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Singh Bisht S, Meena RK, Bhandari MS, Pal Singh P, Sharma U, Bisht A, Verma PK. Exploring Steroidal Saponin Composition and Morphometric Characteristics of Rhizomes from Trillium govanianum Wall. ex D. Don: Inference for Medicinal Properties and Genetic Stock Improvement. Chem Biodivers 2024; 21:e202400588. [PMID: 38651315 DOI: 10.1002/cbdv.202400588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/20/2024] [Accepted: 04/21/2024] [Indexed: 04/25/2024]
Abstract
Trillium govanianum, a medicinal herb, exhibiting diverse morphometric traits and phytochemicals across developmental stages of plants. The changes in the chemical profile and steroidal saponin levels in the rhizome of T. govanianum across different developmental stages were previously unknown. This study categorizes rhizomes into three types based on scar presence: juvenile (5-10 scars, Type I), young (11-19 scars, Type II), and mature (21-29 scars, Type III). Rhizomes show varying sizes (length 1.2-4.7 cm, girth 0.3-1.6 cm), weight (0.18-5.0 g), and extractive yields (9.7-16.1 % w w-1), with notable differences in saponin content (5.95-21.9 mg g-1). Ultra-high performance liquid chromatography-MS/MS (UHPLC-QTOF-MS/MS)-based chemical profiling identifies 31 phytochemicals, mainly including diverse saponins. Ultra-high performance liquid chromatography coupled with evaporative light scattering detection (UHPLC-ELSD)-based quantitative analysis of seven key saponins reveals stage-specific accumulation patterns, with protodioscin (P) and dioscin (DS) predominant in mature rhizomes. Statistical analysis confirms significant variation (p=0.001) in saponin levels across developmental stages with chemical constituent protodioscin (P=4.03±0.03-15.76±0.14 mg g-1, PAve=9.79±3.03 mg g-1) and dioscin (DS=1.23±0.06-3.93±0.07 mg g-1, DSAve=2.59±0.70 mg g-1), with acceptable power (p=0.738; |δ|>0.5) statistics for effective sample size (n=27 samples used in the study) of T. govanianum. Principal Component Analysis (PCA) and Euclidean clustering further highlighted chemotype distinctions.
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Affiliation(s)
- Surendra Singh Bisht
- Chemistry and Bioprospecting Division, ICFRE-Forest Research Institute, 248006, Dehradun, India
| | - Rajendra K Meena
- Genetics and Tree Improvement Division, ICFRE-Forest Research Institute, Dehradun, 248 195, India
| | - Maneesh S Bhandari
- Genetics and Tree Improvement Division, ICFRE-Forest Research Institute, Dehradun, 248 195, India
| | - Prithvi Pal Singh
- C-H Activation and Phytochemistry Lab, CSIR-Institute of Himalayan Bioresource Technology, 176061, Palampur, India
| | - Upendra Sharma
- C-H Activation and Phytochemistry Lab, CSIR-Institute of Himalayan Bioresource Technology, 176061, Palampur, India
| | - Aman Bisht
- Chemistry and Bioprospecting Division, ICFRE-Forest Research Institute, 248006, Dehradun, India
| | - Praveen K Verma
- Botany Division, ICFRE-Forest Research Institute, 248006, Dehradun, India
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Singh PP, Anmol, Suresh PS, Sharma U. NADES extraction, UHPLC-ELSD-based quantification, and network pharmacology-guided target identification of fourteen specialised metabolites from Trillium govanianum Wall. ex D.Don. PHYTOCHEMICAL ANALYSIS : PCA 2024. [PMID: 38659229 DOI: 10.1002/pca.3357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/06/2024] [Accepted: 03/23/2024] [Indexed: 04/26/2024]
Abstract
INTRODUCTION Trillium govanianum Wall. ex D.Don is a folk medicinal herb rich in structurally diverse steroidal saponins. The annual demand for this herb in India is about 200-500 metric tons, highlighting the need for a thorough quality assessment. OBJECTIVE The objective of this study is to develop an easy and reliable ultrahigh-performance liquid chromatography-evaporative light scattering detector (UHPLC-ELSD)-based quality assessment method with 14 specialised metabolites of T. govanianum and identify the potential targets of this herb using network pharmacology. MATERIAL AND METHODS A UHPLC-ELSD method was developed and validated with 14 markers of T. govanianum. The developed method and natural deep eutectic solvent (NADES)-assisted extraction were utilised for the recovery enhancement study of targeted specialised metabolites from rhizome samples (collected from five geographically distinct areas). In addition, the network pharmacology approach was performed for these 14 markers to predict the plausible biological targets of T. govanianum. RESULT The developed method showed good linearity (r2: 0.940-0.998), limit of detection (LOD) (2.4-9.0 μg), limit of quantification (LOQ) (7.92-29.7 μg), precision (intra-day relative standard deviations [RSDs] 0.77%-1.96% and inter-day RSDs 2.19-4.97%), and accuracy (83.24%-118.90%). NADES sample TG-1* showed the highest recovery (yield: 167.66 ± 4.39 mg/g of dry weight) of total saponin content (TSC) as compared to its hydroethanolic extract (yield: 103.95 ± 5.36 mg/g of dry weight). Sample TG-1* was the most favourable (yield: 167.66 ± 4.39 mg/g) in terms of TSC as compared to other analysed samples (32.68 ± 1.04-88.22 ± 6.79 mg/g). Govanoside D (yield: 3.43-28.06 mg/g), 22β-hydroxyprotodioscin (yield: 3.22-114.79 mg/g), and dioscin (yield: 1.07-20.82 mg/g) were quantified as the major metabolites. Furthermore, network pharmacology analysis of targeted 14 markers indicated that these molecules could be possible therapeutic agents for managing neuralgia, diabetes mellitus, and hyperalgesia. CONCLUSION The current study represents the first report for the simultaneous quantification and a network pharmacology-based analysis of 14 chemical marker compounds isolated from T. govanianum.
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Affiliation(s)
- Prithvi Pal Singh
- C-H Activation and Phytochemistry Lab, Chemical Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Anmol
- C-H Activation and Phytochemistry Lab, Chemical Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Patil Shivprasad Suresh
- C-H Activation and Phytochemistry Lab, Chemical Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Upendra Sharma
- C-H Activation and Phytochemistry Lab, Chemical Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Li Z, Li Y, Geng L, Wang J, Ouyang Y, Li J. Genome-wide methylation, transcriptome and characteristic metabolites reveal the balance between diosgenin and brassinosteroids in Dioscorea zingiberensis. HORTICULTURE RESEARCH 2024; 11:uhae056. [PMID: 38659444 PMCID: PMC11040209 DOI: 10.1093/hr/uhae056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 02/14/2024] [Indexed: 04/26/2024]
Abstract
Diosgenin (DG) is a bioactive metabolite isolated from Dioscorea species, renowned for its medicinal properties. Brassinosteroids (BRs) are a class of crucial plant steroidal hormones. Cholesterol and campesterol are important intermediates of DG and BR biosynthesis, respectively. DG and BRs are structurally similar components; however, the regulatory network and metabolic interplays have not been fully elucidated. In an effort to decode these complex networks, we conducted a comprehensive study integrating genome-wide methylation, transcriptome and characteristic metabolite data from Dioscorea zingiberensis. Leveraging these data, we were able to construct a comprehensive regulatory network linking DG and BRs. Mass spectrometry results enabled us to clarify the alterations in cholesterol, campesterol, diosgenin, and castasterone (one of the major active BRs). The DG content decreased by 27.72% at 6 h after brassinolide treatment, whereas the content increased by 85.34% at 6 h after brassinazole treatment. Moreover, we pinpointed DG/BR-related genes, such as CASs, CYP90s, and B3-ARFs, implicated in the metabolic pathways of DG and BRs. Moreover, CASs and CYP90s exhibit hypomethylation, which is closely related to their high transcription. These findings provide robust evidence for the homeostasis between DG and BRs. In conclusion, our research revealed the existence of a balance between DG and BRs in D. zingiberensis. Furthermore, our work not only provides new insights into the relationship between the two pathways but also offers a fresh perspective on the functions of secondary metabolites.
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Affiliation(s)
- Zihao Li
- State Key Laboratory of Hybrid Rice, College Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yi Li
- State Key Laboratory of Hybrid Rice, College Life Sciences, Wuhan University, Wuhan 430072, China
| | - Luyu Geng
- State Key Laboratory of Hybrid Rice, College Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jiachen Wang
- State Key Laboratory of Hybrid Rice, College Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiaru Li
- State Key Laboratory of Hybrid Rice, College Life Sciences, Wuhan University, Wuhan 430072, China
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Lu J, Yao J, Pu J, Wang D, Liu J, Zhang Y, Zha L. Transcriptome analysis of three medicinal plants of the genus Polygonatum: identification of genes involved in polysaccharide and steroidal saponins biosynthesis. FRONTIERS IN PLANT SCIENCE 2023; 14:1293411. [PMID: 38046616 PMCID: PMC10691381 DOI: 10.3389/fpls.2023.1293411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 10/30/2023] [Indexed: 12/05/2023]
Abstract
Polysaccharides and saponins are the main active components of Polygonati Rhizoma. Studying the molecular mechanism of their synthesis pathway is helpful in improving the content of active components at the molecular level. At present, transcriptome analysis of three Polygonatum species (Polygonatum sibiricum Red., Polygonatum cyrtonema Hua, Polygonatum kingianum Coll. et Hemsl.) has been reported, but no comparative study has been found on the transcriptome data of the three species. Transcriptome sequencing was performed on the rhizomes of three Polygonatum species based on high-throughput sequencing technology, and all transcripts were assembled. A total of 168,108 unigenes were generated after the removal of redundancy, of which 121,642 were annotated in seven databases. Through differential analysis and expression analysis of key enzyme genes in the synthesis pathway of three Polygonatum polysaccharides and steroidal saponins, 135 differentially expressed genes encoding 18 enzymes and 128 differentially expressed genes encoding 28 enzymes were identified, respectively. Numerous transcription factors are involved in the carbohydrate synthesis pathway. Quantitative real-time PCR was used to further verify the gene expression level. In this paper, we present a public transcriptome dataset of three medicinal plants of the genus Polygonatum, and analyze the key enzyme genes of polysaccharide and steroidal saponins synthesis pathway, which lays a foundation for improving the active component content of Polygonati Rhizoma by molecular means.
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Affiliation(s)
- Jimei Lu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Jinchen Yao
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Jingzhe Pu
- Anhui Institute for Food and Drug Control, Hefei, China
| | - Duomei Wang
- Anhui Institute for Food and Drug Control, Hefei, China
| | - Junling Liu
- Anhui Institute for Food and Drug Control, Hefei, China
| | - Yazhong Zhang
- Anhui Institute for Food and Drug Control, Hefei, China
| | - Liangping Zha
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
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Singh PP, Suresh PS, Anmol, Sharma U. Govanosides C-F, unprecedented steroidal saponins with rare sugars from rhizomes of Trillium govanianum and their antagonistic effects on acetylcholinesterase. Steroids 2023; 199:109293. [PMID: 37549778 DOI: 10.1016/j.steroids.2023.109293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023]
Abstract
Four previously undescribed steroidal saponins named govanosides C-F (1-4) and nine known compounds (5-13) were isolated from the rhizomes of Trillium govanianum Wall. ex D.Don. Govanosides C-E contained a rare sugar moiety i.e., 6-deoxy allose, while govanoside F has acetylated rhamnose moiety in its glycan part. Also, this is the first report on the isolation of feruloyl sucrose derivatives (11-12) and (E)-4-hydroxy-dodec-2-enedioic acid (13) from the Trillium genus. The structure of isolated compounds was deduced using 1D and 2D NMR, HRESIMS, LC-MS/MS, GC-MS, and saccharide linkage analysis. Steroidal scaffold isolates (1-10) were evaluated for their antagonistic effects on acetylcholinesterase inhibitory activity. Govanoside C (1) significantly inhibited acetylcholinesterase (IC50: 2.38 μM). Molecular docking experiments have also been performed to depict the molecule's interaction and binding free energy with acetylcholinesterase.
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Affiliation(s)
- Prithvi Pal Singh
- C-H Activation & Phytochemistry Lab, Chemical Technology Division CSIR-IHBT, Palampur, Himachal Pradesh 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Patil Shivprasad Suresh
- C-H Activation & Phytochemistry Lab, Chemical Technology Division CSIR-IHBT, Palampur, Himachal Pradesh 176061, India
| | - Anmol
- C-H Activation & Phytochemistry Lab, Chemical Technology Division CSIR-IHBT, Palampur, Himachal Pradesh 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Upendra Sharma
- C-H Activation & Phytochemistry Lab, Chemical Technology Division CSIR-IHBT, Palampur, Himachal Pradesh 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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He M, Zhang G, Huo D, Yang S. Combined Metabolome and Transcriptome Analysis of Creamy Yellow and Purple Colored Panax notoginseng Roots. Life (Basel) 2023; 13:2100. [PMID: 37895482 PMCID: PMC10607970 DOI: 10.3390/life13102100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/03/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023] Open
Abstract
Panax notoginseng (Burk.) F.H. Chen is a species of the Araliaceae family that inhabits southwestern China, Burma, and Nepal. It is cultivated on a commercial scale in Yunnan province, China, owing to its significance in traditional Chinese medicine. Panax notoginseng roots are usually yellow-white (HS); however, purple roots (ZS) have also been reported. The majority of P. notoginseng research has concentrated on the identification and production of natural chemicals in HS; however, there is little to no information about the composition of ZS. Using UPLC-MS/MS, we investigated the global metabolome profile of both ZS- and HS-type roots and discovered 834 metabolites from 11 chemical groups. There were 123 differentially accumulated metabolites (DAM) in the HS and ZS roots, which were classified as lipids and lipid-like molecules, polyketides, organoheterocyclic chemicals, and organooxygen compounds. We investigated the associated compounds in the DAMs because of the importance of anthocyanins in color and saponins and ginsenosides in health benefits. In general, we discovered that pigment compounds such as petunidin 3-glucoside, delphinidin 3-glucoside, and peonidin-3-O-beta-galactoside were more abundant in ZS. The saponin (eight compounds) and ginsenoside (26 compounds) content of the two varieties of roots differed as well. Transcriptome sequencing revealed that flavonoid and anthocyanin production genes were more abundant in ZS than in HS. Similarly, we found differences in gene expression in genes involved in terpenoid production and related pathways. Overall, these findings suggest that the purple roots of P. notoginseng contain varying amounts of ginsenosides and anthocyanins compared to roots with a creamy yellow color.
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Affiliation(s)
- Muhan He
- Office of Academic Affairs, Yunnan Forestry Technological College, Kunming 650224, China; (M.H.); (D.H.)
| | - Guanghui Zhang
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming 650201, China;
| | - Dongfang Huo
- Office of Academic Affairs, Yunnan Forestry Technological College, Kunming 650224, China; (M.H.); (D.H.)
| | - Shengchao Yang
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming 650201, China;
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Kumar P, Singh K, Lone JF, Bhushan A, Gupta P, Gairola S. Morpho-anatomical, Molecular, and Chemical Standardization of Trillium govanianum Wall. ex D. Don: An Endangered Medicinal Herb Native to the Himalayas. Pharmacogn Mag 2023. [DOI: 10.1177/09731296221145070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023] Open
Abstract
Background Trillium govanianum Wall. ex D. Don occurring at high altitudes in the Himalayas and known by the common name ‘Nag Chhatri,’ has high medicinal value. Its rhizome samples have substantial therapeutic potential and possess anti-cancer and anti-aging properties. Due to similar common names and morphology, there is an issue with adulteration and misidentification of actual rhizome samples with rhizomes of other species. So, there is a need to develop valid scientific methods to identify raw herbal samples of authentic ‘Nagchatri’ ( T. govanianum). Objectives The present study focused on developing botanical, molecular, and chemical standards for identifying raw herbal samples of T. govanianum. Materials and Methods Samples were collected from four locations in the Northwestern Himalayas. Botanical characters were studied by stereomicroscope and compound microscope. Molecular identification was done by DNA barcoding and chemical identification by chemical fingerprinting (TLC and HPTLC), LC-MS profiling, and NMR studies. Results The botanical characters involved detailed morpho-anatomical characterization of herbal samples. The DNA barcoding exhibited a 100% identification match of generated barcode sequences with NCBI database sequences for all the selected markers. Chemical profiling revealed diosgenin, makisterone A, and 20-hydroxy ecdysone as major constituents in the rhizome sample, confirming the authenticity of the species. Conclusion The integrated authentication approach employing botanical standardization, DNA barcoding, and chemical profiling will be a promising tool for accurately identifying the genuine raw herbal material of T. govanianum.
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Affiliation(s)
- Pankaj Kumar
- Plant Sciences and Agrotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, Jammu and Kashmir, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Kanwaljeet Singh
- Plant Sciences and Agrotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, Jammu and Kashmir, India
| | - Javaid Fayaz Lone
- Plant Sciences and Agrotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, Jammu and Kashmir, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Anil Bhushan
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
- Natural Product and Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu, Jammu and Kashmir, India
| | - Prasoon Gupta
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
- Natural Product and Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu, Jammu and Kashmir, India
| | - Sumeet Gairola
- Plant Sciences and Agrotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, Jammu and Kashmir, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
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Tyagi P, Singh D, Mathur S, Singh A, Ranjan R. Upcoming progress of transcriptomics studies on plants: An overview. FRONTIERS IN PLANT SCIENCE 2022; 13:1030890. [PMID: 36589087 PMCID: PMC9798009 DOI: 10.3389/fpls.2022.1030890] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/27/2022] [Indexed: 06/17/2023]
Abstract
Transcriptome sequencing or RNA-Sequencing is a high-resolution, sensitive and high-throughput next-generation sequencing (NGS) approach used to study non-model plants and other organisms. In other words, it is an assembly of RNA transcripts from individual or whole samples of functional and developmental stages. RNA-Seq is a significant technique for identifying gene predictions and mining functional analysis that improves gene ontology understanding mechanisms of biological processes, molecular functions, and cellular components, but there is limited information available on this topic. Transcriptomics research on different types of plants can assist researchers to understand functional genes in better ways and regulatory processes to improve breeding selection and cultivation practices. In recent years, several advancements in RNA-Seq technology have been made for the characterization of the transcriptomes of distinct cell types in biological tissues in an efficient manner. RNA-Seq technologies are briefly introduced and examined in terms of their scientific applications. In a nutshell, it introduces all transcriptome sequencing and analysis techniques, as well as their applications in plant biology research. This review will focus on numerous existing and forthcoming strategies for improving transcriptome sequencing technologies for functional gene mining in various plants using RNA- Seq technology, based on the principles, development, and applications.
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Seth R, Devi A, Sharma B, Masand M, Singh G, Pal P, Holkar A, Sharma S, Sharma V, Negi S, Sharma RK. An Integrative Transcriptional Network Revealed Spatial Molecular Interplay Underlying Alantolactone and Inulin Biosynthesis in Inula racemosa Hook f. Int J Mol Sci 2022; 23:ijms231911213. [PMID: 36232516 PMCID: PMC9570477 DOI: 10.3390/ijms231911213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/04/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
Inula racemosa Hook. f. (Pushkarmula), a perennial Himalayan herb known for its aromatic and phytopharmaceutical attributes, is not yet explored at genomic/transcriptomic scale. In this study, efforts were made to unveil the global transcriptional atlas underlying organ-specific specialized metabolite biosynthesis by integrating RNA-Seq analysis of 433 million sequenced reads with the phytochemical analysis of leaf, stem, and root tissues. Overall, 7242 of 83,772 assembled nonredundant unigenes were identified exhibiting spatial expression in leaf (3761), root (2748), and stem (733). Subsequently, integration of the predicted transcriptional interactome network of 2541 unigenes (71,841 edges) with gene ontology and KEGG pathway enrichment analysis revealed isoprenoid, terpenoid, diterpenoid, and gibberellin biosynthesis with antimicrobial activities in root tissue. Interestingly, the root-specific expression of germacrene-mediated alantolactone biosynthesis (GAS, GAO, G8H, IPP, DMAP, and KAO) and antimicrobial activities (BZR1, DEFL, LTP) well-supported with both quantitative expression profiling and phytochemical accumulation of alantolactones (726.08 μg/10 mg) and isoalantolactones (988.59 μg/10 mg), which suggests “roots” as the site of alantolactone biosynthesis. A significant interaction of leaf-specific carbohydrate metabolism with root-specific inulin biosynthesis indicates source (leaf) to sink (root) regulation of inulin. Our findings comprehensively demonstrate the source-sink transcriptional regulation of alantolactone and inulin biosynthesis, which can be further extended for upscaling the targeted specialized metabolites. Nevertheless, the genomic resource created in this study can also be utilized for development of genome-wide functionally relevant molecular markers to expedite the breeding strategies for genetic improvement of I. racemosa.
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Affiliation(s)
- Romit Seth
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, Himachal Pradesh, India
| | - Amna Devi
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Balraj Sharma
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Mamta Masand
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Gopal Singh
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, Himachal Pradesh, India
| | - Poonam Pal
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Ashlesha Holkar
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Shikha Sharma
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Vishal Sharma
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, Himachal Pradesh, India
| | - Shivanti Negi
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, Himachal Pradesh, India
| | - Ram Kumar Sharma
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
- Correspondence: or
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Devi A, Seth R, Masand M, Singh G, Holkar A, Sharma S, Singh A, Sharma RK. Spatial Genomic Resource Reveals Molecular Insights into Key Bioactive-Metabolite Biosynthesis in Endangered Angelica glauca Edgew. Int J Mol Sci 2022; 23:ijms231911064. [PMID: 36232367 PMCID: PMC9569870 DOI: 10.3390/ijms231911064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/04/2022] [Accepted: 09/07/2022] [Indexed: 11/25/2022] Open
Abstract
Angelica glauca Edgew, which is an endangered medicinal and aromatic herb, is a rich source of numerous industrially important bioactive metabolites, including terpenoids, phenolics, and phthalides. Nevertheless, genomic interventions for the sustainable utilization and restoration of its genetic resources are greatly offset due to the scarcity of the genomic resources and key regulators of the underlying specialized metabolism. To unravel the global atlas of the specialized metabolism, the first spatial transcriptome sequencing of the leaf, stem, and root generated 109 million high-quality paired-end reads, assembled de novo into 81,162 unigenes, which exhibit a 61.53% significant homology with the six public protein databases. The organ-specific clustering grouped 1136 differentially expressed unigenes into four subclusters differentially enriched in the leaf, stem, and root tissues. The prediction of the transcriptional-interactome network by integrating enriched gene ontology (GO) and the KEGG metabolic pathways identified the key regulatory unigenes that correspond to terpenoid, flavonoid, and carotenoid biosynthesis in the leaf tissue, followed by the stem and root tissues. Furthermore, the stem and root-specific significant enrichments of phenylalanine ammonia lyase (PAL), cinnamate-4-hydroxylase (C4H), and caffeic acid 3-O-methyltransferase (COMT) indicate that phenylalanine mediated the ferulic acid biosynthesis in the stem and root. However, the root-specific expressions of NADPH-dependent alkenal/one oxidoreductase (NADPH-AOR), S-adenosyl-L-methionine-dependent methyltransferases (SDMs), polyketide cyclase (PKC), and CYP72A15 suggest the “root” as the primary site of phthalide biosynthesis. Additionally, the GC-MS and UPLC analyses corresponded to the organ-specific gene expressions, with higher contents of limonene and phthalide compounds in the roots, while there was a higher accumulation of ferulic acid in the stem, followed by in the root and leaf tissues. The first comprehensive genomic resource with an array of candidate genes of the key metabolic pathways can be potentially utilized for the targeted upscaling of aromatic and pharmaceutically important bioactive metabolites. This will also expedite genomic-assisted conservation and breeding strategies for the revival of the endangered A. glauca.
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Affiliation(s)
- Amna Devi
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Romit Seth
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, Himachal Pradesh, India
| | - Mamta Masand
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Gopal Singh
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Ashlesha Holkar
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Shikha Sharma
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Ashok Singh
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
- Environmental Technology, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, Himachal Pradesh, India
| | - Ram Kumar Sharma
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
- Correspondence: or
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Rattan S, Kumar P, Kaur E, Sood A, Acharya V, Warghat AR. Comparative transcriptome and tissue-specific expression analysis of genes reveal tissue-cultured plants as an alternative source for phenylethanoids and phenylpropanoids in Rhodiola imbricata (Edgew.). Gene X 2022; 836:146672. [PMID: 35714804 DOI: 10.1016/j.gene.2022.146672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/30/2022] [Accepted: 06/10/2022] [Indexed: 11/29/2022] Open
Abstract
Rhodiola imbricata (Crassulaceae) is a traditional trans-Himalayan endangered medicinal herb with immense therapeutic applications. Over the years, over-exploitation, un-managed harvesting, and lack of captive cultivation procedures persuaded threat to its wild habitat. Plant tissue culture and RNA-Seq-based molecular bioprospection of key regulatory genes aid the understanding of molecular dynamics involved in specialized metabolites (phenylethanoids and phenylpropanoids) biosynthesis and its sustainable production. Hence, comparative transcriptomic analysis was performed using leaf and root tissues from the wild and tissue-cultured plants, revealing tissue-specific production of salidroside and rosavin. The transcriptome profiling resulted in 345 million high-quality reads yielding 92,380 unique transcripts with an N50 of 1260 bp. Tissue-specific gene expression analysis revealed that both phenylethanoids and phenylpropanoids biosynthesis are predominantly associated with the shikimate pathway. In addition to RNA-Seq data, the downstream biosynthesis pathways genes viz., phospho-2-dehydro-3-deoxyheptonate aldolase (DAHPS), 3-dehydroquinate synthase (DHQS), shikimate kinase (SK), chorismate mutase (CM), arogenate dehydrogenase (TYRAAT), aromatic-L-amino-acid decarboxylase (TDC), phenylalanine ammonia-lyase (PAL), 4-coumarate-CoA ligase (4-CL), cinnamoyl-CoA reductase (CCR), and cinnamyl alcohol dehydrogenase (CAD) showed higher expression pattern in wild plant tissues compared to tissue-cultured plants. The transcript fold expression determined by RT-qPCR results followed similar patterns as those observed in RNA-seq and targeted metabolite profiling data. Salidroside and rosavin content in wild plants exhibited 2.40 fold and 1.77 fold increase accumulation compared to the tissue-cultured plant. The present investigation explained the tissue and condition-specific significant differences between the expression of proposed biosynthetic pathway genes and salidroside and rosavin content. Additionally, NAC, bHLH, and ARF were the most abundant transcription factor families found in the transcriptomic analysis of R. imbricata. The generated transcriptome dataset provides a valuable gene(s)/transcription factors hub that can be used for the sustainable production of salidroside and rosavin in R. imbricata under tissue culture conditions.
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Affiliation(s)
- Shiv Rattan
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Pankaj Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India
| | - Ekjot Kaur
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Archit Sood
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India
| | - Vishal Acharya
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ashish R Warghat
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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12
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Berrios L. Examining the genomic features of human and plant-associated Burkholderia strains. Arch Microbiol 2022; 204:335. [PMID: 35587294 DOI: 10.1007/s00203-022-02953-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 04/01/2022] [Accepted: 05/02/2022] [Indexed: 11/28/2022]
Abstract
Humans and plants have evolved in the near omnipresence of a microbial milieu, and the factors that govern host-microbe interactions continue to require scientific exploration. To better understand if and to what degree patterns between microbial genomic features and host association (i.e., human and plant) exist, I analyzed the genomes of select Burkholderia strains-a bacterial genus comprised of both human and plant-associated strains-that were isolated from either humans or plants. To this end, I uncovered host-specific, genomic patterns related to metabolic pathway potentials in addition to convergent features that may be related to pathogenic overlap between hosts. Together, these findings detail the genomic associations of human and plant-associated Burkholderia strains and provide a framework for future investigations that seek to link host-host transmission potentials.
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Affiliation(s)
- Louis Berrios
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
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13
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Li D, Wang Q, Chen S, Liu H, Pan K, Li J, Luo C, Wang H. De novo assembly and analysis of Polygonatum cyrtonema Hua and identification of genes involved in polysaccharide and saponin biosynthesis. BMC Genomics 2022; 23:195. [PMID: 35272619 PMCID: PMC8915509 DOI: 10.1186/s12864-022-08421-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 02/25/2022] [Indexed: 12/05/2022] Open
Abstract
Background The investigation of molecular mechanisms involved in polysaccharides and saponin metabolism is critical for genetic engineering of Polygonatum cyrtonema Hua to raise major active ingredient content. Up to now, the transcript sequences are available for different tissues of P. cyrtonema, a wide range scanning about temporal transcript at different ages’ rhizomes was still absent in P. cyrtonema. Results Transcriptome sequencing for rhizomes at different ages was performed. Sixty-two thousand six hundred thirty-five unigenes were generated by assembling transcripts from all samples. A total of 89 unigenes encoding key enzymes involved in polysaccharide biosynthesis and 56 unigenes encoding key enzymes involved in saponin biosynthesis. The content of total polysaccharide and total saponin was positively correlated with the expression patterns of mannose-6-phosphate isomerase (MPI), GDP-L-fucose synthase (TSTA3), UDP-apiose/xylose synthase (AXS), UDP-glucose 6-dehydrogenase (UGDH), Hydroxymethylglutaryl CoA synthase (HMGS), Mevalonate kinase (MVK), 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (ispF), (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase (ispG), 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (ispH), Farnesyl diphosphate synthase (FPPS). Finally, a number of key genes were selected and quantitative real-time PCR were performed to validate the transcriptome analysis results. Conclusions These results create the link between polysaccharides and saponin biosynthesis and gene expression, provide insight for underlying key active substances, and reveal novel candidate genes including TFs that are worth further exploration for their functions and values. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08421-y.
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Affiliation(s)
- Dandan Li
- Agronomy College, Guizhou University, Huaxi, Guiyang, Guizhou, 550025, P. R. China.,Guizhou Key Laboratory of Propagation and Cultivation on Medicinal Plants, Huaxi, Guiyang, Guizhou, 550025, P. R. China
| | - Qing Wang
- Construction Service Center of Wudang District Agricultural Science and Technology Zone, Wudang, Guiyang, Guizhou, 550018, P. R. China
| | - Songshu Chen
- Agronomy College, Guizhou University, Huaxi, Guiyang, Guizhou, 550025, P. R. China
| | - Hongchang Liu
- Agronomy College, Guizhou University, Huaxi, Guiyang, Guizhou, 550025, P. R. China.,Guizhou Key Laboratory of Propagation and Cultivation on Medicinal Plants, Huaxi, Guiyang, Guizhou, 550025, P. R. China
| | - Keqin Pan
- Agronomy College, Guizhou University, Huaxi, Guiyang, Guizhou, 550025, P. R. China
| | - Jinling Li
- Agronomy College, Guizhou University, Huaxi, Guiyang, Guizhou, 550025, P. R. China.,Guizhou Key Laboratory of Propagation and Cultivation on Medicinal Plants, Huaxi, Guiyang, Guizhou, 550025, P. R. China
| | - Chunli Luo
- Agronomy College, Guizhou University, Huaxi, Guiyang, Guizhou, 550025, P. R. China.,Guizhou Key Laboratory of Propagation and Cultivation on Medicinal Plants, Huaxi, Guiyang, Guizhou, 550025, P. R. China
| | - Hualei Wang
- Agronomy College, Guizhou University, Huaxi, Guiyang, Guizhou, 550025, P. R. China. .,Guizhou Key Laboratory of Propagation and Cultivation on Medicinal Plants, Huaxi, Guiyang, Guizhou, 550025, P. R. China.
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14
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Li Y, Tan C, Li Z, Guo J, Li S, Chen X, Wang C, Dai X, Yang H, Song W, Hou L, Xu J, Tong Z, Xu A, Yuan X, Wang W, Yang Q, Chen L, Sun Z, Wang K, Pan B, Chen J, Bao Y, Liu F, Qi X, Gang DR, Wen J, Li J. The genome of Dioscorea zingiberensis sheds light on the biosynthesis, origin and evolution of the medicinally important diosgenin saponins. HORTICULTURE RESEARCH 2022; 9:uhac165. [PMID: 36204203 PMCID: PMC9531337 DOI: 10.1093/hr/uhac165] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 07/18/2022] [Indexed: 05/05/2023]
Abstract
Diosgenin saponins isolated from Dioscorea species such as D. zingiberensis exhibit a broad spectrum of pharmacological activities. Diosgenin, the aglycone of diosgenin saponins, is an important starting material for the production of steroidal drugs. However, how plants produce diosgenin saponins and the origin and evolution of the diosgenin saponin biosynthetic pathway remain a mystery. Here we report a high-quality, 629-Mb genome of D. zingiberensis anchored on 10 chromosomes with 30 322 protein-coding genes. We reveal that diosgenin is synthesized in leaves ('source'), then converted into diosgenin saponins, and finally transported to rhizomes ('sink') for storage in plants. By evaluating the distribution and evolutionary patterns of diosgenin saponins in Dioscorea species, we find that diosgenin saponin-containing may be an ancestral trait in Dioscorea and is selectively retained. The results of comparative genomic analysis indicate that tandem duplication coupled with a whole-genome duplication event provided key evolutionary resources for the diosgenin saponin biosynthetic pathway in the D. zingiberensis genome. Furthermore, comparative transcriptome and metabolite analysis among 13 Dioscorea species suggests that specific gene expression patterns of pathway genes promote the differential evolution of the diosgenin saponin biosynthetic pathway in Dioscorea species. Our study provides important insights and valuable resources for further understanding the biosynthesis, evolution, and utilization of plant specialized metabolites such as diosgenin saponins.
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Affiliation(s)
- Yi Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Chao Tan
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zihao Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jingzhe Guo
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Song Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Xin Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Chen Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Xiaokang Dai
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Huan Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Wei Song
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Lixiu Hou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jiali Xu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Ziyu Tong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Anran Xu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Xincheng Yuan
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Weipeng Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Qingyong Yang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lingling Chen
- College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Zongyi Sun
- Grandomics Biosciences, Beijing 102200, China
| | - Kai Wang
- Grandomics Biosciences, Beijing 102200, China
| | - Bo Pan
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, 666303, China
| | - Jianghua Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence in Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Kunming, 650223, China
| | - Yinghua Bao
- Henry Fok College of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, China
| | - Faguang Liu
- Henry Fok College of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, China
| | - Xiaoquan Qi
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - David R Gang
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164, USA
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA
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15
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Liu X, Gong X, Liu Y, Liu J, Zhang H, Qiao S, Li G, Tang M. Application of High-Throughput Sequencing on the Chinese Herbal Medicine for the Data-Mining of the Bioactive Compounds. FRONTIERS IN PLANT SCIENCE 2022; 13:900035. [PMID: 35909744 PMCID: PMC9331165 DOI: 10.3389/fpls.2022.900035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/10/2022] [Indexed: 05/11/2023]
Abstract
The Chinese Herbal Medicine (CHM) has been used worldwide in clinic to treat the vast majority of human diseases, and the healing effect is remarkable. However, the functional components and the corresponding pharmacological mechanism of the herbs are unclear. As one of the main means, the high-throughput sequencing (HTS) technologies have been employed to discover and parse the active ingredients of CHM. Moreover, a tremendous amount of effort is made to uncover the pharmacodynamic genes associated with the synthesis of active substances. Here, based on the genome-assembly and the downstream bioinformatics analysis, we present a comprehensive summary of the application of HTS on CHM for the synthesis pathways of active ingredients from two aspects: active ingredient properties and disease classification, which are important for pharmacological, herb molecular breeding, and synthetic biology studies.
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Affiliation(s)
- Xiaoyan Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Xun Gong
- Department of Rheumatology and Immunology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Yi Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
- Institute of Animal Husbandry, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Junlin Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Hantao Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Sen Qiao
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Gang Li
- Department of Vascular Surgery, The Second Affiliated Hospital of Shandong First Medical University, Taian, China
- Gang Li,
| | - Min Tang
- School of Life Sciences, Jiangsu University, Zhenjiang, China
- *Correspondence: Min Tang,
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16
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Chen Y, Wu J, Yu D, Du X. Advances in steroidal saponins biosynthesis. PLANTA 2021; 254:91. [PMID: 34617240 DOI: 10.1007/s00425-021-03732-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 09/11/2021] [Indexed: 06/13/2023]
Abstract
This work reviews recent advances in the pathways and key enzymes of steroidal saponins biosynthesis and sets the foundation for the biotechnological production of these useful compounds through transformation of microorganisms. Steroidal saponins, due to their specific chemical structures and active effects, have long been important natural products and that are irreplaceable in hormone production and other pharmaceutical industries. This article comprehensively reviewed the previous and current research progress and summarized the biosynthesis pathways and key biosynthetic enzymes of steroidal saponins that have been discovered in plants and microoganisms. On the basis of the general biosynthetic pathway in plants, it was found that the starting components, intermediates and catalysing enzymes were diverse between plants and microorganisms; however, the functions of their related enzymes tended to be similar. The biosynthesis pathways of steroidal saponins in microorganisms and marine organisms have not been revealed as clearly as those in plants and need further investigation. The elucidation of biosynthetic pathways and key enzymes is essential for understanding the synthetic mechanisms of these compounds and provides researchers with important information to further develop and implement the massive production of steroidal saponins by biotechnological approaches and methodologies.
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Affiliation(s)
- Yiyang Chen
- Key Laboratory of Chinese Materia Medica, Ministry of Education, Pharmaceutical College, Heilongjiang University of Chinese Medicine, 24 Heping Road, Harbin, 150040, China
| | - Junkai Wu
- Key Laboratory of Chinese Materia Medica, Ministry of Education, Pharmaceutical College, Heilongjiang University of Chinese Medicine, 24 Heping Road, Harbin, 150040, China
| | - Dan Yu
- Key Laboratory of Chinese Materia Medica, Ministry of Education, Pharmaceutical College, Heilongjiang University of Chinese Medicine, 24 Heping Road, Harbin, 150040, China
| | - Xiaowei Du
- Key Laboratory of Chinese Materia Medica, Ministry of Education, Pharmaceutical College, Heilongjiang University of Chinese Medicine, 24 Heping Road, Harbin, 150040, China.
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17
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Guo J, Huang Z, Sun J, Cui X, Liu Y. Research Progress and Future Development Trends in Medicinal Plant Transcriptomics. FRONTIERS IN PLANT SCIENCE 2021; 12:691838. [PMID: 34394145 PMCID: PMC8355584 DOI: 10.3389/fpls.2021.691838] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 06/29/2021] [Indexed: 05/17/2023]
Abstract
Transcriptomics is one of the most popular topics in biology in recent times. Transcriptome sequencing (RNA-Seq) is a high-throughput, high-sensitivity, and high-resolution technique that can be used to study model and non-model organisms. Transcriptome sequencing is also an important method for studying the genomes of medicinal plants, a topic on which limited information is available. The study of medicinal plants through transcriptomics can help researchers analyze functional genes and regulatory mechanisms of medicinal plants and improve breeding selection and cultivation techniques. This article analyzes and compares the applications of transcriptome sequencing in medicinal plants over the past decade and briefly introduces the methods of transcriptome sequencing and analysis, their applications in medicinal plant research, and potential development trends. We will focus on the research and application progress of transcriptome sequencing in the following four areas: the mining of functional genes in medicinal plants, development of molecular markers, biosynthetic pathways of secondary metabolites, and developmental mechanisms of medicinal plants. Our review will provide ideas for the mining of functional genes of medicinal plants and breeding new varieties.
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Affiliation(s)
- Junda Guo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Zhen Huang
- Yuxi Walvax Biotechnology Co., Ltd., Yuxi, China
| | - Jialing Sun
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Xiuming Cui
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Yunnan Provincial Key Laboratory of Panax Notoginseng, Kunming, China
- Key Laboratory of Panax Notoginseng Resources Sustainable Development and Utilization of State Administration of Traditional Chinese Medicine, Kunming, China
- Kunming Key Laboratory of Sustainable Development and Utilization of Famous-Region Drug, Kunming, China
| | - Yuan Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Yunnan Provincial Key Laboratory of Panax Notoginseng, Kunming, China
- Key Laboratory of Panax Notoginseng Resources Sustainable Development and Utilization of State Administration of Traditional Chinese Medicine, Kunming, China
- Kunming Key Laboratory of Sustainable Development and Utilization of Famous-Region Drug, Kunming, China
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18
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Sidharthan VK, Kalaivanan NS, Baranwal VK. Discovery of putative novel viruses in the transcriptomes of endangered plant species native to India and China. Gene 2021; 786:145626. [PMID: 33798682 DOI: 10.1016/j.gene.2021.145626] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/15/2021] [Accepted: 03/26/2021] [Indexed: 11/30/2022]
Abstract
Viruses are abundant entities that infect almost every living organism. In recent years, Next Generation Sequencing coupled with bioinformatic analyses is widely adopted for identification of known and unknown viruses in a plant sample. In the present study, nine putative novel viruses were discovered from public domain transcriptome datasets of five endangered plant species by de novo assembly of reads using CLC and SPAdes followed by BLAST analysis. Of the identified viruses, ten coding-complete and five partial genomic segments were recovered. Based on phylogeny and BLAST analysis, the identified viruses were putatively assigned to various plant viral genera except dactylorhiza hatagirea benylike virus that probably represents a new group of plant virus. The methodology followed can be adopted for the discovery of novel viruses in plant species with little genomic information. Viral genome sequences recovered in the study will serve as a valuable resource for further characterization of identified viruses.
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Affiliation(s)
- V Kavi Sidharthan
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - N S Kalaivanan
- ICAR-National Research Centre for Orchids, Pakyong, Sikkim, India
| | - V K Baranwal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India.
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19
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Kumar P, Acharya V, Warghat AR. Comparative transcriptome analysis infers bulb derived in vitro cultures as a promising source for sipeimine biosynthesis in Fritillaria cirrhosa D. Don (Liliaceae, syn. Fritillaria roylei Hook.) - High value Himalayan medicinal herb. PHYTOCHEMISTRY 2021; 183:112631. [PMID: 33370713 DOI: 10.1016/j.phytochem.2020.112631] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 06/12/2023]
Abstract
Fritillaria cirrhosa D. Don (Liliaceae, syn. Fritillaria roylei Hook.) is a critically endangered medicinal herb of immense importance due to its pharmaceutical bioactive compound, especially sipeimine, used for the treatment of chronic respiratory disorders. However, the industrial demand for sipeimine solely depends on its endangered natural habitat. Therefore; there is an utmost need for its biodiversity conservation as well as for the sustainable utilization of phytochemicals. Plant cell culture and transcriptomics-based molecular bioprospection of key regulatory genes involved in sipeimine biosynthesis as such will play a crucial role in exploring the unexplored traits, that are in supply crisis or nearly in extinction stage. De novo comparative transcriptome sequencing of the bulb (in vivo), callus, and regenerated plantlets (in vitro) resulted in more than 150 million high-quality paired-end clean reads that assembled into final 31,428 transcripts. Functional annotation and unigenes classification with multiple public databases such as KEGG, Refseq, Uniprot, TAIR, GO, and COG, etc. along with chemical structures and functional biocatalytic activity analysis of different steroidal alkaloids facilitated the identification of 30 unigenes specific to sipeimine biosynthesis. Additionally, ABC transporters and TFs like bHLH, MYC, MYB, and WRKY suggests their possible role in metabolite translocation and regulation in vivo as well as in vitro tissues. Differential gene expression and quantitative analysis revealed that the MVA pathway probably the predominant route for 5C intermediate (IPP & DMAPP) biosynthesis. Further, the genes involved in the downstream biosynthesis pathway viz. SQLE, CAS1, SMT1, SMO1, SMO2, SC5DL, DHCR7, DHCR24, CYP710A, 3β-HSD, CYP90D2, and CYP374A6 shown similar expression pattern with RNA-Seq and qRT-PCR findings. The positive correlation between higher expression of proposed biosynthetic pathway genes and relatively higher accumulation of sipeimine in differentiated naturally grown bulb tissues (in vivo), undifferentiated cells (callus), and de-differentiated tissues i.e. regenerated plantlets (in vitro) has been evident from the present study. Comprehensive genomic resources created in F. cirrhosa will provide strong evidence of bulb derived in vitro culture as an alternative promising source for steroidal alkaloids biosynthesis and metabolite upscaling through genetic and metabolic engineering.
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Affiliation(s)
- Pankaj Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India.
| | - Vishal Acharya
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India; Academy of Scientific and Innovative Research, New Delhi, India.
| | - Ashish R Warghat
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India; Academy of Scientific and Innovative Research, New Delhi, India.
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Suresh PS, Singh PP, Padwad YS, Sharma U. Steroidal saponins from Trillium govanianum as α-amylase, α-glucosidase, and dipeptidyl peptidase IV inhibitory agents. J Pharm Pharmacol 2021; 73:487-495. [PMID: 33793831 DOI: 10.1093/jpp/rgaa038] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 10/27/2020] [Indexed: 11/14/2022]
Abstract
OBJECTIVE To provide the scientific basis for the utility of rhizome of Trillium govanianum as nutraceutical supplements in managing physiological glycemic levels. METHODS The in vitro enzyme inhibitory activity of the extract, fractions, and the isolated steroidal saponins from the rhizome part of T. govanianum was carried out against α-amylase, α-glucosidase, and dipeptidyl peptidase IV. The molecular interactions, binding score, and pharmacokinetic parameters (absorption, distribution metabolism, and excretion) of steroidal saponins were analyzed by the Schrodinger molecular docking software. KEY FINDINGS Current study explained that the extract, fractions, and isolated steroidal saponins from T. govanianum possess good α-amylase and α-glucosidase inhibitory activity while moderate dipeptidyl peptidase IV inhibitory activity. Moreover, in vitro results revealed that borassoside E (IC50 7.15 ± 1.78 μM), protodioscin (IC50 6.72 ± 0.04 μM), and diosgenin (IC50 12.75 ± 2.70 μM) are most effective in inhibiting the activity of α-amylase, α-glucosidase, and dipeptidyl peptidase IV, respectively. Current in silico and in vitro studies established an association between the steroidal saponins from T. govanianum and their molecular interactions with α-amylase, α-glucosidase, and dipeptidyl peptidase IV. CONCLUSION The results of this investigation suggest that fractions and steroidal saponins from T. govanianum exhibit good antidiabetic activity which could be used as nutraceutical supplements for the management of systemic glucose level.
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Affiliation(s)
- Patil Shivprasad Suresh
- Chemical Technology Division, CSIR-IHBT, Palampur, India.,Food and Nutraceuticals Division, CSIR-IHBT, Palampur, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, U.P., India
| | - Prithvi Pal Singh
- Chemical Technology Division, CSIR-IHBT, Palampur, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, U.P., India
| | - Yogendra S Padwad
- Food and Nutraceuticals Division, CSIR-IHBT, Palampur, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, U.P., India
| | - Upendra Sharma
- Chemical Technology Division, CSIR-IHBT, Palampur, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, U.P., India
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21
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Rathore S, Walia S, Devi R, Kumar R. Review on Trillium govanianum Wall. ex D. Don: A threatened medicinal plant from the Himalaya. J Herb Med 2020. [DOI: 10.1016/j.hermed.2020.100395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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22
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Gao X, Zhang X, Chen W, Li J, Yang W, Zhang X, Li S, Liu C. Transcriptome analysis of Paris polyphylla var. yunnanensis illuminates the biosynthesis and accumulation of steroidal saponins in rhizomes and leaves. PHYTOCHEMISTRY 2020; 178:112460. [PMID: 32692662 DOI: 10.1016/j.phytochem.2020.112460] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 07/10/2020] [Accepted: 07/12/2020] [Indexed: 06/11/2023]
Abstract
Paris polyphylla var. yunnanensis can synthesize Paris saponins with multiple effective therapies, and its rhizome has become an indispensable ingredient in many patented drugs. However, how Paris saponin content changes in tissues at different stages and the molecular mechanisms underlying the production and accumulation of the bioactive compounds are unclear. This study aimed to uncover the mechanisms underlying the biosynthesis and accumulation by integrating transcriptome sequencing and phytochemical investigation of the leaves and rhizomes at different growth stages. Paris saponin content in leaves was lower during the fruiting stage than the vegetative stage, whereas the content in rhizomes increased during the fruiting stage. The candidate genes related to Paris saponin biosynthesis were determined by transcriptome analyses. Most biosynthetic genes were found to be abundantly expressed in the leaves during the vegetative stage in the light of expression profiles and functional enrichment results. The expression patterns of the differentially expressed genes related to the biosynthesis were positively correlated with the accumulation of saponins in tissues. These findings suggest that both leaves and rhizomes are capable of biosynthesizing Paris saponins, and that aerial plant parts can be used to extract them. The different patterns of biosynthesis and accumulation in the leaves and rhizomes were also determined here. This study will help improve our understanding of the mechanisms underlying the biosynthesis and accumulation of Paris saponins, and aid in the comprehensive development and utilization of this medicinal plant.
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Affiliation(s)
- Xiaoyang Gao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Xuan Zhang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wen Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Jing Li
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenjing Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xingwang Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China; The Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.
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23
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Dragon’s Blood from Dracaena cambodiana in China: Applied History and Induction Techniques toward Formation Mechanism. FORESTS 2020. [DOI: 10.3390/f11040372] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Dragon’s blood that is extracted from Dracaena plants has been widely used as traditional medicine in various ancient cultures. The application of dragon’s blood has a cherished history in China, even though the original plants were not discovered for some period. Dracaena cochinchinensis and Dracaena cambodiana were successively discovered in southern China during the 1970s–1980s. In the last half of the century, Chinese scientists have extensively investigated the production of dragon’s blood from these two Dracaena species, whereas these results have not been previously systematically summarized, as in the present paper. Herein, we present the applied history in ancient China and artificially induced technologies for dragon’s blood development based on these two Dracaena species, in particular, using tissue cultures seedlings and tender plants of D. cambodiana. Big data research, including transcriptomic and genomic studies, has suggested that dragon’s blood might be a defense substance that is secreted by Dracaena plants in response to (a)biotic stimuli. This review represents an effort to highlight the progress and achievements from applied history as well as induction techniques that are used for the formation of dragon’s blood that have taken place in China. Such knowledge might aid in the global conservation of wild Dracaena species and contribute to understanding dragon blood formation mechanisms, eventually assisting in the efficient utilization of limited Dracaena plant resources for the sustainable production of dragon’s blood.
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Cai B, Zhang Y, Wang Z, Xu D, Jia Y, Guan Y, Liao A, Liu G, Chun C, Li J. Therapeutic Potential of Diosgenin and Its Major Derivatives against Neurological Diseases: Recent Advances. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:3153082. [PMID: 32215172 PMCID: PMC7079249 DOI: 10.1155/2020/3153082] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 12/16/2019] [Accepted: 12/30/2019] [Indexed: 12/15/2022]
Abstract
Diosgenin (DG), a well-known steroidal sapogenin, is present abundantly in medicinal herbs such as Dioscorea rhizome, Dioscorea villosa, Trigonella foenum-graecum, Smilax China, and Rhizoma polgonati. DG is utilized as a major starting material for the production of steroidal drugs in the pharmaceutical industry. Due to its wide range of pharmacological activities and medicinal properties, it has been used in the treatment of cancers, hyperlipidemia, inflammation, and infections. Numerous studies have reported that DG is useful in the prevention and treatment of neurological diseases. Its therapeutic mechanisms are based on the mediation of different signaling pathways, and targeting these pathways might lead to the development of effective therapeutic agents for neurological diseases. The present review mainly summarizes recent progress using DG and its derivatives as therapeutic agents for multiple neurological disorders along with their various mechanisms in the central nervous system. In particular, those related to therapeutic efficacy for Parkinson's disease, Alzheimer's disease, brain injury, neuroinflammation, and ischemia are discussed. This review article also critically evaluates existing limitations associated with the solubility and bioavailability of DG and discusses imperatives for translational clinical research. It briefly recapitulates recent advances in structural modification and novel formulations to increase the therapeutic efficacy and brain levels of DG. In the present review, databases of PubMed, Web of Science, and Scopus were used for studies of DG and its derivatives in the treatment of central nervous system diseases published in English until December 10, 2019. Three independent researchers examined articles for eligibility. A total of 150 articles were screened from the above scientific literature databases. Finally, a total of 46 articles were extracted and included in this review. Keywords related to glioma, ischemia, memory, aging, cognitive impairment, Alzheimer, Parkinson, and neurodegenerative disorders were searched in the databases based on DG and its derivatives.
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Affiliation(s)
- Bangrong Cai
- Henan Research Center for Special Processing Technology of Chinese Medicine, School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Ying Zhang
- Department of Biochemistry, Department of Biomedical Sciences, Research Center for Aging and Geriatrics, Research Institute of Medical Sciences, Chonnam National University Medical School, Gwangju 501-190, Republic of Korea
| | - Zengtao Wang
- Department of Medicinal Chemistry, College of Pharmacy JiangXi University of Traditional Chinese Medicine, Nanchang 330004, China
| | - Dujuan Xu
- Henan Research Center for Special Processing Technology of Chinese Medicine, School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Yongyan Jia
- Henan Research Center for Special Processing Technology of Chinese Medicine, School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Yanbin Guan
- Henan Research Center for Special Processing Technology of Chinese Medicine, School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Aimei Liao
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Gaizhi Liu
- Henan Research Center for Special Processing Technology of Chinese Medicine, School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - ChangJu Chun
- Research Institute of Drug Development, College of Pharmacy, Chonnam National University, Gwangju, Republic of Korea
| | - Jiansheng Li
- Collaborative Innovation Center for Respiratory Disease Diagnosis and Treatment and Chinese Medicine Development of Henan Province, Henan Key Laboratory of Chinese Medicine for Respiratory Disease, Henan University of Chinese Medicine, China
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25
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Singh G, Pal P, Masand M, Seth R, Kumar A, Singh S, Sharma RK. Comparative transcriptome analysis revealed gamma-irradiation mediated disruption of floral integrator gene(s) leading to prolonged vegetative phase in Stevia rebaudiana Bertoni. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 148:90-102. [PMID: 31951945 DOI: 10.1016/j.plaphy.2020.01.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/02/2020] [Accepted: 01/03/2020] [Indexed: 06/10/2023]
Abstract
Stevia rebaudiana Bert. is getting global attention because of its ability to synthesize commercially important low/no calorie natural sweeteners (LNCSs) steviol glycosides (SGs). Considering, higher accumulation of SGs in vegetative phase followed by decrement during reproductive phase necessitate the understanding of different molecular components of floral transition to develop superior varieties/cultivars with prolonged vegetative phase in Stevia. Current comparative transcriptional analysis of low dose (5 kR) gamma-irradiated mutant genotype (SMG) with prolonged vegetative phase vis-à-vis background genotype (SBG) identified DGEs of major floral transition pathways, and expressed according to their physiological fate irrespective to SMG & SBG. Contrarily, reduced expression of floral integrator genes (FT and LEAFY) in mutant genotype suggests their involvement in prolonged vegetative phase phenotype. Likewise, GO and KEGG enrichment of photosynthesis and carbon assimilation efficiency might be associated with prolonged vegetative phase and higher accumulation of Stevioside content in mutant genotype. Furthermore, deviation of flowering related transcription factors (higher expressions except MIKS-type MADS-box SMG_PV compared to SBG_F) may possibly be correlated with low expression of floral integrator genes. Findings of current studies will facilitate the genetic manipulations and crop improvement efforts in Stevia through conventional breeding and genome editing approaches for increased SGs biosynthesis.
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Affiliation(s)
- Gopal Singh
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Poonam Pal
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Mamta Masand
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Romit Seth
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Ashok Kumar
- Agrotechnology of Medicinal, Aromatic and Commercially Important Plants (AMACIP) Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Sanatsujat Singh
- Agrotechnology of Medicinal, Aromatic and Commercially Important Plants (AMACIP) Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Ram Kumar Sharma
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India.
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Parmar R, Seth R, Singh P, Singh G, Kumar S, Sharma RK. Transcriptional profiling of contrasting genotypes revealed key candidates and nucleotide variations for drought dissection in Camellia sinensis (L.) O. Kuntze. Sci Rep 2019; 9:7487. [PMID: 31097754 PMCID: PMC6522520 DOI: 10.1038/s41598-019-43925-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 05/01/2019] [Indexed: 12/20/2022] Open
Abstract
Tea is popular health beverage consumed by millions of people worldwide. Drought is among the acute abiotic stress severely affecting tea cultivation, globally. In current study, transcriptome sequencing of four diverse tea genotypes with inherent contrasting genetic response to drought (tolerant & sensitive) generated more than 140 million reads. De novo and reference-based assembly and functional annotation of 67,093 transcripts with multifarious public protein databases yielded 54,484 (78.2%) transcripts with significant enrichment of GO and KEGG drought responsive pathways in tolerant genotypes. Comparative DGE and qRT analysis revealed key role of ABA dependent & independent pathways, potassium & ABC membrane transporters (AtABCG22, AtABCG11, AtABCC5 & AtABCC4) and antioxidant defence system against oxidative stress in tolerant genotypes, while seems to be failed in sensitive genotypes. Additionally, highly expressed UPL3HECT E3 ligases and RING E3 ligases possibly enhance drought tolerance by actively regulating functional modification of stress related genes. Further, ascertainment of, 80803 high quality putative SNPs with functional validation of key non-synonymous SNPs suggested their implications for developing high-throughput genotyping platform in tea. Futuristically, functionally relevant genomic resources can be potentially utilized for gene discovery, genetic engineering and marker-assisted genetic improvement for better yield and quality in tea under drought conditions.
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Affiliation(s)
- Rajni Parmar
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-IHBT, Palampur, Himachal Pradesh, 176061, India
| | - Romit Seth
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India.,Department of Biotechnology, Guru Nanak Dev University, Amritsar, 143005, India
| | - Pradeep Singh
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India.,Department of Biotechnology, Guru Nanak Dev University, Amritsar, 143005, India
| | - Gopal Singh
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-IHBT, Palampur, Himachal Pradesh, 176061, India
| | - Sanjay Kumar
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-IHBT, Palampur, Himachal Pradesh, 176061, India
| | - Ram Kumar Sharma
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India. .,Academy of Scientific and Innovative Research (AcSIR), CSIR-IHBT, Palampur, Himachal Pradesh, 176061, India.
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Yang Z, Yang L, Liu C, Qin X, Liu H, Chen J, Ji Y. Transcriptome analyses of Paris polyphylla var. chinensis, Ypsilandra thibetica, and Polygonatum kingianum characterize their steroidal saponin biosynthesis pathway. Fitoterapia 2019; 135:52-63. [PMID: 30999023 DOI: 10.1016/j.fitote.2019.04.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 04/01/2019] [Accepted: 04/13/2019] [Indexed: 10/27/2022]
Abstract
Steroidal saponins, one of the most diverse groups of plant-derived natural products, elicit biological and pharmacological activities; however, the genes involved in their biosynthesis and the corresponding biosynthetic pathway in monocotyledon plants remain unclear. This study aimed to identify genes involved in the biosynthesis of steroidal saponins by performing a comparative analysis among transcriptomes of Paris polyphylla var. chinensis (PPC), Ypsilandra thibetica (YT), and Polygonatum kingianum (PK). De novo transcriptome assemblies generated 57,537, 140,420, and 151,773 unigenes from PPC, YT, and PK, respectively, of which 56.54, 47.81, and 44.30% were successfully annotated, respectively. Among the transcriptomes for PPC, YT, and PK, we identified 194, 169, and 131; 17, 14, and 26; and, 80, 122, and 113 unigenes corresponding to terpenoid backbone biosynthesis; sesquiterpenoid and triterpenoid biosynthesis; and, steroid biosynthesis pathways, respectively. These genes are putatively involved in the biosynthesis of cholesterol that is the primary precursor of steroidal saponins. Phylogenetic analyses indicated that lanosterol synthase may be exclusive to dicotyledon plant species, and the cytochrome P450 unigenes were closely related to clusters CYP90B1 and CYP734A1, which are UDP-glycosyltransferases unigenes homologous with the UGT73 family. Thus, unigenes of β-glucosidase may be candidate genes for catalysis of later period modifications of the steroidal saponin skeleton. Our data provide evidence to support the hypothesis that monocotyledons biosynthesize steroidal saponins from cholesterol via the cycloartenol pathway.
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Affiliation(s)
- Zhenyan Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, PR China; Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Population, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, PR China
| | - Lifang Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, PR China; School of Life Science, Yunnan University, Kunming 650201, Yunnan, PR China
| | - Changkun Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, PR China; Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Population, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, PR China
| | - Xujie Qin
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, PR China
| | - Haiyang Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, PR China
| | - Jiahui Chen
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, PR China.
| | - Yunheng Ji
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, PR China; Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Population, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, PR China.
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Drapal M, de Carvalho EB, Rouard M, Amah D, Sardos J, Van den Houwe I, Brown A, Roux N, Swennen R, Fraser PD. Metabolite profiling characterises chemotypes of Musa diploids and triploids at juvenile and pre-flowering growth stages. Sci Rep 2019; 9:4657. [PMID: 30874619 PMCID: PMC6420674 DOI: 10.1038/s41598-019-41037-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 02/22/2019] [Indexed: 11/16/2022] Open
Abstract
Bananas (Musa spp.) are consumed worldwide as dessert and cooking types. Edible banana varieties are for the most part seedless and sterile and therefore vegetatively propagated. This confers difficulties for breeding approaches against pressing biotic and abiotic threats and for the nutritional enhancement of banana pulp. A panel of banana accessions, representative of the diversity of wild and cultivated bananas, was analysed to assess the range of chemotypes available globally. The focus of this assessment was banana leaves at two growth stages (juvenile and pre-flowering), to see when during the plant growth metabolic differences can be established. The metabolic data corresponded to genomic trends reported in previous studies and demonstrated a link between metabolites/pathways and the genomes of M. acuminata and M. balbisiana. Furthermore, the vigour and resistance traits of M. balbisiana was connected to the phenolic composition and showed differences with the number of B genes in the hybrid accessions. Differences in the juvenile and pre-flowering data led to low correlation between the growth stages for prediction purposes.
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Affiliation(s)
- Margit Drapal
- School of Biological Sciences, Royal Holloway, University of London, Egham Hill, Egham, Surrey, TW20 0EX, UK
| | | | - Mathieu Rouard
- Bioversity France, Parc Scientifique Agropolis II, 34397, Montpellier, Cedex 5, France
| | - Delphine Amah
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Julie Sardos
- Bioversity France, Parc Scientifique Agropolis II, 34397, Montpellier, Cedex 5, France
| | | | - Allan Brown
- International Institute of Tropical Agriculture, Arusha, Tanzania
| | - Nicolas Roux
- Bioversity France, Parc Scientifique Agropolis II, 34397, Montpellier, Cedex 5, France
| | - Rony Swennen
- International Institute of Tropical Agriculture, Arusha, Tanzania.,Bioversity International, W. De Croylaan 42, 3001, Heverlee, Belgium.,Department of Biosystem, KU Leuven University, Oude Markt 13 - bus 5005, 3000, Leuven, Belgium
| | - Paul D Fraser
- School of Biological Sciences, Royal Holloway, University of London, Egham Hill, Egham, Surrey, TW20 0EX, UK.
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Drapal M, Barros de Carvalho E, Ovalle Rivera TM, Becerra Lopez-Lavalle LA, Fraser PD. Capturing Biochemical Diversity in Cassava ( Manihot esculenta Crantz) through the Application of Metabolite Profiling. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:986-993. [PMID: 30557498 PMCID: PMC6346375 DOI: 10.1021/acs.jafc.8b04769] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 12/10/2018] [Accepted: 12/17/2018] [Indexed: 05/19/2023]
Abstract
Cassava ( Manihot esculenta Crantz) is the predominant staple food in Sub-Saharan Africa (SSA) and an industrial crop in South East Asia. Despite focused breeding efforts for increased yield, resistance, and nutritional value, cassava breeding has not advanced at the same rapidity as other staple crops. In the present study, metabolomic techniques were implemented to characterize the chemotypes of selected cassava accessions and assess potential resources for the breeding program. The metabolite data analyzed was applied to describe the biochemical diversity available in the panel, identifying South American accessions as the most diverse. Genotypes with distinct phenotypic traits showed a representative metabolite profile and could be clearly identified, even if the phenotypic trait was a root characteristic, e.g., high amylose content.
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Affiliation(s)
- Margit Drapal
- School
of Biological Sciences, Royal Holloway,
University of London, Egham Hill, Egham, Surrey TW20 0EX, U.K.
| | | | | | | | - Paul D. Fraser
- School
of Biological Sciences, Royal Holloway,
University of London, Egham Hill, Egham, Surrey TW20 0EX, U.K.
- E-mail: . Phone: +44 1784
443894
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30
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Upadhyay S, Jeena GS, Shukla RK. Recent advances in steroidal saponins biosynthesis and in vitro production. PLANTA 2018; 248:519-544. [PMID: 29748819 DOI: 10.1007/s00425-018-2911-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 04/27/2018] [Indexed: 06/08/2023]
Abstract
Steroidal saponins exhibited numerous pharmacological activities due to the modification of their backbone by different cytochrome P450s (P450) and UDP glycosyltransferases (UGTs). Plant-derived steroidal saponins are not sufficient for utilizing them for commercial purpose so in vitro production of saponin by tissue culture, root culture, embryo culture, etc, is necessary for its large-scale production. Saponin glycosides are the important class of plant secondary metabolites, which consists of either steroidal or terpenoidal backbone. Due to the existence of a wide range of medicinal properties, saponin glycosides are pharmacologically very important. This review is focused on important medicinal properties of steroidal saponin, its occurrence, and biosynthesis. In addition to this, some recently identified plants containing steroidal saponins in different parts were summarized. The high throughput transcriptome sequencing approach elaborates our understanding related to the secondary metabolic pathway and its regulation even in the absence of adequate genomic information of non-model plants. The aim of this review is to encapsulate the information related to applications of steroidal saponin and its biosynthetic enzymes specially P450s and UGTs that are involved at later stage modifications of saponin backbone. Lastly, we discussed the in vitro production of steroidal saponin as the plant-based production of saponin is time-consuming and yield a limited amount of saponins. A large amount of plant material has been used to increase the production of steroidal saponin by employing in vitro culture technique, which has received a lot of attention in past two decades and provides a way to conserve medicinal plants as well as to escape them for being endangered.
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Affiliation(s)
- Swati Upadhyay
- Biotechnology Division (CSIR-CIMAP), Central Institute of Medicinal and Aromatic Plants, (CSIR-CIMAP) P.O. CIMAP (a laboratory under Council of Scientific and Industrial Research, India), Near Kukrail Picnic Spot, Lucknow, 226015, India
| | - Gajendra Singh Jeena
- Biotechnology Division (CSIR-CIMAP), Central Institute of Medicinal and Aromatic Plants, (CSIR-CIMAP) P.O. CIMAP (a laboratory under Council of Scientific and Industrial Research, India), Near Kukrail Picnic Spot, Lucknow, 226015, India
| | - Rakesh Kumar Shukla
- Biotechnology Division (CSIR-CIMAP), Central Institute of Medicinal and Aromatic Plants, (CSIR-CIMAP) P.O. CIMAP (a laboratory under Council of Scientific and Industrial Research, India), Near Kukrail Picnic Spot, Lucknow, 226015, India.
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31
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de Brito Francisco R, Martinoia E. The Vacuolar Transportome of Plant Specialized Metabolites. PLANT & CELL PHYSIOLOGY 2018; 59:1326-1336. [PMID: 29452376 DOI: 10.1093/pcp/pcy039] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/05/2018] [Indexed: 05/21/2023]
Abstract
The plant vacuole is a cellular compartment that is essential to plant development and growth. Often plant vacuoles accumulate specialized metabolites, also called secondary metabolites, which constitute functionally and chemically diverse compounds that exert in planta many essential functions and improve the plant's fitness. These metabolites provide, for example, chemical defense against herbivorous and pathogens or chemical attractants (color and fragrance) to attract pollinators. The chemical composition of the vacuole is dynamic, and is altered during development and as a response to environmental changes. To some extent these alterations rely on vacuolar transporters, which import and export compounds into and out of the vacuole, respectively. During the past decade, significant progress was made in the identification and functional characterization of the transporters implicated in many aspects of plant specialized metabolism. Still, deciphering the molecular players underlying such processes remains a challenge for the future. In this review, we present a comprehensive summary of the most recent achievements in this field.
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Affiliation(s)
| | - Enrico Martinoia
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
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32
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Zhu JH, Li HL, Guo D, Wang Y, Dai HF, Mei WL, Peng SQ. Identification, characterization and expression analysis of genes involved in steroidal saponin biosynthesis in Dracaena cambodiana. JOURNAL OF PLANT RESEARCH 2018; 131:555-562. [PMID: 29234988 DOI: 10.1007/s10265-017-1004-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/22/2017] [Indexed: 05/24/2023]
Abstract
Dracaena cambodiana is a traditional medicinal plant used for producing dragon's blood. The plants and dragon's blood of D. cambodiana contain a rich variety of steroidal saponins. However, little is known about steroidal saponin biosynthesis and its regulation in D. cambodiana. Here, 122 genes encoding enzymes involved in steroidal saponin biosynthesis were identified based on transcriptome data, with 29 of them containing complete open reading frames (ORF). Transcript expression analysis revealed that several genes related to steroidal saponin biosynthesis showed distinct tissue-specific expression patterns; the expression levels of genes encoding the key enzymes involved in the biosynthesis and early modification of steroidal saponins were significantly down-regulated in the stems in response to the inducer of dragon's blood, exhibiting positive correlations with the content of steroidal saponins. These results provide insights on the steroidal saponins biosynthetic pathway and mechanisms underlying induced formation of dragon's blood in D. cambodiana.
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Affiliation(s)
- Jia-Hong Zhu
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Hui-Liang Li
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Dong Guo
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Ying Wang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Hao-Fu Dai
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Wen-Li Mei
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.
| | - Shi-Qing Peng
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.
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33
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Nguyen LT, Reverter A, Cánovas A, Venus B, Anderson ST, Islas-Trejo A, Dias MM, Crawford NF, Lehnert SA, Medrano JF, Thomas MG, Moore SS, Fortes MRS. STAT6, PBX2, and PBRM1 Emerge as Predicted Regulators of 452 Differentially Expressed Genes Associated With Puberty in Brahman Heifers. Front Genet 2018; 9:87. [PMID: 29616079 PMCID: PMC5869259 DOI: 10.3389/fgene.2018.00087] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 03/02/2018] [Indexed: 12/17/2022] Open
Abstract
The liver plays a central role in metabolism and produces important hormones. Hepatic estrogen receptors and the release of insulin-like growth factor 1 (IGF1) are critical links between liver function and the reproductive system. However, the role of liver in pubertal development is not fully understood. To explore this question, we applied transcriptomic analyses to liver samples of pre- and post-pubertal Brahman heifers and identified differentially expressed (DE) genes and genes encoding transcription factors (TFs). Differential expression of genes suggests potential biological mechanisms and pathways linking liver function to puberty. The analyses identified 452 DE genes and 82 TF with significant contribution to differential gene expression by using a regulatory impact factor metric. Brain-derived neurotrophic factor was observed as the most down-regulated gene (P = 0.003) in post-pubertal heifers and we propose this gene influences pubertal development in Brahman heifers. Additionally, co-expression network analysis provided evidence for three TF as key regulators of liver function during pubertal development: the signal transducer and activator of transcription 6, PBX homeobox 2, and polybromo 1. Pathway enrichment analysis identified transforming growth factor-beta and Wnt signaling pathways as significant annotation terms for the list of DE genes and TF in the co-expression network. Molecular information regarding genes and pathways described in this work are important to further our understanding of puberty onset in Brahman heifers.
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Affiliation(s)
- Loan T Nguyen
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia.,Faculty of Biotechnology, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Antonio Reverter
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, QLD, Australia
| | - Angela Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Bronwyn Venus
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Stephen T Anderson
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Alma Islas-Trejo
- Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Marina M Dias
- Departamento de Zootecnia, Faculdade de Ciências Agráìrias e Veterináìrias, Universidade Estadual Paulista Júlio de Mesquita Filho, São Paulo, Brazil
| | - Natalie F Crawford
- Department of Animal Science, Colorado State University, Fort Collins, CO, United States
| | - Sigrid A Lehnert
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, QLD, Australia
| | - Juan F Medrano
- Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Milt G Thomas
- Department of Animal Science, Colorado State University, Fort Collins, CO, United States
| | - Stephen S Moore
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Marina R S Fortes
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia.,Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
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34
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Singh G, Singh G, Singh P, Parmar R, Paul N, Vashist R, Swarnkar MK, Kumar A, Singh S, Singh AK, Kumar S, Sharma RK. Molecular dissection of transcriptional reprogramming of steviol glycosides synthesis in leaf tissue during developmental phase transitions in Stevia rebaudiana Bert. Sci Rep 2017; 7:11835. [PMID: 28928460 PMCID: PMC5605536 DOI: 10.1038/s41598-017-12025-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 09/01/2017] [Indexed: 12/18/2022] Open
Abstract
Stevia is a natural source of commercially important steviol glycosides (SGs), which share biosynthesis route with gibberellic acids (GAs) through plastidal MEP and cytosolic MVA pathways. Ontogeny-dependent deviation in SGs biosynthesis is one of the key factor for global cultivation of Stevia, has not been studied at transcriptional level. To dissect underlying molecular mechanism, we followed a global transcriptome sequencing approach and generated more than 100 million reads. Annotation of 41,262 de novo assembled transcripts identified all the genes required for SGs and GAs biosynthesis. Differential gene expression and quantitative analysis of important pathway genes (DXS, HMGR, KA13H) and gene regulators (WRKY, MYB, NAC TFs) indicated developmental phase dependent utilization of metabolic flux between SGs and GAs synthesis. Further, identification of 124 CYPs and 45 UGTs enrich the genomic resources, and their PPI network analysis with SGs/GAs biosynthesis proteins identifies putative candidates involved in metabolic changes, as supported by their developmental phase-dependent expression. These putative targets can expedite molecular breeding and genetic engineering efforts to enhance SGs content, biomass and yield. Futuristically, the generated dataset will be a useful resource for development of functional molecular markers for diversity characterization, genome mapping and evolutionary studies in Stevia.
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Affiliation(s)
- Gopal Singh
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
- Academy of Scientific and Innovative Research, New Delhi, India
| | - Gagandeep Singh
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Pradeep Singh
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Rajni Parmar
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
- Academy of Scientific and Innovative Research, New Delhi, India
| | - Navgeet Paul
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Radhika Vashist
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Mohit Kumar Swarnkar
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Ashok Kumar
- Agrotechnology of Medicinal, Aromatic and Commercially Important Plants, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Sanatsujat Singh
- Agrotechnology of Medicinal, Aromatic and Commercially Important Plants, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Anil Kumar Singh
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
- ICAR-Indian Institute of Agricultural Biotechnology, PDU Campus, IINRG, Namkum, Ranchi, Jharkhand, India
| | - Sanjay Kumar
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Ram Kumar Sharma
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India.
- Academy of Scientific and Innovative Research, New Delhi, India.
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