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Javan SL, Kashkooli AB, Shojaeiyan A, Majidian S. Transcriptomic data reveals the dynamics of terpenoids biosynthetic pathway of fenugreek. BMC Genomics 2024; 25:390. [PMID: 38649807 PMCID: PMC11034138 DOI: 10.1186/s12864-024-10253-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/26/2024] [Indexed: 04/25/2024] Open
Abstract
Medicinal plants are rich sources for treating various diseases due their bioactive secondary metabolites. Fenugreek (Trigonella foenum-graecum) is one of the medicinal plants traditionally used in human nutrition and medicine which contains an active substance, called diosgenin, with anticancer properties. Biosynthesis of this important anticancer compound in fenugreek can be enhanced using eliciting agents which involves in manipulation of metabolite and biochemical pathways stimulating defense responses. Methyl jasmonate elicitor was used to increase diosgenin biosynthesis in fenugreek plants. However, the molecular mechanism and gene expression profiles underlying diosgening accumulation remain unexplored. In the current study we performed an extensive analysis of publicly available RNA-sequencing datasets to elucidate the biosynthesis and expression profile of fenugreek plants treated with methyl jasmonate. For this purpose, seven read datasets of methyl jasmonate treated plants were obtained that were covering several post-treatment time points (6-120 h). Transcriptomics analysis revealed upregulation of several key genes involved in diosgenein biosynthetic pathway including Squalene synthase (SQS) as the first committed step in diosgenin biosynthesis as well as Squalene Epoxidase (SEP) and Cycloartenol Synthase (CAS) upon methyl jasmonate application. Bioinformatics analysis, including gene ontology enrichment and pathway analysis, further supported the involvement of these genes in diosgenin biosynthesis. The bioinformatics analysis led to a comprehensive validation, with expression profiling across three different fenugreek populations treated with the same methyl jasmonate application. Initially, key genes like SQS, SEP, and CAS showed upregulation, followed by later upregulation of Δ24, suggesting dynamic pathway regulation. Real-time PCR confirmed consistent upregulation of SQS and SEP, peaking at 72 h. Additionally, candidate genes Δ24 and SMT1 highlighted roles in directing metabolic flux towards diosgenin biosynthesis. This integrated approach validates the bioinformatics findings and elucidates fenugreek's molecular response to methyl jasmonate elicitation, offering insights for enhancing diosgenin yield. The assembled transcripts and gene expression profiles are deposited in the Zenodo open repository at https://doi.org/10.5281/zenodo.8155183 .
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Affiliation(s)
- Sara Lamei Javan
- Department of Horticultural Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | | | - AbdolAli Shojaeiyan
- Department of Horticultural Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Sina Majidian
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Switzerland SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
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Maleki M, Shojaeiyan A, Mokhtassi-Bidgoli A. Differential responses of two fenugreek (Trigonella foenum-graecum L.) landraces pretreated with melatonin to prolonged drought stress and subsequent recovery. BMC PLANT BIOLOGY 2024; 24:161. [PMID: 38429697 PMCID: PMC10908034 DOI: 10.1186/s12870-024-04835-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 02/18/2024] [Indexed: 03/03/2024]
Abstract
BACKGROUND Drought impairs growth, disturbs photosynthesis, and induces senescence in plants, which results in crop productivity reduction and ultimately jeopardizes human food security. The objective of this study was to determine major parameters associated with drought tolerance and recovery ability of fenugreek (Trigonella foenum-graecum L.), by examining differential biochemical and phenological responses and underlying enzyme activities as well as melatonin roles during drought stress and re-watering for two contrasting landraces. Moreover, the relative expression of three key genes involved in the biosynthesis pathway of diosgenin, including SQS, CAS, and BG, was investigated. RESULTS Depending on the conditions, drought stress enhanced the activity of antioxidant enzymes and the osmoregulating compounds, non-enzymatic antioxidants, hydrogen peroxide content, and lipid peroxidation levels in most cases. Severe drought stress accelerated flowering time in Shushtar landrace (SHR) but had no significant effects on Varamin (VR). Pretreatment with melatonin delayed flowering time in SHR and caused high drought resistance in this landrace. Furthermore, melatonin significantly enhanced drought adaptability in VR by improving plant recovery ability. DISCUSSION Based on our results plants' responses to drought stress and melatonin pretreatment were completely landrace-specific. Drought stress caused an increase in the relative expression of CAS gene and ultimately the accumulation of steroidal saponins in SHR. Melatonin compensated for the decrease in biomass production due to drought stress and finally increased steroidal saponins performance in SHR. Our study showed that melatonin can improve drought stress and recovery in fenugreek, but different factors such as genotype, melatonin concentration, and plant age should be considered.
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Affiliation(s)
- Masoud Maleki
- Department of Horticultural Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Abdolali Shojaeiyan
- Department of Horticultural Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
| | - Ali Mokhtassi-Bidgoli
- Department of Agronomy, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
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Liao H, Quan H, Huang B, Ji H, Zhang T, Chen J, Zhou J. Integrated transcriptomic and metabolomic analysis reveals the molecular basis of tissue-specific accumulation of bioactive steroidal alkaloids in Fritillaria unibracteata. PHYTOCHEMISTRY 2023; 214:113831. [PMID: 37598994 DOI: 10.1016/j.phytochem.2023.113831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 08/22/2023]
Abstract
Fritillaria unibracteata is an endangered medicinal plant whose bulb has been used as a Chinese herb to suppress cough, asthma and excessive phlegm for centuries. Steroidal alkaloids, which are synthesized via the steroid synthesis pathways, are their significant bioactive constituents. However, few studies on genes involved in steroidal alkaloid biosynthesis in F. unibracteata have been reported, mainly due to the lack of the F. unibracteata genome. In this paper, comparative transcriptomic and metabolomic analyses of four different tissues of F. unibracteata (leaves, flowers, stems, and bulbs) were performed. Imperialine, peiminine, and peimisine were among the significant bioactive compounds that were considerably abundant in bulb tissue, according to the metabolomic findings. Then, 83.60 Gb transcriptome sequencing of four different tissues was performed, of which one gene encoding phosphomevalonate kinase was directly functionally characterized to verify the accuracy of sequences obtained from the transcriptome. A total of 9217 differentially expressed unigenes (DEGs) were identified in four different tissues of F. unibracteata. GO and KEGG enrichments revealed that phenylpropanoid biosynthesis, MVA-mediated terpenoid backbone biosynthesis, and steroid biosynthesis were enriched in bulb tissue, whereas enrichment of MEP-mediated terpenoid backbone biosynthesis, photosynthesis, photosynthesis-antenna protein and carotenoid biosynthesis was observed in aerial tissues. Moreover, clustering analysis indicated that the downstream steroid biosynthesis pathway was more important in steroidal alkaloid biosynthesis compared to the upstream terpenoid backbone biosynthesis pathway. Hence, MVA-mediated biosynthesis of steroidal alkaloids was proposed, in which 15 bulb-clustered DEGs were positively correlated with a high accumulation of bioactive steroid alkaloids, further validating our proposal. In addition, 36 CYP450s showing a positive correlation with bioactive steroidal alkaloids provided candidate enzymes to catalyze the subsequent steps of steroidal alkaloid biosynthesis. In addition, the transcription factors and ABC transporters clustered in bulb tissue might be responsible for the regulation and transportation of steroidal alkaloid biosynthesis. Protein-protein interaction analysis implied a highly complex steroid alkaloid biosynthesis network in which delta (24)-sterol reductase might be one of the central catalysts. Based on the integrated transcriptome and metabolome, this current study is a first step in understanding the tissue-specific biosynthesis of steroidal alkaloids in F. unibracteata. Furthermore, key genes and regulators identified herein could facilitate metabolic engineering to improve steroidal alkaloids in F. unibracteata.
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Affiliation(s)
- Hai Liao
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, 610031, China.
| | - Huige Quan
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, 610031, China.
| | - Binhan Huang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, 610031, China.
| | - Huiyue Ji
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, 610031, China.
| | - Tian Zhang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, 610031, China.
| | - Jiao Chen
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, 610031, China.
| | - Jiayu Zhou
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, 610031, China.
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4
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Szeliga M, Bakera B, Święcicka M, Tyrka M, Rakoczy-Trojanowska M. Identification of candidate genes responsible for chasmogamy in wheat. BMC Genomics 2023; 24:170. [PMID: 37016302 PMCID: PMC10074802 DOI: 10.1186/s12864-023-09252-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 03/15/2023] [Indexed: 04/06/2023] Open
Abstract
BACKGROUND The flowering biology of wheat plants favours self-pollination which causes obstacles in wheat hybrid breeding. Wheat flowers can be divided into two groups, the first one is characterized by flowering and pollination within closed flowers (cleistogamy), while the second one possesses the ability to open flowers during processes mentioned above (chasmogamy). The swelling of lodicules is involved in the flowering of cereals and among others their morphology, calcium and potassium content differentiate between cleistogamic and non-cleistogamous flowers. A better understanding of the chasmogamy mechanism can lead to the development of tools for selection of plants with the desired outcrossing rate. To learn more, the sequencing of transcriptomes (RNA-Seq) and Representational Difference Analysis products (RDA-Seq) were performed to investigate the global transcriptomes of wheat lodicules in two highly chasmogamous (HCH, Piko and Poezja) and two low chasmogamous (LCH, Euforia and KWS Dacanto) varieties at two developmental stages-pre-flowering and early flowering. RESULTS The differentially expressed genes were enriched in five, main pathways: "metabolism", "organismal systems", "genetic information processing", "cellular processes" and "environmental information processing", respectively. Important genes with opposite patterns of regulation between the HCH and LCH lines have been associated with the lodicule development i.e. expression levels of MADS16 and MADS58 genes may be responsible for quantitative differences in chasmogamy level in wheat. CONCLUSIONS We conclude that the results provide a new insight into lodicules involvement in the wheat flowering process. This study generated important genomic information to support the exploitation of the chasmogamy in wheat hybrid breeding programs.
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Affiliation(s)
- Magdalena Szeliga
- Rzeszow University of Technology, Powstańców Warszawy 12, 35-959, Rzeszów, Poland.
| | - Beata Bakera
- Faculty of Biology, Institute of Experimental Plant Biology and Biotechnology, University of Warsaw, Miecznikowa Street 1, 02-096, Warsaw, Poland
| | - Magdalena Święcicka
- Warsaw University of Life Sciences, Nowoursynowska 166, 02-787, Warsaw, Poland
| | - Mirosław Tyrka
- Rzeszow University of Technology, Powstańców Warszawy 12, 35-959, Rzeszów, Poland
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Li Y, Yang H, Li Z, Li S, Li J. Advances in the Biosynthesis and Molecular Evolution of Steroidal Saponins in Plants. Int J Mol Sci 2023; 24:ijms24032620. [PMID: 36768941 PMCID: PMC9917158 DOI: 10.3390/ijms24032620] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
Steroidal saponins are an important type of plant-specific metabolite that are essential for plants' responses to biotic and abiotic stresses. Because of their extensive pharmacological activities, steroidal saponins are also important industrial raw materials for the production of steroidal drugs. In recent years, more and more studies have explored the biosynthesis of steroidal saponins in plants, but most of them only focused on the biosynthesis of their molecular skeleton, diosgenin, and their subsequent glycosylation modification mechanism needs to be further studied. In addition, the biosynthetic regulation mechanism of steroidal saponins, their distribution pattern, and their molecular evolution in plants remain unclear. In this review, we summarized and discussed recent studies on the biosynthesis, molecular regulation, and function of steroidal saponins. Finally, we also reviewed the distribution and molecular evolution of steroidal saponins in plants. The elucidation of the biosynthesis, regulation, and molecular evolutionary mechanisms of steroidal saponins is crucial to provide new insights and references for studying their distribution, diversity, and evolutionary history in plants. Furthermore, a deeper understanding of steroidal saponin biosynthesis will contribute to their industrial production and pharmacological applications.
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Affiliation(s)
| | | | | | | | - Jiaru Li
- Correspondence: ; Tel.: +86-27-6875-3599
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Amiri F, Moghadam A, Tahmasebi A, Niazi A. Identification of key genes involved in secondary metabolite biosynthesis in Digitalis purpurea. PLoS One 2023; 18:e0277293. [PMID: 36893121 PMCID: PMC9997893 DOI: 10.1371/journal.pone.0277293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 10/25/2022] [Indexed: 03/10/2023] Open
Abstract
The medicinal plant Digitalis purpurea produces cardiac glycosides that are useful in the pharmaceutical industry. These bioactive compounds are in high demand due to ethnobotany's application to therapeutic procedures. Recent studies have investigated the role of integrative analysis of multi-omics data in understanding cellular metabolic status through systems metabolic engineering approach, as well as its application to genetically engineering metabolic pathways. In spite of numerous omics experiments, most molecular mechanisms involved in metabolic pathways biosynthesis in D. purpurea remain unclear. Using R Package Weighted Gene Co-expression Network Analysis, co-expression analysis was performed on the transcriptome and metabolome data. As a result of our study, we identified transcription factors, transcriptional regulators, protein kinases, transporters, non-coding RNAs, and hub genes that are involved in the production of secondary metabolites. Since jasmonates are involved in the biosynthesis of cardiac glycosides, the candidate genes for Scarecrow-Like Protein 14 (SCL14), Delta24-sterol reductase (DWF1), HYDRA1 (HYD1), and Jasmonate-ZIM domain3 (JAZ3) were validated under methyl jasmonate treatment (MeJA, 100 μM). Despite early induction of JAZ3, which affected downstream genes, it was dramatically suppressed after 48 hours. SCL14, which targets DWF1, and HYD1, which induces cholesterol and cardiac glycoside biosynthesis, were both promoted. The correlation between key genes and main metabolites and validation of expression patterns provide a unique insight into the biosynthesis mechanisms of cardiac glycosides in D. purpurea.
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Affiliation(s)
- Fatemeh Amiri
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
| | - Ali Moghadam
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
- * E-mail:
| | | | - Ali Niazi
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
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7
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Tiedge K, Li X, Merrill AT, Davisson D, Chen Y, Yu P, Tantillo DJ, Last RL, Zerbe P. Comparative transcriptomics and metabolomics reveal specialized metabolite drought stress responses in switchgrass (Panicum virgatum). THE NEW PHYTOLOGIST 2022; 236:1393-1408. [PMID: 36028985 PMCID: PMC9912200 DOI: 10.1111/nph.18443] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/09/2022] [Indexed: 05/13/2023]
Abstract
Switchgrass (Panicum virgatum) is a bioenergy model crop valued for its energy efficiency and drought tolerance. The related monocot species rice (Oryza sativa) and maize (Zea mays) deploy species-specific, specialized metabolites as core stress defenses. By contrast, specialized chemical defenses in switchgrass are largely unknown. To investigate specialized metabolic drought responses in switchgrass, we integrated tissue-specific transcriptome and metabolite analyses of the genotypes Alamo and Cave-in-Rock that feature different drought tolerance. The more drought-susceptible Cave-in-Rock featured an earlier onset of transcriptomic changes and significantly more differentially expressed genes in response to drought compared to Alamo. Specialized pathways showed moderate differential expression compared to pronounced transcriptomic alterations in carbohydrate and amino acid metabolism. However, diterpenoid-biosynthetic genes showed drought-inducible expression in Alamo roots, contrasting largely unaltered triterpenoid and phenylpropanoid pathways. Metabolomic analyses identified common and genotype-specific flavonoids and terpenoids. Consistent with transcriptomic alterations, several root diterpenoids showed significant drought-induced accumulation, whereas triterpenoid abundance remained predominantly unchanged. Structural analysis verified select drought-responsive diterpenoids as oxygenated furanoditerpenoids. Drought-dependent transcriptome and metabolite profiles provide the foundation to understand the molecular mechanisms underlying switchgrass drought responses. Accumulation of specialized root diterpenoids and corresponding pathway transcripts supports a role in drought stress tolerance.
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Affiliation(s)
- Kira Tiedge
- Department of Plant BiologyUniversity of California, DavisDavisCA95616USA
- Groningen Institute for Evolutionary Life SciencesUniversity of Groningen9747AG Groningenthe Netherlands
| | - Xingxing Li
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMI48824USA
- DOE Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingMI48824USA
| | - Amy T. Merrill
- Department of ChemistryUniversity of California, DavisDavisCA95616USA
| | - Danielle Davisson
- Department of Plant BiologyUniversity of California, DavisDavisCA95616USA
| | - Yuxuan Chen
- Department of Plant BiologyUniversity of California, DavisDavisCA95616USA
| | - Ping Yu
- NMR FacilityUniversity of California, DavisDavisCA95616USA
| | - Dean J. Tantillo
- Department of ChemistryUniversity of California, DavisDavisCA95616USA
| | - Robert L. Last
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMI48824USA
- DOE Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingMI48824USA
- Department Plant BiologyMichigan State UniversityEast LansingMI48824USA
| | - Philipp Zerbe
- Department of Plant BiologyUniversity of California, DavisDavisCA95616USA
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Exploring the medicinally important secondary metabolites landscape through the lens of transcriptome data in fenugreek (Trigonella foenum graecum L.). Sci Rep 2022; 12:13534. [PMID: 35941189 PMCID: PMC9359999 DOI: 10.1038/s41598-022-17779-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 07/30/2022] [Indexed: 11/08/2022] Open
Abstract
Fenugreek (Trigonella foenum-graecum L.) is a self-pollinated leguminous crop belonging to the Fabaceae family. It is a multipurpose crop used as herb, spice, vegetable and forage. It is a traditional medicinal plant in India attributed with several nutritional and medicinal properties including antidiabetic and anticancer. We have performed a combined transcriptome assembly from RNA sequencing data derived from leaf, stem and root tissues. Around 209,831 transcripts were deciphered from the assembly of 92% completeness and an N50 of 1382 bases. Whilst secondary metabolites of medicinal value, such as trigonelline, diosgenin, 4-hydroxyisoleucine and quercetin, are distributed in several tissues, we report transcripts that bear sequence signatures of enzymes involved in the biosynthesis of such metabolites and are highly expressed in leaves, stem and roots. One of the antidiabetic alkaloid, trigonelline and its biosynthesising enzyme, is highly abundant in leaves. These findings are of value to nutritional and the pharmaceutical industry.
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Camlica M, Yaldiz G. Gum yield, optimization of gum isolation, diosgenin and crude protein contents of fenugreek genotypes and cultivars grown under irrigated and dryland conditions. J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2022.104571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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10
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Zhou C, Yang Y, Tian J, Wu Y, An F, Li C, Zhang Y. 22R- but not 22S-hydroxycholesterol is recruited for diosgenin biosynthesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:940-951. [PMID: 34816537 DOI: 10.1111/tpj.15604] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 11/08/2021] [Accepted: 11/17/2021] [Indexed: 05/05/2023]
Abstract
Diosgenin is an important compound in the pharmaceutical industry and it is biosynthesized in several eudicot and monocot species, herein represented by fenugreek (a eudicot), and Dioscorea zingiberensis (a monocot). Formation of diosgenin can be achieved by the early C22,16-oxidations of cholesterol followed by a late C26-oxidation. This study reveals that, in both fenugreek and D. zingiberensis, the early C22,16-oxygenase(s) shows strict 22R-stereospecificity for hydroxylation of the substrates. Evidence against the recently proposed intermediacy of 16S,22S-dihydroxycholesterol in diosgenin biosynthesis was also found. Moreover, in contrast to the eudicot fenugreek, which utilizes a single multifunctional cytochrome P450 (TfCYP90B50) to perform the early C22,16-oxidations, the monocot D. zingiberensis has evolved two separate cytochrome P450 enzymes, with DzCYP90B71 being specific for the 22R-oxidation and DzCYP90G6 for the C16-oxidation. We suggest that the DzCYP90B71/DzCYP90G6 pair represent more broadly conserved catalysts for diosgenin biosynthesis in monocots.
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Affiliation(s)
- Chen Zhou
- Shanghai Key Laboratory of Bio-Energy Crops, Research Center for Natural Products, School of Life Sciences, Shanghai University, 333 Nanchen Road, Shanghai, 200444, China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, 368 Youyi Road, Wuhan, 430062, China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, 201 Jiufeng Road, Wuhan, 430074, China
| | - Yuhui Yang
- Shanghai Key Laboratory of Bio-Energy Crops, Research Center for Natural Products, School of Life Sciences, Shanghai University, 333 Nanchen Road, Shanghai, 200444, China
| | - Jingyi Tian
- Shanghai Key Laboratory of Bio-Energy Crops, Research Center for Natural Products, School of Life Sciences, Shanghai University, 333 Nanchen Road, Shanghai, 200444, China
| | - Yihan Wu
- School of Environmental and Chemical Engineering, Shanghai University, 333 Nanchen Road, Shanghai, 200444, China
| | - Faliang An
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Changfu Li
- Shanghai Key Laboratory of Bio-Energy Crops, Research Center for Natural Products, School of Life Sciences, Shanghai University, 333 Nanchen Road, Shanghai, 200444, China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, 201 Jiufeng Road, Wuhan, 430074, China
| | - Yansheng Zhang
- Shanghai Key Laboratory of Bio-Energy Crops, Research Center for Natural Products, School of Life Sciences, Shanghai University, 333 Nanchen Road, Shanghai, 200444, China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, 201 Jiufeng Road, Wuhan, 430074, China
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Hu Z, Wang C, Pan L, Han S, Jin M, Xiang Y, Zheng L, Li Z, Cao R, Qin B. Identification and a phased pH control strategy of diosgenin bio-synthesized by an endogenous Bacillus licheniformis Syt1 derived from Dioscorea zingiberensis C. H. Wright. Appl Microbiol Biotechnol 2021; 105:9333-9342. [PMID: 34841464 DOI: 10.1007/s00253-021-11679-z] [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: 07/08/2021] [Revised: 10/07/2021] [Accepted: 11/02/2021] [Indexed: 11/28/2022]
Abstract
Diosgenin is widely used as one precursor of steroidal drugs in pharmaceutical industry. Currently, there is no choice but to traditionally extract diosgenin from Dioscorea zingiberensis C. H. Wright (DZW) or other plants. In this work, an environmentally friendly approach, in which diosgenin can be bio-synthesized by the endophytic bacterium Bacillus licheniformis Syt1 isolated from DZW, is proposed. Diosgenin produced by the strain was identified by high-performance liquid chromatography (HPLC), nuclear magnetic resonance (NMR), and Fourier transform infrared spectroscopy (FTIR). The thermal gravimetric analysis (TGA) showed that the melting point of the diosgenin product was 204 °C. The optical rotation measurement exhibited that the optical rotation was α20589 = - 126.1° ± 1.5° (chloroform, c = 1%): negative sign means that the product is left-handed, which is very important to further produce steroid hormone drugs. Cholesterol may be the intermediate product in the diosgenin biosynthesis pathway. In the batch fermentation process to produce diosgenin using the strain, pH values played an important role. A phased pH control strategy from 5.5 to 7.5 was proved to be more effective to improve production yield than any single pH control, which could get the highest diosgenin yield of 85 ± 8.6 mg L-1. The proposed method may replace phyto-chemistry extraction to produce diosgenin in the industry in the future.Key points• An endophytic Bacillus licheniformis Syt1 derived from host can produce diosgenin.• A dynamic pH industrial control strategy is better than any single pH control.• Proposed diosgenin-produced method hopefully replaces phyto-chemistry extraction.
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Affiliation(s)
- Zhongqiu Hu
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Chunli Wang
- YangLing Demonstration Zone Hospital, Yangling, Shaanxi, 712100, People's Republic of China
| | - Lintao Pan
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Shiyao Han
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Miao Jin
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Yongsheng Xiang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Lifei Zheng
- College of Science, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Zhonghong Li
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Rang Cao
- College of Grassland Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Baofu Qin
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
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Nayak SN, Aravind B, Malavalli SS, Sukanth BS, Poornima R, Bharati P, Hefferon K, Kole C, Puppala N. Omics Technologies to Enhance Plant Based Functional Foods: An Overview. Front Genet 2021; 12:742095. [PMID: 34858472 PMCID: PMC8631721 DOI: 10.3389/fgene.2021.742095] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/13/2021] [Indexed: 11/25/2022] Open
Abstract
Functional foods are natural products of plants that have health benefits beyond necessary nutrition. Functional foods are abundant in fruits, vegetables, spices, beverages and some are found in cereals, millets, pulses and oilseeds. Efforts to identify functional foods in our diet and their beneficial aspects are limited to few crops. Advances in sequencing and availability of different omics technologies have given opportunity to utilize these tools to enhance the functional components of the foods, thus ensuring the nutritional security. Integrated omics approaches including genomics, transcriptomics, proteomics, metabolomics coupled with artificial intelligence and machine learning approaches can be used to improve the crops. This review provides insights into omics studies that are carried out to find the active components and crop improvement by enhancing the functional compounds in different plants including cereals, millets, pulses, oilseeds, fruits, vegetables, spices, beverages and medicinal plants. There is a need to characterize functional foods that are being used in traditional medicines, as well as utilization of this knowledge to improve the staple foods in order to tackle malnutrition and hunger more effectively.
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Affiliation(s)
- Spurthi N. Nayak
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - B. Aravind
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - Sachin S. Malavalli
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - B. S. Sukanth
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - R. Poornima
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - Pushpa Bharati
- Department of Food Science and Nutrition, University of Agricultural Sciences, Dharwad, India
| | - Kathleen Hefferon
- Department of Microbiology, Cornell University, Ithaca, NY, United States
| | - Chittaranjan Kole
- President, International Phytomedomics and Nutriomics Consortium (ipnc.info), Daejeon, South Korea
| | - Naveen Puppala
- New Mexico State University-Agricultural Science Center at Clovis, New Mexico, NM, United States
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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: 11] [Impact Index Per Article: 3.7] [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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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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Epping J, Laibach N. An underutilized orphan tuber crop-Chinese yam : a review. PLANTA 2020; 252:58. [PMID: 32959173 PMCID: PMC7505826 DOI: 10.1007/s00425-020-03458-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 09/11/2020] [Indexed: 05/09/2023]
Abstract
MAIN CONCLUSION The diversification of food crops can improve our diets and address the effects of climate change, and in this context the orphan crop Chinese yam shows significant potential as a functional food. As the effects of climate change become increasingly visible even in temperate regions, there is an urgent need to diversify our crops in order to address hunger and malnutrition. This has led to the re-evaluation of neglected species such as Chinese yam (Dioscorea polystachya Turcz.), which has been cultivated for centuries in East Asia as a food crop and as a widely-used ingredient in traditional Chinese medicine. The tubers are rich in nutrients, but also contain bioactive metabolites such as resistant starches, steroidal sapogenins (like diosgenin), the storage protein dioscorin, and mucilage polysaccharides. These health-promoting products can help to prevent cardiovascular disease, diabetes, and disorders of the gut microbiome. Whereas most edible yams are tropical species, Chinese yam could be cultivated widely in Europe and other temperate regions to take advantage of its nutritional and bioactive properties. However, this is a laborious process and agronomic knowledge is fragmented. The underground tubers contain most of the starch, but are vulnerable to breaking and thus difficult to harvest. Breeding to improve tuber shape is complex given the dioecious nature of the species, the mostly vegetative reproduction via bulbils, and the presence of more than 100 chromosomes. Protocols have yet to be established for in vitro cultivation and genetic transformation, which limits the scope of research. This article summarizes the sparse research landscape and evaluates the nutritional and medical applications of Chinese yam. By highlighting the potential of Chinese yam tubers, we aim to encourage the adoption of this orphan crop as a novel functional food.
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Affiliation(s)
- Janina Epping
- Institute of Plant Biology and Biotechnology, University of Muenster, Schlossplatz 8, 48143, Muenster, Germany.
| | - Natalie Laibach
- Institute for Food and Resource Economics, University of Bonn, Meckenheimer Allee 174, 53115, Bonn, Germany
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Abd El-Wahab MMH, Aljabri M, Sarhan MS, Osman G, Wang S, Mabrouk M, El-Shabrawi HM, Gabr AMM, Abd El-Haliem AM, O’Sullivan DM, El-Soda M. High-Density SNP-Based Association Mapping of Seed Traits in Fenugreek Reveals Homology with Clover. Genes (Basel) 2020; 11:E893. [PMID: 32764325 PMCID: PMC7464718 DOI: 10.3390/genes11080893] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 07/28/2020] [Accepted: 08/02/2020] [Indexed: 12/02/2022] Open
Abstract
Fenugreek as a self-pollinated plant is ideal for genome-wide association mapping where traits can be marked by their association with natural mutations. However, fenugreek is poorly investigated at the genomic level due to the lack of information regarding its genome. To fill this gap, we genotyped a collection of 112 genotypes with 153,881 SNPs using double digest restriction site-associated DNA sequencing. We used 38,142 polymorphic SNPs to prove the suitability of the population for association mapping. One significant SNP was associated with both seed length and seed width, and another SNP was associated with seed color. Due to the lack of a comprehensive genetic map, it is neither possible to align the newly developed markers to chromosomes nor to predict the underlying genes. Therefore, systematic targeting of those markers to homologous genomes of other legumes can overcome those problems. A BLAST search using the genomic fenugreek sequence flanking the identified SNPs showed high homology with several members of the Trifolieae tribe indicating the potential of translational approaches to improving our understanding of the fenugreek genome. Using such a comprehensively-genotyped fenugreek population is the first step towards identifying genes underlying complex traits and to underpin fenugreek marker-assisted breeding programs.
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Affiliation(s)
- Mustafa M. H. Abd El-Wahab
- Department of Agronomy, Faculty of Agriculture, Cairo University, Giza 12613, Egypt; (M.M.H.A.E.-W.); (M.M.)
| | - Maha Aljabri
- Department of Biology, Faculty of Applied Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia; (M.A.); (G.O.)
- Research Laboratories Centre, Faculty of Applied Science, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Mohamed S. Sarhan
- Environmental Studies and Research Unit, Cairo University, Giza 12613, Egypt;
| | - Gamal Osman
- Department of Biology, Faculty of Applied Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia; (M.A.); (G.O.)
- Research Laboratories Centre, Faculty of Applied Science, Umm Al-Qura University, Makkah 21955, Saudi Arabia
- Agricultural Genetic Engineering Research Institute (AGERI), ARC, Giza 12915, Egypt
| | - Shichen Wang
- Genomics and Bioinformatics Service Texas A&M AgriLife Research, Amarillo College Station, Amarillo, TX 77845, USA;
| | - Mahmoud Mabrouk
- Department of Agronomy, Faculty of Agriculture, Cairo University, Giza 12613, Egypt; (M.M.H.A.E.-W.); (M.M.)
| | - Hattem M. El-Shabrawi
- Plant Biotechnology Department, National Research Center, Giza 12622, Egypt; (H.M.E.-S.); (A.M.M.G.)
| | - Ahmed M. M. Gabr
- Plant Biotechnology Department, National Research Center, Giza 12622, Egypt; (H.M.E.-S.); (A.M.M.G.)
| | - Ahmed M. Abd El-Haliem
- Plant Physiology, University of Amsterdam, Swammerdam Institute for Life Sciences Amsterdam, 1098 XH Amsterdam, The Netherlands;
| | - Donal M. O’Sullivan
- School of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading RG6 6AR, UK;
| | - Mohamed El-Soda
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza 12613, Egypt
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Szeliga M, Ciura J, Tyrka M. Representational Difference Analysis of Transcripts Involved in Jervine Biosynthesis. Life (Basel) 2020; 10:life10060088. [PMID: 32575579 PMCID: PMC7344996 DOI: 10.3390/life10060088] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 12/28/2022] Open
Abstract
Veratrum-type steroidal alkaloids (VSA) are the major bioactive ingredients that strongly determine the pharmacological activities of Veratrum nigrum. Biosynthesis of VSA at the molecular and genetic levels is not well understood. Next-generation sequencing of representational difference analysis (RDA) products after elicitation and precursor feeding was applied to identify candidate genes involved in VSA biosynthesis. A total of 12,048 contigs with a median length of 280 bases were received in three RDA libraries obtained after application of methyl jasmonate, squalene and cholesterol. The comparative analysis of annotated sequences was effective in identifying candidate genes. GABAT2 transaminase and hydroxylases active at C-22, C-26, C-11, and C-16 positions in late stages of jervine biosynthesis were selected. Moreover, genes coding pyrroline-5-carboxylate reductase and enzymes from the short-chain dehydrogenases/reductases family (SDR) associated with the reduction reactions of the VSA biosynthesis process were proposed. The data collected contribute to better understanding of jervine biosynthesis and may accelerate implementation of biotechnological methods of VSA biosynthesis.
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Affiliation(s)
- Magdalena Szeliga
- Department of Biotechnology and Bioinformatics, Faculty of Chemistry, Rzeszow University of Technology, Powstańców Warszawy 6 Ave, 35-959 Rzeszow, Poland; (J.C.); (M.T.)
- Correspondence:
| | - Joanna Ciura
- Department of Biotechnology and Bioinformatics, Faculty of Chemistry, Rzeszow University of Technology, Powstańców Warszawy 6 Ave, 35-959 Rzeszow, Poland; (J.C.); (M.T.)
- Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Mirosław Tyrka
- Department of Biotechnology and Bioinformatics, Faculty of Chemistry, Rzeszow University of Technology, Powstańców Warszawy 6 Ave, 35-959 Rzeszow, Poland; (J.C.); (M.T.)
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Mohammadi M, Mashayekh T, Rashidi-Monfared S, Ebrahimi A, Abedini D. New insights into diosgenin biosynthesis pathway and its regulation in Trigonella foenum-graecum L. PHYTOCHEMICAL ANALYSIS : PCA 2020; 31:229-241. [PMID: 31469464 DOI: 10.1002/pca.2887] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 07/17/2019] [Accepted: 07/21/2019] [Indexed: 05/05/2023]
Abstract
INTRODUCTION Throughout history, thousands of medicinal and aromatic plants have been widely utilised by people worldwide. Owing to them possessing of valuable compounds with little side effects in comparison with chemical drugs, herbs have been of interest to humans for a number of purposes. Diosgenin, driven from fenugreek, Trigonella foenum-graecum L., has extensively drawn scientist's attention owing to having curable properties and being a precursor of steroid hormones synthesis. Nonetheless, complete knowledge about the biosynthesis pathway of this metabolite is still elusive. OBJECTIVE In the present research, we isolated the full-length CDS of 14 genes involving in diosgenin formation and measured their expression rate in various genotypes, which had illustrated different amount of diosgenin. METHODOLOGY The genes were successfully isolated, and functional motifs were also assessed using in silico approaches. RESULTS Moreover, combining transcript and metabolite analysis revealed that there are many genes playing the role in diosgenin formation, some of which are highly influential. Among them, ∆24 -reductase, which converts cycloartenol to cycloartanol, is the first-committed and rate-limiting enzyme in this pathway. Additionally, no transcripts indicating to the presence or expression of lanosterol synthase were detected, contradicting the previous hypothesis about the biosynthetic pathway of diosgenin in fenugreek. CONCLUSION Considering all these, therefore, we propose the most possible pathway of diosgenin. This knowledge will then pave the way toward cloning the genes as well as engineering the diosgenin biosynthesis pathway.
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Affiliation(s)
- Mohammad Mohammadi
- Agricultural Biotechnology Department, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Tooba Mashayekh
- Agricultural Biotechnology Department, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Sajad Rashidi-Monfared
- Agricultural Biotechnology Department, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Amin Ebrahimi
- Agronomy and Plant Breeding Department, Faculty of Agriculture, Shahrood University of Technology, Semnan, Iran
| | - Davar Abedini
- Agricultural Biotechnology Department, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
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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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Comparative analysis of proteomic and metabolomic profiles of different species of Paris. J Proteomics 2019; 200:11-27. [PMID: 30890455 DOI: 10.1016/j.jprot.2019.02.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 01/12/2019] [Accepted: 02/01/2019] [Indexed: 02/08/2023]
Abstract
An extract prepared from species of Paris is the most widely consumed herbal product in China. The genus Paris includes a variety of genotypes with different medicinal component contents but only two are defined as official sources. Closely related species have different medicinal properties because of differential expression of proteins and metabolites. To better understand the molecular basis of these differences, we examined proteomic and metabolomic changes in rhizomes of P. polyphylla var. chinensis, P. polyphylla var. yunnanensis, and P. fargesii var. fargesii using a technique known as sequential window acquisition of all theoretical mass spectra as well as gas chromatography-time-of-flight mass spectrometry. In total, 419 proteins showed significant abundance changes, and 33 metabolites could be used to discriminate Paris species. A complex analysis of proteomic and metabolomic data revealed a higher efficiency of sucrose utilization and an elevated protein abundance in the sugar metabolic pathway of P. polyphylla var. chinensis. The pyruvate content and efficiency of acetyl-CoA-utilization in saponin biosynthesis were also higher in P. polyphylla var. chinensis than in the other two species. The results expand our understanding of the proteome and metabolome of Paris and offer new insights into the species-specific traits of these herbaceous plants. SIGNIFICANCE: The traditional Chinese medicine Paris is the most widely consumed herbal product for the treatment of joint pain, rheumatoid arthritis and antineoplastic. All Paris species have roughly the same morphological characteristics; however, different members have different medicinal compound contents. Efficient exploitation of genetic diversity is a key factor in the development of rare medicinal plants with improved agronomic traits and malleability to challenging environmental conditions. Nevertheless, only a partial understanding of physiological and molecular mechanisms of different plants of Paris can be achieved without proteomics. To better understand the molecular basis of these differences and facilitate the use of other Paris species, we examine proteomic metabolomic changes in rhizomes of Paris using the technique known as SWATH-MS and GC/TOF-MS. Our research has provided information that can be used in other studies to compare metabolic traits in different Paris species. Our findings can also serve as a theoretical basis for the selection and cultivation of other Paris species with a higher medicinal value.
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Zhou C, Li X, Zhou Z, Li C, Zhang Y. Comparative Transcriptome Analysis Identifies Genes Involved in Diosgenin Biosynthesis in Trigonella foenum-graecum L. Molecules 2019; 24:molecules24010140. [PMID: 30609669 PMCID: PMC6337231 DOI: 10.3390/molecules24010140] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 12/25/2018] [Accepted: 12/26/2018] [Indexed: 01/01/2023] Open
Abstract
Trigonella foenum-graecum L. (fenugreek) is a valuable resource of producing diosgenin which serves as a substrate for synthesizing more than two hundred kinds of steroidal drugs. Phytochemical analysis indicated that methyl jasmonate (MeJA) efficiently induced diosgenin biosynthesis in fenugreek seedlings. Though early steps up to cholesterol have recently been elucidated in plants, cytochrome P450 (CYP)- and glycosyltransferase (GT)-encoding genes involved in the late steps from cholesterol to diosgenin remain unknown. This study established comparative fenugreek transcriptome datasets from the MeJA-treated seedlings and the corresponding control lines. Differential gene expression analysis identified a number of MeJA-induced CYP and GT candidate genes. Further gene expression pattern analysis across a different MeJA-treating time points, together with a phylogenetic analysis, suggested specific family members of CYPs and GTs that may participate in the late steps during diosgenin biosynthesis. MeJA-induced transcription factors (TFs) that may play regulatory roles in diosgenin biosynthesis were also discussed. This study provided a valuable genetic resource to functionally characterize the genes involved in diosgenin biosynthesis, which will push forward the production of diosgenin in microbial organisms using a promising synthetic biology strategy.
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Affiliation(s)
- Chen Zhou
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xiaohua Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zilin Zhou
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Changfu Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
- Shanghai Key Laboratory of Bio-Energy Crops, Research Center for Natural Products, School of Life Sciences, Shanghai University, Shanghai 200444, China.
| | - Yansheng Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
- Shanghai Key Laboratory of Bio-Energy Crops, Research Center for Natural Products, School of Life Sciences, Shanghai University, Shanghai 200444, China.
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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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Sethi G, Shanmugam MK, Warrier S, Merarchi M, Arfuso F, Kumar AP, Bishayee A. Pro-Apoptotic and Anti-Cancer Properties of Diosgenin: A Comprehensive and Critical Review. Nutrients 2018; 10:nu10050645. [PMID: 29783752 PMCID: PMC5986524 DOI: 10.3390/nu10050645] [Citation(s) in RCA: 150] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 05/04/2018] [Accepted: 05/16/2018] [Indexed: 12/15/2022] Open
Abstract
Novel and alternative options are being adopted to combat the initiation and progression of human cancers. One of the approaches is the use of molecules isolated from traditional medicinal herbs, edible dietary plants and seeds that play a pivotal role in the prevention/treatment of cancer, either alone or in combination with existing chemotherapeutic agents. Compounds that modulate these oncogenic processes are potential candidates for cancer therapy and may eventually make it to clinical applications. Diosgenin is a naturally occurring steroidal sapogenin and is one of the major bioactive compounds found in dietary fenugreek (Trigonella foenum-graecum) seeds. In addition to being a lactation aid, diosgenin has been shown to be hypocholesterolemic, gastro- and hepato-protective, anti-oxidant, anti-inflammatory, anti-diabetic, and anti-cancer. Diosgenin has a unique structural similarity to estrogen. Several preclinical studies have reported on the pro-apoptotic and anti-cancer properties of diosgenin against a variety of cancers, both in in vitro and in vivo. Diosgenin has also been reported to reverse multi-drug resistance in cancer cells and sensitize cancer cells to standard chemotherapy. Remarkably, diosgenin has also been reported to be used by pharmaceutical companies to synthesize steroidal drugs. Several novel diosgenin analogs and nano-formulations have been synthesized with improved anti-cancer efficacy and pharmacokinetic profile. In this review we discuss in detail the multifaceted anti-cancer properties of diosgenin that have found application in pharmaceutical, functional food, and cosmetic industries; and the various intracellular molecular targets modulated by diosgenin that abrogate the oncogenic process.
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Affiliation(s)
- Gautam Sethi
- Department for Management of Science and Technology Development, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam.
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam.
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore.
| | - Muthu K Shanmugam
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore.
| | - Sudha Warrier
- Division of Cancer Stem Cells and Cardiovascular Regeneration, Manipal Institute of Regenerative Medicine, Manipal University, Bangalore 560065, India.
| | - Myriam Merarchi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore.
| | - Frank Arfuso
- Stem Cell and Cancer Biology Laboratory, School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia.
| | - Alan Prem Kumar
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore.
| | - Anupam Bishayee
- Department of Pharmaceutical Sciences, College of Pharmacy, Larkin University, 18301 N. Miami Avenue, Miami, FL 33169, USA.
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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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Comparative Transcriptome Analysis Identifies Putative Genes Involved in Dioscin Biosynthesis in Dioscorea zingiberensis. Molecules 2018; 23:molecules23020454. [PMID: 29463020 PMCID: PMC6017347 DOI: 10.3390/molecules23020454] [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: 01/22/2018] [Revised: 02/12/2018] [Accepted: 02/17/2018] [Indexed: 12/17/2022] Open
Abstract
Dioscorea zingiberensis is a perennial herb native to China. The rhizome of D. zingiberensis has long been used as a traditional Chinese medicine to treat rheumatic arthritis. Dioscin is the major bioactive ingredient conferring the medicinal property described in Chinese pharmacopoeia. Several previous studies have suggested cholesterol as the intermediate to the biosynthesis of dioscin, however, the biosynthetic steps to dioscin after cholesterol remain unknown. In this study, a comprehensive D. zingiberensis transcriptome derived from its leaf and rhizome was constructed. Based on the annotation using various public databases, all possible enzymes in the biosynthetic steps to cholesterol were identified. In the late steps beyond cholesterol, cholesterol undergoes site-specific oxidation by cytochrome P450s (CYPs) and glycosylation by UDP-glycosyltransferases (UGTs) to yield dioscin. From the D. zingiberensis transcriptome, a total of 485 unigenes were annotated as CYPs and 195 unigenes with a sequence length above 1000 bp were annotated as UGTs. Transcriptomic comparison revealed 165 CYP annotated unigenes correlating to dioscin biosynthesis in the plant. Further phylogenetic analysis suggested that among those CYP candidates four of them would be the most likely candidates involved in the biosynthetic steps from cholesterol to dioscin. Additionally, from the UGT annotated unigenes, six of them were annotated as 3-O-UGTs and two of them were annotated as rhamnosyltransferases, which consisted of potential UGT candidates involved in dioscin biosynthesis. To further explore the function of the UGT candidates, two 3-O-UGT candidates, named Dz3GT1 and Dz3GT2, were cloned and functionally characterized. Both Dz3GT1 and Dz3GT2 were able to catalyze a C3-glucosylation activity on diosgenin. In conclusion, this study will facilitate our understanding of dioscin biosynthesis pathway and provides a basis for further mining the genes involved in dioscin biosynthesis.
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Kim JK, Park SU. An update on the biological and pharmacological activities of diosgenin. EXCLI JOURNAL 2018; 17:24-28. [PMID: 29383016 PMCID: PMC5780621 DOI: 10.17179/excli2017-894] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 12/13/2017] [Indexed: 01/03/2023]
Affiliation(s)
- Jae Kwang Kim
- Division of Life Sciences and Convergence Research Center for Insect Vectors, Incheon National University, Incheon 22012, Korea
| | - Sang Un Park
- Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 34134, Korea
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Rai MK, Shekhawat JK, Kataria V, Shekhawat N. De novo assembly of leaf transcriptome, functional annotation and genomic resources development in Prosopis cineraria , a multipurpose tree of Indian Thar Desert. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.plgene.2017.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Ciura J, Szeliga M, Grzesik M, Tyrka M. Changes in fenugreek transcriptome induced by methyl jasmonate and steroid precursors revealed by RNA-Seq. Genomics 2017; 110:S0888-7543(17)30132-5. [PMID: 29107013 DOI: 10.1016/j.ygeno.2017.10.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 09/27/2017] [Accepted: 10/20/2017] [Indexed: 12/14/2022]
Abstract
Changes in fenugreek transcriptome related to enhanced production of steroids were induced by methyl jasmonate, cholesterol and squalene, and recorded using RNA-seq. A total of 112,850 unigenes were obtained after de novo assembling of next generation sequencing data, and used for functional annotations. In steroidal saponins pathway, transcripts involved in mevalonate, terpenoid backbone and plant sterol synthesis were annotated. Overexpression of several transcripts from phytosterol biosynthesis pathway was confirmed by quantitative RT-PCR. In diosgenin biosynthesis pathway, fatty acid ω-hydroxylase (CYP86A2) and steroid 22-alpha-hydroxylase (CYP90B1) genes were annotated in all induced transcriptomes. Moreover, direct sequencing confirmed increased levels of CYP90B1, unspecific monooxygenase and 26-hydroxylase genes in plants with elevated level of diosgenin. New unigenes corresponding to enzymes involved in biosynthesis of diosgenin from cycloartenol via cholesterol were obtained and the role of CYP72A family in steroidal saponin biosynthesis was proposed. Additional support for biosynthetic pathway from cycloartenol to diosgenin was provided.
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Affiliation(s)
- Joanna Ciura
- Department of Biotechnology and Bioinformatics, Faculty of Chemistry, Rzeszów University of Technology, ul. Powstańców Warszawy 6, 35-595 Rzeszów, Poland.
| | - Magdalena Szeliga
- Department of Biotechnology and Bioinformatics, Faculty of Chemistry, Rzeszów University of Technology, ul. Powstańców Warszawy 6, 35-595 Rzeszów, Poland
| | - Michalina Grzesik
- Department of Biotechnology and Bioinformatics, Faculty of Chemistry, Rzeszów University of Technology, ul. Powstańców Warszawy 6, 35-595 Rzeszów, Poland
| | - Mirosław Tyrka
- Department of Biotechnology and Bioinformatics, Faculty of Chemistry, Rzeszów University of Technology, ul. Powstańców Warszawy 6, 35-595 Rzeszów, Poland.
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