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Han T, Miao G. Strategies, Achievements, and Potential Challenges of Plant and Microbial Chassis in the Biosynthesis of Plant Secondary Metabolites. Molecules 2024; 29:2106. [PMID: 38731602 PMCID: PMC11085123 DOI: 10.3390/molecules29092106] [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: 03/08/2024] [Revised: 04/27/2024] [Accepted: 04/27/2024] [Indexed: 05/13/2024] Open
Abstract
Diverse secondary metabolites in plants, with their rich biological activities, have long been important sources for human medicine, food additives, pesticides, etc. However, the large-scale cultivation of host plants consumes land resources and is susceptible to pest and disease problems. Additionally, the multi-step and demanding nature of chemical synthesis adds to production costs, limiting their widespread application. In vitro cultivation and the metabolic engineering of plants have significantly enhanced the synthesis of secondary metabolites with successful industrial production cases. As synthetic biology advances, more research is focusing on heterologous synthesis using microorganisms. This review provides a comprehensive comparison between these two chassis, evaluating their performance in the synthesis of various types of secondary metabolites from the perspectives of yield and strategies. It also discusses the challenges they face and offers insights into future efforts and directions.
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Affiliation(s)
- Taotao Han
- Department of Bioengineering, Huainan Normal University, Huainan 232038, China;
| | - Guopeng Miao
- Department of Bioengineering, Huainan Normal University, Huainan 232038, China;
- Key Laboratory of Bioresource and Environmental Biotechnology of Anhui Higher Education Institutes, Huainan Normal University, Huainan 232038, China
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Titova MV, Lunkova MK, Tyurina TM, Prudnikova ON, Popova EV, Klychnikov OI, Metalnikov PS, Ikhalaynen YA, Vasileva EN, Rodin IA, Nosov AM. Suspension cell cultures of Panax vietnamensis as a biotechnological source of ginsenosides: growth, cytology, and ginsenoside profile assessment. FRONTIERS IN PLANT SCIENCE 2024; 15:1349494. [PMID: 38469323 PMCID: PMC10926444 DOI: 10.3389/fpls.2024.1349494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/25/2024] [Indexed: 03/13/2024]
Abstract
Introduction Panax vietnamensis is a valuable medicinal plant and a source of a broad spectrum of biologically active ginsenosides of different structural groups. Overexploitation and low adaptability to planation cultivation have made this species vulnerable to human pressure and prompted the development of cell cultivation in vitro as a sustainable alternative to harvesting wild plants for their bioactive components. Despite high interest in biotechnological production, little is known about the main factors affecting cell growth and ginsenoside biosynthesis of this species under in vitro conditions. In this study, the potential of cell cultures of P. vietnamensis as a biotechnological source of ginsenosides was was assessed. Methods Six suspension cell lines that were developed from different sections of a single rhizome through a multi-step culture optimization process and maintained for over 3 years on media with different mineral salt base and varying contents of auxins and cytokinins. These cell lines were evaluated for productivity parameters and cytological characteristics. Ginsenoside profiles were assessed using a combination of the reversed-phase ultra-high-performance liquid chromatography-Orbitrap-tandem mass spectrometry (UHPLC-Orbitrap-MS/MS) and ultra-performance liquid chromatography-time of flight-mass spectrometry (UPLC-TOF-MS). Results All lines demonstrated good growth with a specific growth rate of 0.1-0.2 day-1, economic coefficient of 0.31-0.70, productivity on dry weight (DW) of 0.30-0.83 gDW (L·day)-1, and maximum biomass accumulation varying from 10 to 22 gDW L-1. Ginsenosides of the protopanaxadiol (Rb1, Rb2/Rb3, malonyl-Rb1, and malonyl-Rb2/Rb3), oleanolic acid (R0 and chikusetsusaponin IV), and ocotillol (vinaginsenoside R1) groups and their isomers were identified in cell biomass extracts. Chikusetsusaponin IV was identified in P. vietnamensis cell culture for the first time. Discussion These results suggest that suspension cell cultures of Vietnamese ginseng have a high potential for the biotechnological production of biomass containing ginsenosides, particularly of the oleanolic acid and ocotillol groups.
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Affiliation(s)
- Maria V. Titova
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Maria K. Lunkova
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana M. Tyurina
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Olga N. Prudnikova
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Elena V. Popova
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Oleg I. Klychnikov
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
- Department of Biochemistry, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Pavel S. Metalnikov
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Yuri A. Ikhalaynen
- Department of Analytical Chemistry, Faculty of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Elizaveta N. Vasileva
- Department of Analytical Chemistry, Faculty of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Igor A. Rodin
- Department of Analytical Chemistry, Faculty of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Alexander M. Nosov
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
- Department of Plant Physiology, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
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Mmereke KM, Venkataraman S, Moiketsi BN, Khan MR, Hassan SH, Rantong G, Masisi K, Kwape TE, Gaobotse G, Zulfiqar F, Kumar Sharma S, Malik S, Makhzoum A. Nanoparticle elicitation: A promising strategy to modulate the production of bioactive compounds in hairy roots. Food Res Int 2024; 178:113910. [PMID: 38309862 DOI: 10.1016/j.foodres.2023.113910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/15/2023] [Accepted: 12/21/2023] [Indexed: 02/05/2024]
Abstract
Hairy root culture is one of the promising biotechnological tools to obtain the stable and sustainable production of specialized metabolites from plants under controlled environment conditions. Various strategies have been adopted to enhance the accumulation of bioactive compounds in hairy roots yet their utilization at the commercial scale is restricted to only a few products. Recently, nanotechnology has been emerged as an active technique that has revolutionized the many sectors in an advantageous way. Elicitation using nanoparticles has been recognized as an effective strategy for enhancing the bioactive compounds of interest in plants. Nanoparticles elicit the activity of defense-related compounds through activation of the specific transcription factors involved in specialized metabolites production. This review discusses the recent progress in using nanoparticles to enhance specialized metabolite biosynthesis using hairy root culture system and the significant achievements in this area of research. Biotic and abiotic elicitors to improve the production of bioactive compounds in hairy roots, different types of nanoparticles as eliciting agents, their properties as dependent on shape, most widely used nanoparticles in plant hairy root systems are described in detail. Further challenges involved in application of nanoparticles, their toxicity in plant cells and risks associated to human health are also envisaged. No doubt, nanoparticle elicitation is a remarkable approach to obtain phytochemicals from hairy roots to be utilized in various sectors including food, medicines, cosmetics or agriculture but it is quite essential to understand the inter-relationships between the nanoparticles and the plant systems in terms of specifics such as type, dosage and time of exposure as well as other important parameters.
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Affiliation(s)
- Kamogelo M Mmereke
- Department of Biological Sciences & Biotechnology, Botswana International University of Science & Technology, Palapye, Botswana
| | - Srividhya Venkataraman
- Virology Laboratory, Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Bertha Nametso Moiketsi
- Department of Biological Sciences & Biotechnology, Botswana International University of Science & Technology, Palapye, Botswana
| | - Muhammad Rehan Khan
- Department of Agricultural Science, University of Naples Federico II, Via Università 133, 80055 Portici, Italy; URD Agro-Biotechnologies Industrielles (ABI), CEBB, AgroParisTech, 3 Rue des Rouges-Terres, 51110 Pomacle, France
| | - Sayyeda Hira Hassan
- Department of Biosciences and Territory, University of Molise, 86090 Pesche, Italy
| | - Gaolathe Rantong
- Department of Biological Sciences & Biotechnology, Botswana International University of Science & Technology, Palapye, Botswana
| | - Kabo Masisi
- Department of Biological Sciences & Biotechnology, Botswana International University of Science & Technology, Palapye, Botswana
| | - Tebogo E Kwape
- Department of Biological Sciences & Biotechnology, Botswana International University of Science & Technology, Palapye, Botswana
| | - Goabaone Gaobotse
- Department of Biological Sciences & Biotechnology, Botswana International University of Science & Technology, Palapye, Botswana
| | - Faisal Zulfiqar
- Department of Horticultural Sciences, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | | | - Sonia Malik
- Physiology, Ecology and Environment (P2E) Laboratory, University of Orleans, INRAE, USC1328, 45067 Orleans, France.
| | - Abdullah Makhzoum
- Department of Biological Sciences & Biotechnology, Botswana International University of Science & Technology, Palapye, Botswana.
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Shi M, Wang C, Wang P, Yun F, Liu Z, Ye F, Wei L, Liao W. Role of methylation in vernalization and photoperiod pathway: a potential flowering regulator? HORTICULTURE RESEARCH 2023; 10:uhad174. [PMID: 37841501 PMCID: PMC10569243 DOI: 10.1093/hr/uhad174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 08/23/2023] [Indexed: 10/17/2023]
Abstract
Recognized as a pivotal developmental transition, flowering marks the continuation of a plant's life cycle. Vernalization and photoperiod are two major flowering pathways orchestrating numerous florigenic signals. Methylation, including histone, DNA and RNA methylation, is one of the recent foci in plant development. Considerable studies reveal that methylation seems to show an increasing potential regulatory role in plant flowering via altering relevant gene expression without altering the genetic basis. However, little has been reviewed about whether and how methylation acts on vernalization- and photoperiod-induced flowering before and after FLOWERING LOCUS C (FLC) reactivation, what role RNA methylation plays in vernalization- and photoperiod-induced flowering, how methylation participates simultaneously in both vernalization- and photoperiod-induced flowering, the heritability of methylation memory under the vernalization/photoperiod pathway, and whether and how methylation replaces vernalization/photoinduction to regulate flowering. Our review provides insight about the crosstalk among the genetic control of the flowering gene network, methylation (methyltransferases/demethylases) and external signals (cold, light, sRNA and phytohormones) in vernalization and photoperiod pathways. The existing evidence that RNA methylation may play a potential regulatory role in vernalization- and photoperiod-induced flowering has been gathered and represented for the first time. This review speculates about and discusses the possibility of substituting methylation for vernalization and photoinduction to promote flowering. Current evidence is utilized to discuss the possibility of future methylation reagents becoming flowering regulators at the molecular level.
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Affiliation(s)
- Meimei Shi
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Chunlei Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Peng Wang
- Vegetable and Flower Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Fahong Yun
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Zhiya Liu
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Fujin Ye
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Lijuan Wei
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Weibiao Liao
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
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Xu F, Valappil AK, Mathiyalagan R, Tran TNA, Ramadhania ZM, Awais M, Yang DC. In Vitro Cultivation and Ginsenosides Accumulation in Panax ginseng: A Review. PLANTS (BASEL, SWITZERLAND) 2023; 12:3165. [PMID: 37687411 PMCID: PMC10489967 DOI: 10.3390/plants12173165] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/03/2023] [Accepted: 08/10/2023] [Indexed: 09/10/2023]
Abstract
The use of in vitro tissue culture for herbal medicines has been recognized as a valuable source of botanical secondary metabolites. The tissue culture of ginseng species is used in the production of bioactive compounds such as phenolics, polysaccharides, and especially ginsenosides, which are utilized in the food, cosmetics, and pharmaceutical industries. This review paper focuses on the in vitro culture of Panax ginseng and accumulation of ginsenosides. In vitro culture has been applied to study organogenesis and biomass culture, and is involved in direct organogenesis for rooting and shooting from explants and in indirect morphogenesis for somatic embryogenesis via the callus, which is a mass of disorganized cells. Biomass production was conducted with different types of tissue cultures, such as adventitious roots, cell suspension, and hairy roots, and subsequently on a large scale in a bioreactor. This review provides the cumulative knowledge of biotechnological methods to increase the ginsenoside resources of P. ginseng. In addition, ginsenosides are summarized at enhanced levels of activity and content with elicitor treatment, together with perspectives of new breeding tools which can be developed in P. ginseng in the future.
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Affiliation(s)
- Fengjiao Xu
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si 17104, Gyeonggi-do, Republic of Korea; (F.X.); (T.N.A.T.); (Z.M.R.); (M.A.)
| | - Anjali Kariyarath Valappil
- Department of Biopharmaceutical Biotechnology, College of Life Science, Kyung Hee University, Yongin-si 17104, Gyeonggi-do, Republic of Korea; (A.K.V.); (R.M.)
| | - Ramya Mathiyalagan
- Department of Biopharmaceutical Biotechnology, College of Life Science, Kyung Hee University, Yongin-si 17104, Gyeonggi-do, Republic of Korea; (A.K.V.); (R.M.)
| | - Thi Ngoc Anh Tran
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si 17104, Gyeonggi-do, Republic of Korea; (F.X.); (T.N.A.T.); (Z.M.R.); (M.A.)
| | - Zelika Mega Ramadhania
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si 17104, Gyeonggi-do, Republic of Korea; (F.X.); (T.N.A.T.); (Z.M.R.); (M.A.)
| | - Muhammad Awais
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si 17104, Gyeonggi-do, Republic of Korea; (F.X.); (T.N.A.T.); (Z.M.R.); (M.A.)
| | - Deok Chun Yang
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si 17104, Gyeonggi-do, Republic of Korea; (F.X.); (T.N.A.T.); (Z.M.R.); (M.A.)
- Department of Biopharmaceutical Biotechnology, College of Life Science, Kyung Hee University, Yongin-si 17104, Gyeonggi-do, Republic of Korea; (A.K.V.); (R.M.)
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Zhao Y, Liu G, Yang F, Liang Y, Gao Q, Xiang C, Li X, Yang R, Zhang G, Jiang H, Yu L, Yang S. Multilayered regulation of secondary metabolism in medicinal plants. MOLECULAR HORTICULTURE 2023; 3:11. [PMID: 37789448 PMCID: PMC10514987 DOI: 10.1186/s43897-023-00059-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 04/27/2023] [Indexed: 10/05/2023]
Abstract
Medicinal plants represent a huge reservoir of secondary metabolites (SMs), substances with significant pharmaceutical and industrial potential. However, obtaining secondary metabolites remains a challenge due to their low-yield accumulation in medicinal plants; moreover, these secondary metabolites are produced through tightly coordinated pathways involving many spatiotemporally and environmentally regulated steps. The first regulatory layer involves a complex network of transcription factors; a second, more recently discovered layer of complexity in the regulation of SMs is epigenetic modification, such as DNA methylation, histone modification and small RNA-based mechanisms, which can jointly or separately influence secondary metabolites by regulating gene expression. Here, we summarize the findings in the fields of genetic and epigenetic regulation with a special emphasis on SMs in medicinal plants, providing a new perspective on the multiple layers of regulation of gene expression.
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Affiliation(s)
- Yan Zhao
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, 650201, Kunming, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Guanze Liu
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, 650201, Kunming, China
| | - Feng Yang
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanli Liang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, 650201, Kunming, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Qingqing Gao
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, 650201, Kunming, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Chunfan Xiang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, 650201, Kunming, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Xia Li
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, 650201, Kunming, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Run Yang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, 650201, Kunming, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Guanghui Zhang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, 650201, Kunming, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Huifeng Jiang
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
| | - Lei Yu
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, 650214, China.
| | - Shengchao Yang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, 650201, Kunming, China.
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Kolackova M, Janova A, Dobesova M, Zvalova M, Chaloupsky P, Krystofova O, Adam V, Huska D. Role of secondary metabolites in distressed microalgae. ENVIRONMENTAL RESEARCH 2023; 224:115392. [PMID: 36746204 DOI: 10.1016/j.envres.2023.115392] [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: 11/22/2022] [Revised: 01/09/2023] [Accepted: 01/28/2023] [Indexed: 06/18/2023]
Abstract
Proficient photosynthetic microalgae/cyanobacteria produce a remarkable amount of various biomolecules. Secondary metabolites (SM) represent high value products for global biotrend application. Production improvement can be achieved by nutritional, environmental, and physiological stress as a first line tools for their stimulation. In recent decade, an increasing interest in algal stress biology and omics techniques have deepened knowledge in this area. However, deep understanding and connection of specific stress elucidator are missing. Hence, the present review summarizes recent evidence with an emphasis on the carotenoids, phenolic, and less-discussed compounds (glycerol, proline, mycosporins-like amino acids). Even when they are synthesized at very low concentrations, it highlights the need to expand knowledge in this area using genome-editing tools and omics approaches.
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Affiliation(s)
- Martina Kolackova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00, Brno, Czech Republic
| | - Anna Janova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00, Brno, Czech Republic
| | - Marketa Dobesova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00, Brno, Czech Republic
| | - Monika Zvalova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00, Brno, Czech Republic
| | - Pavel Chaloupsky
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00, Brno, Czech Republic
| | - Olga Krystofova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00, Brno, Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00, Brno, Czech Republic
| | - Dalibor Huska
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00, Brno, Czech Republic.
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Santiago R, Monreal JA. Editorial: XVII Spanish Portuguese Congress on Plant Biology (BP2021) - plant biochemistry and metabolism. FRONTIERS IN PLANT SCIENCE 2023; 14:1189060. [PMID: 37123859 PMCID: PMC10140626 DOI: 10.3389/fpls.2023.1189060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 03/28/2023] [Indexed: 05/03/2023]
Affiliation(s)
- Rogelio Santiago
- Misión Biológica de Galicia, Spanish Council for Scientific Research (MBG-CSIC), Pontevedra, Spain
- Agrobiología Ambiental, Calidad de Suelos y Plantas Universidade de Vigo (UVIGO), Unidad Asociada a la MBG Consejo Superior de Investigaciones Científicas (CSIC), Vigo, Spain
- *Correspondence: Rogelio Santiago, ; José A. Monreal,
| | - José A. Monreal
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
- *Correspondence: Rogelio Santiago, ; José A. Monreal,
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Kong J, Garcia V, Zehraoui E, Stammitti L, Hilbert G, Renaud C, Maury S, Delaunay A, Cluzet S, Lecourieux F, Lecourieux D, Teyssier E, Gallusci P. Zebularine, a DNA Methylation Inhibitor, Activates Anthocyanin Accumulation in Grapevine Cells. Genes (Basel) 2022; 13:genes13071256. [PMID: 35886036 PMCID: PMC9316115 DOI: 10.3390/genes13071256] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/07/2022] [Accepted: 07/12/2022] [Indexed: 02/01/2023] Open
Abstract
Through its role in the regulation of gene expression, DNA methylation can participate in the control of specialized metabolite production. We have investigated the link between DNA methylation and anthocyanin accumulation in grapevine using the hypomethylating drug, zebularine and Gamay Teinturier cell suspensions. In this model, zebularine increased anthocyanin accumulation in the light, and induced its production in the dark. To unravel the underlying mechanisms, cell transcriptome, metabolic content, and DNA methylation were analyzed. The up-regulation of stress-related genes, as well as a decrease in cell viability, revealed that zebularine affected cell integrity. Concomitantly, the global DNA methylation level was only slightly decreased in the light and not modified in the dark. However, locus-specific analyses demonstrated a decrease in DNA methylation at a few selected loci, including a CACTA DNA transposon and a small region upstream from the UFGT gene, coding for the UDP glucose:flavonoid-3-O-glucosyltransferase, known to be critical for anthocyanin biosynthesis. Moreover, this decrease was correlated with an increase in UFGT expression and in anthocyanin content. In conclusion, our data suggest that UFGT expression could be regulated through DNA methylation in Gamay Teinturier, although the functional link between changes in DNA methylation and UFGT transcription still needs to be demonstrated.
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Affiliation(s)
- Junhua Kong
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - Virginie Garcia
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - Enric Zehraoui
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - Linda Stammitti
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - Ghislaine Hilbert
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - Christel Renaud
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - Stéphane Maury
- INRAe, EA1207 USC1328 Laboratoire de Biologie des Ligneux et des Grandes Cultures, Université d’Orléans, 45067 Orléans, France; (S.M.); (A.D.)
| | - Alain Delaunay
- INRAe, EA1207 USC1328 Laboratoire de Biologie des Ligneux et des Grandes Cultures, Université d’Orléans, 45067 Orléans, France; (S.M.); (A.D.)
| | - Stéphanie Cluzet
- Unité de Recherche Oenologie, Faculté des Sciences Pharmaceutiques, University Bordeaux, EA4577, USC 1366 INRA, Equipe Molécules d’Intérêt Biologique (GESVAB), ISVV, CEDEX, 33882 Villenave d’Ornon, France;
| | - Fatma Lecourieux
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - David Lecourieux
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - Emeline Teyssier
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
- Correspondence: ; Tel.: +33-5-5757-5928
| | - Philippe Gallusci
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
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10
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Escrich A, Cusido RM, Bonfill M, Palazon J, Sanchez-Muñoz R, Moyano E. The Epigenetic Regulation in Plant Specialized Metabolism: DNA Methylation Limits Paclitaxel in vitro Biotechnological Production. FRONTIERS IN PLANT SCIENCE 2022; 13:899444. [PMID: 35874001 PMCID: PMC9305382 DOI: 10.3389/fpls.2022.899444] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Environmental conditions are key factors in the modulation of the epigenetic mechanisms regulating gene expression in plants. Specifically, the maintenance of cell cultures in optimal in vitro conditions alters methylation patterns and, consequently, their genetic transcription and metabolism. Paclitaxel production in Taxus x media cell cultures is reduced during its maintenance in in vitro conditions, compromising the biotechnological production of this valuable anticancer agent. To understand how DNA methylation influences taxane production, the promoters of three genes (GGPPS, TXS, and DBTNBT) involved in taxane biosynthesis have been studied, comparing the methylation patterns between a new line and one of ~14 years old. Our work revealed that while the central promoter of the GGPPS gene is protected from cytosine methylation accumulation, TXS and DBTNBT promoters accumulate methylation at different levels. The DBTNBT promoter of the old line is the most affected, showing a 200 bp regulatory region where all the cytosines were methylated. This evidence the existence of specific epigenetic regulatory mechanisms affecting the last steps of the pathway, such as the DBTNBT promoter. Interestingly, the GGPPS promoter, a regulatory sequence of a non-specific taxane biosynthetic gene, was not affected by this mechanism. In addition, the relationship between the detected methylation points and the predicted transcription factor binding sites (TFBS) showed that the action of TFs would be compromised in the old line, giving a further explanation for the production reduction in in vitro cell cultures. This knowledge could help in designing novel strategies to enhance the biotechnological production of taxanes over time.
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Affiliation(s)
- Ainoa Escrich
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Rosa M. Cusido
- Department of Biology, Healthcare and the Environment, Faculty of Pharmacy and Food Science, Universitat de Barcelona, Barcelona, Spain
| | - Mercedes Bonfill
- Department of Biology, Healthcare and the Environment, Faculty of Pharmacy and Food Science, Universitat de Barcelona, Barcelona, Spain
| | - Javier Palazon
- Department of Biology, Healthcare and the Environment, Faculty of Pharmacy and Food Science, Universitat de Barcelona, Barcelona, Spain
| | - Raul Sanchez-Muñoz
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, Ghent, Belgium
| | - Elisabeth Moyano
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
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11
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Yang BC, Lee MS, Lin MK, Chang WT. 5-Azacytidine increases tanshinone production in Salvia miltiorrhiza hairy roots through epigenetic modulation. Sci Rep 2022; 12:9349. [PMID: 35672334 PMCID: PMC9174287 DOI: 10.1038/s41598-022-12577-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 05/03/2022] [Indexed: 11/26/2022] Open
Abstract
Recent studies have indicated strong connections between epigenetic modulation and secondary metabolites in plants. It is vital to understand the roles of epigenetics in the production of secondary metabolites. In this study, the inhibitor of DNA methylation 5-azacytidine (5-Az) was used on the hairy roots of the medicinal plant Salvia miltiorrhiza to investigate its effect on secondary metabolite production, gene expression, methylation levels in genomic DNA and promoter regions. Our results showed that the contents of tanshinones in S. miltiorrhiza hairy roots increased by 1.5–5 times, and some genes in the biosynthesis pathway showed an upward trend. According to our NGS analysis, the methylation pattern in the promotor of the gene encoding copalyl diphosphate synthase (CPS) was altered, and 51 out of 145 cytosines were demethylated during 5-Az treatment. A total of 36 putative transcription factors (TFs) binding cites were identified in these demethylation sites. Among these TFs binding cites, cis-regulatory elements for the binding of NF-Y and MYB were frequently found in our results. This is the first report to demonstrate a possible mechanism of DNA methylation participating in tanshinone biosynthesis in S. miltiorrhiza hairy roots by modulating the CPS promoter and TFs binding sites.
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Affiliation(s)
- Bo-Cheng Yang
- Department of Chinese Pharmaceutical Sciences and Chinese Medicine Resources, College of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Meng-Shiou Lee
- Department of Chinese Pharmaceutical Sciences and Chinese Medicine Resources, College of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Ming-Kuem Lin
- Department of Chinese Pharmaceutical Sciences and Chinese Medicine Resources, College of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Wen-Te Chang
- Department of Chinese Pharmaceutical Sciences and Chinese Medicine Resources, College of Chinese Medicine, China Medical University, Taichung, Taiwan.
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12
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McKee MC, Wilson SA, Roberts SC. The Interface amongst Conserved and Specialized Pathways in Non-Paclitaxel and Paclitaxel Accumulating Taxus Cultures. Metabolites 2021; 11:metabo11100688. [PMID: 34677403 PMCID: PMC8538509 DOI: 10.3390/metabo11100688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/17/2021] [Accepted: 09/29/2021] [Indexed: 12/02/2022] Open
Abstract
Plant cell cultures derived from Taxus are used to produce valuable metabolites like paclitaxel, a chemotherapeutic drug. Methyl jasmonate elicitation enhances paclitaxel accumulation, but also inhibits culture growth and increases phenylpropanoid biosynthesis, two side effects that detract from taxane accumulation. To understand the connection between all of these processes, a systems approach is applied to investigate cell-wide metabolism in Taxus. Non-paclitaxel and paclitaxel accumulating cultures were elicited over single and multi-generational periods, and subsequent changes in conserved and specialized metabolism were quantified. Methyl jasmonate typically resulted in decreased growth and increased metabolite content in paclitaxel accumulating cultures. Conversely, elicitation typically resulted in either no change or decrease in accumulation of metabolites in the non-paclitaxel accumulating cultures. In both sets of cultures, variability was seen in the response to methyl jasmonate across generations of cell growth. Consolidation of these data determined that paclitaxel accumulation and basal levels of phenolic and flavonoid compounds are indirectly correlated with aggregate size. These approaches assess alternative metabolic pathways that are linked to paclitaxel biosynthesis and provide a comprehensive strategy to both understand the relationship between conserved and specialized metabolism in plants and in the design of strategies to increase natural product yields in plant cell culture.
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Affiliation(s)
- Michelle C. McKee
- Biology & Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA
| | - Sarah A. Wilson
- Chemical Engineering, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Susan C. Roberts
- Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA 01609, USA
- Correspondence:
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13
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Arya SS, Lenka SK, Cahill DM, Rookes JE. Designer nanoparticles for plant cell culture systems: Mechanisms of elicitation and harnessing of specialized metabolites. Bioessays 2021; 43:e2100081. [PMID: 34608646 DOI: 10.1002/bies.202100081] [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: 03/21/2021] [Revised: 09/08/2021] [Accepted: 09/08/2021] [Indexed: 11/07/2022]
Abstract
Plant cell culture systems have become an attractive and sustainable approach to produce high-value and commercially significant metabolites under controlled conditions. Strategies involving elicitor supplementation into plant cell culture media are employed to mimic natural conditions for increasing the metabolite yield. Studies on nanoparticles (NPs) that have investigated elicitation of specialized metabolism have shown the potential of NPs to be a substitute for biotic elicitors such as phytohormones and microbial extracts. Customizable physicochemical characteristics allow the design of monodispersed-, stimulus-responsive-, and hormone-carrying-NPs of precise geometries to enhance their elicitation capabilities based on target metabolite/plant cell culture type. We contextualize advances in NP-mediated elicitation, especially stimulation of specialized metabolic pathways, the underlying mechanisms, impacts on gene regulation, and NP-associated cytotoxicity. The novelty of the concept lies in unleashing the potential of designer NPs to enhance yield, harness metabolites, and transform nanoelicitation from exploratory investigations to a commercially viable strategy.
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Affiliation(s)
- Sagar S Arya
- School of Life and Environmental Sciences, Deakin University, Geelong Campus at Waurn Ponds, Geelong, Victoria, Australia.,TERI-Deakin Nanobiotechnology Centre, The Energy and Resources Institute, Gurugram, Haryana, India
| | - Sangram K Lenka
- TERI-Deakin Nanobiotechnology Centre, The Energy and Resources Institute, Gurugram, Haryana, India
| | - David M Cahill
- School of Life and Environmental Sciences, Deakin University, Geelong Campus at Waurn Ponds, Geelong, Victoria, Australia
| | - James E Rookes
- School of Life and Environmental Sciences, Deakin University, Geelong Campus at Waurn Ponds, Geelong, Victoria, Australia
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14
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Balestrini R, Brunetti C, Cammareri M, Caretto S, Cavallaro V, Cominelli E, De Palma M, Docimo T, Giovinazzo G, Grandillo S, Locatelli F, Lumini E, Paolo D, Patanè C, Sparvoli F, Tucci M, Zampieri E. Strategies to Modulate Specialized Metabolism in Mediterranean Crops: From Molecular Aspects to Field. Int J Mol Sci 2021; 22:ijms22062887. [PMID: 33809189 PMCID: PMC7999214 DOI: 10.3390/ijms22062887] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/10/2021] [Accepted: 03/10/2021] [Indexed: 12/21/2022] Open
Abstract
Plant specialized metabolites (SMs) play an important role in the interaction with the environment and are part of the plant defense response. These natural products are volatile, semi-volatile and non-volatile compounds produced from common building blocks deriving from primary metabolic pathways and rapidly evolved to allow a better adaptation of plants to environmental cues. Specialized metabolites include terpenes, flavonoids, alkaloids, glucosinolates, tannins, resins, etc. that can be used as phytochemicals, food additives, flavoring agents and pharmaceutical compounds. This review will be focused on Mediterranean crop plants as a source of SMs, with a special attention on the strategies that can be used to modulate their production, including abiotic stresses, interaction with beneficial soil microorganisms and novel genetic approaches.
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Affiliation(s)
- Raffaella Balestrini
- National Research Council (CNR)-Institute of Sustainable Plant Protection (IPSP), Viale Mattioli 25 and Strada delle Cacce 73, 10125 and 10135 Torino, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy; (C.B.); (E.L.); (E.Z.)
- Correspondence: ; Tel.: +39-01165-02927
| | - Cecilia Brunetti
- National Research Council (CNR)-Institute of Sustainable Plant Protection (IPSP), Viale Mattioli 25 and Strada delle Cacce 73, 10125 and 10135 Torino, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy; (C.B.); (E.L.); (E.Z.)
| | - Maria Cammareri
- CNR-Institute of Bioscience and Bioresources (IBBR), Via Università 133, 80055 Portici, Italy; (M.C.); (M.D.P.); (T.D.); (S.G.); (M.T.)
| | - Sofia Caretto
- CNR-Institute of Sciences of Food Production, Via Monteroni, 73100 Lecce, Italy; (S.C.); (G.G.)
| | - Valeria Cavallaro
- CNR-Institute of Bioeconomy (IBE), Via Paolo Gaifami, 18, 95126 Catania, Italy; (V.C.); (C.P.)
| | - Eleonora Cominelli
- CNR-Institute of Agricultural Biology and Biotechnology, Via Edoardo Bassini 15, 20133 Milan, Italy; (E.C.); (F.L.); (D.P.); (F.S.)
| | - Monica De Palma
- CNR-Institute of Bioscience and Bioresources (IBBR), Via Università 133, 80055 Portici, Italy; (M.C.); (M.D.P.); (T.D.); (S.G.); (M.T.)
| | - Teresa Docimo
- CNR-Institute of Bioscience and Bioresources (IBBR), Via Università 133, 80055 Portici, Italy; (M.C.); (M.D.P.); (T.D.); (S.G.); (M.T.)
| | - Giovanna Giovinazzo
- CNR-Institute of Sciences of Food Production, Via Monteroni, 73100 Lecce, Italy; (S.C.); (G.G.)
| | - Silvana Grandillo
- CNR-Institute of Bioscience and Bioresources (IBBR), Via Università 133, 80055 Portici, Italy; (M.C.); (M.D.P.); (T.D.); (S.G.); (M.T.)
| | - Franca Locatelli
- CNR-Institute of Agricultural Biology and Biotechnology, Via Edoardo Bassini 15, 20133 Milan, Italy; (E.C.); (F.L.); (D.P.); (F.S.)
| | - Erica Lumini
- National Research Council (CNR)-Institute of Sustainable Plant Protection (IPSP), Viale Mattioli 25 and Strada delle Cacce 73, 10125 and 10135 Torino, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy; (C.B.); (E.L.); (E.Z.)
| | - Dario Paolo
- CNR-Institute of Agricultural Biology and Biotechnology, Via Edoardo Bassini 15, 20133 Milan, Italy; (E.C.); (F.L.); (D.P.); (F.S.)
| | - Cristina Patanè
- CNR-Institute of Bioeconomy (IBE), Via Paolo Gaifami, 18, 95126 Catania, Italy; (V.C.); (C.P.)
| | - Francesca Sparvoli
- CNR-Institute of Agricultural Biology and Biotechnology, Via Edoardo Bassini 15, 20133 Milan, Italy; (E.C.); (F.L.); (D.P.); (F.S.)
| | - Marina Tucci
- CNR-Institute of Bioscience and Bioresources (IBBR), Via Università 133, 80055 Portici, Italy; (M.C.); (M.D.P.); (T.D.); (S.G.); (M.T.)
| | - Elisa Zampieri
- National Research Council (CNR)-Institute of Sustainable Plant Protection (IPSP), Viale Mattioli 25 and Strada delle Cacce 73, 10125 and 10135 Torino, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy; (C.B.); (E.L.); (E.Z.)
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15
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Zhao DK, Zhao Y, Chen SY, Kennelly EJ. Solanum steroidal glycoalkaloids: structural diversity, biological activities, and biosynthesis. Nat Prod Rep 2021; 38:1423-1444. [DOI: 10.1039/d1np00001b] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Chemical structures of typical Solanum steroidal glycoalkaloids from eggplant, tomato, and potato.
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Affiliation(s)
- Da-Ke Zhao
- Biocontrol Engineering Research Center of Plant Disease and Pest, Biocontrol Engineering Research Center of Crop Disease and Pest, School of Ecology and Environment, Yunnan University, Kunming, 650504, P. R. China
| | - Yi Zhao
- Department of Biological Sciences, Lehman College, City University of New York, Bronx, New York, 10468, USA
- PhD Program in Biology, The Graduate Center, City University of New York, New York, 10016, USA
| | - Sui-Yun Chen
- Biocontrol Engineering Research Center of Plant Disease and Pest, Biocontrol Engineering Research Center of Crop Disease and Pest, School of Ecology and Environment, Yunnan University, Kunming, 650504, P. R. China
| | - Edward J. Kennelly
- Department of Biological Sciences, Lehman College, City University of New York, Bronx, New York, 10468, USA
- PhD Program in Biology, The Graduate Center, City University of New York, New York, 10016, USA
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16
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Application of the MSAP Technique to Evaluate Epigenetic Changes in Plant Conservation. Int J Mol Sci 2020; 21:ijms21207459. [PMID: 33050382 PMCID: PMC7589462 DOI: 10.3390/ijms21207459] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 09/29/2020] [Accepted: 10/08/2020] [Indexed: 02/08/2023] Open
Abstract
Epigenetic variation, and particularly DNA methylation, is involved in plasticity and responses to changes in the environment. Conservation biology studies have focused on the measurement of this variation to establish demographic parameters, diversity levels and population structure to design the appropriate conservation strategies. However, in ex situ conservation approaches, the main objective is to guarantee the characteristics of the conserved material (phenotype and epi-genetic). We review the use of the Methylation Sensitive Amplified Polymorphism (MSAP) technique to detect changes in the DNA methylation patterns of plant material conserved by the main ex situ plant conservation methods: seed banks, in vitro slow growth and cryopreservation. Comparison of DNA methylation patterns before and after conservation is a useful tool to check the fidelity of the regenerated plants, and, at the same time, may be related with other genetic variations that might appear during the conservation process (i.e., somaclonal variation). Analyses of MSAP profiles can be useful in the management of ex situ plant conservation but differs in the approach used in the in situ conservation. Likewise, an easy-to-use methodology is necessary for a rapid interpretation of data, in order to be readily implemented by conservation managers.
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17
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Pucker B, Rückert C, Stracke R, Viehöver P, Kalinowski J, Weisshaar B. Twenty-Five Years of Propagation in Suspension Cell Culture Results in Substantial Alterations of the Arabidopsis Thaliana Genome. Genes (Basel) 2019; 10:E671. [PMID: 31480756 PMCID: PMC6770967 DOI: 10.3390/genes10090671] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 08/23/2019] [Accepted: 08/29/2019] [Indexed: 01/16/2023] Open
Abstract
Arabidopsis thaliana is one of the best studied plant model organisms. Besides cultivation in greenhouses, cells of this plant can also be propagated in suspension cell culture. At7 is one such cell line that was established about 25 years ago. Here, we report the sequencing and the analysis of the At7 genome. Large scale duplications and deletions compared to the Columbia-0 (Col-0) reference sequence were detected. The number of deletions exceeds the number of insertions, thus indicating that a haploid genome size reduction is ongoing. Patterns of small sequence variants differ from the ones observed between A. thaliana accessions, e.g., the number of single nucleotide variants matches the number of insertions/deletions. RNA-Seq analysis reveals that disrupted alleles are less frequent in the transcriptome than the native ones.
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Affiliation(s)
- Boas Pucker
- Genetics and Genomics of Plants, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615 Bielefeld, NRW, Germany.
| | - Christian Rückert
- Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615 Bielefeld, NRW, Germany
| | - Ralf Stracke
- Genetics and Genomics of Plants, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615 Bielefeld, NRW, Germany
| | - Prisca Viehöver
- Genetics and Genomics of Plants, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615 Bielefeld, NRW, Germany
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615 Bielefeld, NRW, Germany
| | - Bernd Weisshaar
- Genetics and Genomics of Plants, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615 Bielefeld, NRW, Germany
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