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Singh VK, Ahmed S, Saini DK, Gahlaut V, Chauhan S, Khandare K, Kumar A, Sharma PK, Kumar J. Manipulating epigenetic diversity in crop plants: Techniques, challenges and opportunities. Biochim Biophys Acta Gen Subj 2024; 1868:130544. [PMID: 38104668 DOI: 10.1016/j.bbagen.2023.130544] [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: 09/18/2023] [Revised: 12/04/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
Epigenetic modifications act as conductors of inheritable alterations in gene expression, all while keeping the DNA sequence intact, thereby playing a pivotal role in shaping plant growth and development. This review article presents an overview of techniques employed to investigate and manipulate epigenetic diversity in crop plants, focusing on both naturally occurring and artificially induced epialleles. The significance of epigenetic modifications in facilitating adaptive responses is explored through the examination of how various biotic and abiotic stresses impact them. Further, environmental chemicals are explored for their role in inducing epigenetic changes, particularly focusing on inhibitors of DNA methylation like 5-AzaC and zebularine, as well as inhibitors of histone deacetylation including trichostatin A and sodium butyrate. The review delves into various approaches for generating epialleles, including tissue culture techniques, mutagenesis, and grafting, elucidating their potential to induce heritable epigenetic modifications in plants. In addition, the ground breaking CRISPR/Cas is emphasized for its accuracy in targeting specific epigenetic changes. This presents a potent tools for deciphering the intricacies of epigenetic mechanisms. Furthermore, the intricate relationship between epigenetic modifications and non-coding RNA expression, including siRNAs and miRNAs, is investigated. The emerging role of exo-RNAi in epigenetic regulation is also introduced, unveiling its promising potential for future applications. The article concludes by addressing the opportunities and challenges presented by these techniques, emphasizing their implications for crop improvement. Conclusively, this extensive review provides valuable insights into the intricate realm of epigenetic changes, illuminating their significance in phenotypic plasticity and their potential in advancing crop improvement.
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Affiliation(s)
| | - Shoeb Ahmed
- Ch. Charan Singh University, Meerut 250004, India
| | - Dinesh Kumar Saini
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States
| | - Vijay Gahlaut
- University Centre for Research and Development, Chandigarh University, Mohali 140413, Punjab, India
| | | | - Kiran Khandare
- Center of Innovative and Applied Bioprocessing, Mohali 140308, Punjab, India
| | - Ashutosh Kumar
- Center of Innovative and Applied Bioprocessing, Mohali 140308, Punjab, India
| | - Pradeep Kumar Sharma
- Ch. Charan Singh University, Meerut 250004, India; Maharaja Suhel Dev State University, Azamgarh 276404, U.P., India
| | - Jitendra Kumar
- National Agri-Food Biotechnology Institute, Sector-81, Mohali 140306, Punjab, India.
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Türkoğlu A, Haliloğlu K, Demirel F, Aydin M, Çiçek S, Yiğider E, Demirel S, Piekutowska M, Szulc P, Niedbała G. Machine Learning Analysis of the Impact of Silver Nitrate and Silver Nanoparticles on Wheat ( Triticum aestivum L.): Callus Induction, Plant Regeneration, and DNA Methylation. PLANTS (BASEL, SWITZERLAND) 2023; 12:4151. [PMID: 38140479 PMCID: PMC10747064 DOI: 10.3390/plants12244151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023]
Abstract
The objective of this study was to comprehend the efficiency of wheat regeneration, callus induction, and DNA methylation through the application of mathematical frameworks and artificial intelligence (AI)-based models. This research aimed to explore the impact of treatments with AgNO3 and Ag-NPs on various parameters. The study specifically concentrated on analyzing RAPD profiles and modeling regeneration parameters. The treatments and molecular findings served as input variables in the modeling process. It included the use of AgNO3 and Ag-NPs at different concentrations (0, 2, 4, 6, and 8 mg L-1). The in vitro and epigenetic characteristics were analyzed using several machine learning (ML) methods, including support vector machine (SVM), random forest (RF), extreme gradient boosting (XGBoost), k-nearest neighbor classifier (KNN), and Gaussian processes classifier (GP) methods. This study's results revealed that the highest values for callus induction (CI%) and embryogenic callus induction (EC%) occurred at a concentration of 2 mg L-1 of Ag-NPs. Additionally, the regeneration efficiency (RE) parameter reached its peak at a concentration of 8 mg L-1 of AgNO3. Taking an epigenetic approach, AgNO3 at a concentration of 2 mg L-1 demonstrated the highest levels of genomic template stability (GTS), at 79.3%. There was a positive correlation seen between increased levels of AgNO3 and DNA hypermethylation. Conversely, elevated levels of Ag-NPs were associated with DNA hypomethylation. The models were used to estimate the relationships between the input elements, including treatments, concentration, GTS rates, and Msp I and Hpa II polymorphism, and the in vitro output parameters. The findings suggested that the XGBoost model exhibited superior performance scores for callus induction (CI), as evidenced by an R2 score of 51.5%, which explained the variances. Additionally, the RF model explained 71.9% of the total variance and showed superior efficacy in terms of EC%. Furthermore, the GP model, which provided the most robust statistics for RE, yielded an R2 value of 52.5%, signifying its ability to account for a substantial portion of the total variance present in the data. This study exemplifies the application of various machine learning models in the cultivation of mature wheat embryos under the influence of treatments and concentrations involving AgNO3 and Ag-NPs.
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Affiliation(s)
- Aras Türkoğlu
- Department of Field Crops, Faculty of Agriculture, Necmettin Erbakan University, Konya 42310, Türkiye
| | - Kamil Haliloğlu
- Department of Field Crops, Faculty of Agriculture, Ataturk University, Erzurum 25240, Türkiye;
| | - Fatih Demirel
- Department of Agricultural Biotechnology, Faculty of Agriculture, Igdır University, Igdir 76000, Türkiye;
| | - Murat Aydin
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ataturk University, Erzurum 25240, Türkiye; (M.A.); (S.Ç.); (E.Y.)
| | - Semra Çiçek
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ataturk University, Erzurum 25240, Türkiye; (M.A.); (S.Ç.); (E.Y.)
| | - Esma Yiğider
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ataturk University, Erzurum 25240, Türkiye; (M.A.); (S.Ç.); (E.Y.)
| | - Serap Demirel
- Department of Molecular Biology and Genetics, Faculty of Science, Van Yüzüncü Yıl University, Van 65080, Türkiye;
| | - Magdalena Piekutowska
- Department of Geoecology and Geoinformation, Institute of Biology and Earth Sciences, Pomeranian University in Słupsk, 27 Partyzantów St., 76-200 Słupsk, Poland;
| | - Piotr Szulc
- Department of Agronomy, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland;
| | - Gniewko Niedbała
- Department of Biosystems Engineering, Faculty of Environmental and Mechanical Engineering, Poznań University of Life Sciences, Wojska Polskiego 50, 60-627 Poznań, Poland
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Eren B, Türkoğlu A, Haliloğlu K, Demirel F, Nowosad K, Özkan G, Niedbała G, Pour-Aboughadareh A, Bujak H, Bocianowski J. Investigation of the Influence of Polyamines on Mature Embryo Culture and DNA Methylation of Wheat ( Triticum aestivum L.) Using the Machine Learning Algorithm Method. PLANTS (BASEL, SWITZERLAND) 2023; 12:3261. [PMID: 37765424 PMCID: PMC10536335 DOI: 10.3390/plants12183261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/21/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023]
Abstract
Numerous factors can impact the efficiency of callus formation and in vitro regeneration in wheat cultures through the introduction of exogenous polyamines (PAs). The present study aimed to investigate in vitro plant regeneration and DNA methylation patterns utilizing the inter-primer binding site (iPBS) retrotransposon and coupled restriction enzyme digestion-iPBS (CRED-iPBS) methods in wheat. This investigation involved the application of distinct types of PAs (Put: putrescine, Spd: spermidine, and Spm: spermine) at varying concentrations (0, 0.5, 1, and 1.5 mM). The subsequent outcomes were subjected to predictive modeling using diverse machine learning (ML) algorithms. Based on the specific polyamine type and concentration utilized, the results indicated that 1 mM Put and Spd were the most favorable PAs for supporting endosperm-associated mature embryos. Employing an epigenetic approach, Put at concentrations of 0.5 and 1.5 mM exhibited the highest levels of genomic template stability (GTS) (73.9%). Elevated Spd levels correlated with DNA hypermethylation while reduced Spm levels were linked to DNA hypomethylation. The in vitro and epigenetic characteristics were predicted using ML techniques such as the support vector machine (SVM), extreme gradient boosting (XGBoost), and random forest (RF) models. These models were employed to establish relationships between input variables (PAs, concentration, GTS rates, Msp I polymorphism, and Hpa II polymorphism) and output parameters (in vitro measurements). This comparative analysis aimed to evaluate the performance of the models and interpret the generated data. The outcomes demonstrated that the XGBoost method exhibited the highest performance scores for callus induction (CI%), regeneration efficiency (RE), and the number of plantlets (NP), with R2 scores explaining 38.3%, 73.8%, and 85.3% of the variances, respectively. Additionally, the RF algorithm explained 41.5% of the total variance and showcased superior efficacy in terms of embryogenic callus induction (ECI%). Furthermore, the SVM model, which provided the most robust statistics for responding embryogenic calluses (RECs%), yielded an R2 value of 84.1%, signifying its ability to account for a substantial portion of the total variance present in the data. In summary, this study exemplifies the application of diverse ML models to the cultivation of mature wheat embryos in the presence of various exogenous PAs and concentrations. Additionally, it explores the impact of polymorphic variations in the CRED-iPBS profile and DNA methylation on epigenetic changes, thereby contributing to a comprehensive understanding of these regulatory mechanisms.
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Affiliation(s)
- Barış Eren
- Department of Agricultural Biotechnology, Faculty of Agriculture, Igdır University, Igdir 76000, Türkiye; (B.E.); (F.D.)
| | - Aras Türkoğlu
- Department of Field Crops, Faculty of Agriculture, Necmettin Erbakan University, Konya 42310, Türkiye
| | - Kamil Haliloğlu
- Department of Field Crops, Faculty of Agriculture, Ataturk University, Erzurum 25240, Türkiye;
| | - Fatih Demirel
- Department of Agricultural Biotechnology, Faculty of Agriculture, Igdır University, Igdir 76000, Türkiye; (B.E.); (F.D.)
| | - Kamila Nowosad
- Department of Genetics, Plant Breeding and Seed Production, Wrocław University of Environmental and Life Sciences, Grunwaldzki 24A, 53-363 Wrocław, Poland;
| | - Güller Özkan
- Department of Biology, Faculty of Science, Ankara University, Ankara 06100, Türkiye;
| | - Gniewko Niedbała
- Department of Biosystems Engineering, Faculty of Environmental and Mechanical Engineering, Poznan University of Life Sciences, Wojska Polskiego 50, 60-627 Poznań, Poland;
| | - Alireza Pour-Aboughadareh
- Seed and Plant Improvement Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj P.O. Box 3158854119, Iran;
| | - Henryk Bujak
- Department of Genetics, Plant Breeding and Seed Production, Wrocław University of Environmental and Life Sciences, Grunwaldzki 24A, 53-363 Wrocław, Poland;
- Research Centre for Cultivar Testing (COBORU), Słupia Wielka 34, 63-022 Słupia Wielka, Poland
| | - Jan Bocianowski
- Department of Mathematical and Statistical Methods, Poznan University of Life Sciences, Wojska Polskiego 28, 60-637 Poznań, Poland
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Teano G, Concia L, Wolff L, Carron L, Biocanin I, Adamusová K, Fojtová M, Bourge M, Kramdi A, Colot V, Grossniklaus U, Bowler C, Baroux C, Carbone A, Probst AV, Schrumpfová PP, Fajkus J, Amiard S, Grob S, Bourbousse C, Barneche F. Histone H1 protects telomeric repeats from H3K27me3 invasion in Arabidopsis. Cell Rep 2023; 42:112894. [PMID: 37515769 DOI: 10.1016/j.celrep.2023.112894] [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: 01/21/2021] [Revised: 12/02/2022] [Accepted: 07/13/2023] [Indexed: 07/31/2023] Open
Abstract
While the pivotal role of linker histone H1 in shaping nucleosome organization is well established, its functional interplays with chromatin factors along the epigenome are just starting to emerge. Here we show that, in Arabidopsis, as in mammals, H1 occupies Polycomb Repressive Complex 2 (PRC2) target genes where it favors chromatin condensation and H3K27me3 deposition. We further show that, contrasting with its conserved function in PRC2 activation at genes, H1 selectively prevents H3K27me3 accumulation at telomeres and large pericentromeric interstitial telomeric repeat (ITR) domains by restricting DNA accessibility to Telomere Repeat Binding (TRB) proteins, a group of H1-related Myb factors mediating PRC2 cis recruitment. This study provides a mechanistic framework by which H1 avoids the formation of gigantic H3K27me3-rich domains at telomeric sequences and contributes to safeguard nucleus architecture.
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Affiliation(s)
- Gianluca Teano
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France; Université Paris-Saclay, 91190 Orsay, France
| | - Lorenzo Concia
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Léa Wolff
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Léopold Carron
- Sorbonne Université, CNRS, IBPS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), 75005 Paris, France
| | - Ivona Biocanin
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France; Université Paris-Saclay, 91190 Orsay, France
| | - Kateřina Adamusová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Michael Bourge
- Cytometry Facility, Imagerie-Gif, Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Amira Kramdi
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Vincent Colot
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Chris Bowler
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Célia Baroux
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Alessandra Carbone
- Sorbonne Université, CNRS, IBPS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), 75005 Paris, France
| | - Aline V Probst
- CNRS UMR6293, Université Clermont Auvergne, INSERM U1103, GReD, CRBC, Clermont-Ferrand, France
| | - Petra Procházková Schrumpfová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Simon Amiard
- CNRS UMR6293, Université Clermont Auvergne, INSERM U1103, GReD, CRBC, Clermont-Ferrand, France
| | - Stefan Grob
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Clara Bourbousse
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Fredy Barneche
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France.
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Hung FY, Feng YR, Hsin KT, Shih YH, Chang CH, Zhong W, Lai YC, Xu Y, Yang S, Sugimoto K, Cheng YS, Wu K. Arabidopsis histone H3 lysine 9 methyltransferases KYP/SUVH5/6 are involved in leaf development by interacting with AS1-AS2 to repress KNAT1 and KNAT2. Commun Biol 2023; 6:219. [PMID: 36828846 PMCID: PMC9958104 DOI: 10.1038/s42003-023-04607-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 02/16/2023] [Indexed: 02/26/2023] Open
Abstract
The Arabidopsis H3K9 methyltransferases KRYPTONITE/SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG 4 (KYP/SUVH4), SUVH5 and SUVH6 are redundantly involved in silencing of transposable elements (TEs). Our recent study indicated that KYP/SUVH5/6 can directly interact with the histone deacetylase HDA6 to synergistically regulate TE expression. However, the function of KYP/SUVH5/6 in plant development is still unclear. The transcriptional factors ASYMMETRIC LEAVES1 (AS1) and AS2 form a transcription complex, which is involved in leaf development by repressing the homeobox genes KNOTTED-LIKE FROM ARABIDOPSIS THALIANA 1 (KNAT1) and KNAT2. In this study, we found that KYP and SUVH5/6 directly interact with AS1-AS2 to repress KNAT1 and KNAT2 by altering histone H3 acetylation and H3K9 dimethylation levels. In addition, KYP can directly target the promoters of KNAT1 and KNAT2, and the binding of KYP depends on AS1. Furthermore, the genome-wide occupancy profile of KYP indicated that KYP is enriched in the promoter regions of coding genes, and the binding of KYP is positively correlated with that of AS1 and HDA6. Together, these results indicate that Arabidopsis H3K9 methyltransferases KYP/SUVH5/6 are involved in leaf development by interacting with AS1-AS2 to alter histone H3 acetylation and H3K9 dimethylation from KNAT1 and KNAT2 loci.
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Affiliation(s)
- Fu-Yu Hung
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
- RIKEN, Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Yun-Ru Feng
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Kuan-Ting Hsin
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Yuan-Hsin Shih
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Chung-Han Chang
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Wenjian Zhong
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - You-Cheng Lai
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Yingchao Xu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Songguang Yang
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Keiko Sugimoto
- RIKEN, Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Yi-Sheng Cheng
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Keqiang Wu
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan.
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Sivanesan I, Nayeem S, Venkidasamy B, Kuppuraj SP, RN C, Samynathan R. Genetic and epigenetic modes of the regulation of somatic embryogenesis: a review. Biol Futur 2022; 73:259-277. [DOI: 10.1007/s42977-022-00126-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 06/16/2022] [Indexed: 01/17/2023]
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Liu D, Mu Q, Li X, Xu S, Li Y, Gu T. The callus formation capacity of strawberry leaf explant is modulated by DNA methylation. HORTICULTURE RESEARCH 2022; 9:uhab073. [PMID: 35043170 PMCID: PMC8947209 DOI: 10.1093/hr/uhab073] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 10/16/2021] [Accepted: 11/04/2021] [Indexed: 05/30/2023]
Abstract
Shoot regeneration from leaf tissue requires de-differentiation of cells from a highly differentiated state into an active dividing state, but how this physiological transition occurs and is regulated especially at epigenetic level remains obscure. Here we have characterized the DNA methylome represented by 5-methylcytosine (5mC) in leaf and the callus tissue derived from the leaf explant of woodland strawberry Fragaria vesca. We detected an overall increase of DNA methylation and distinct 5mC enrichment patterns in the CG, CHG and CHH sequence contexts in genetic and transposable elements. Our analyses revealed an intricate relation between DNA methylation and gene expression levels in leaf or leaf-derived callus. However, when considering the genes involved in callus formation and shoot regeneration, e.g. FvePLT3/7, FveWIND3, FveWIND4, FveLOG4 and FveIAA14, their dynamic transcription levels were associated with the differentially methylated regions located in the promoters or gene bodies, indicating a regulatory role of DNA methylation in the transcriptional regulation of pluripotency acquisition in strawberry. Furthermore, application of a DNA methyltransferase inhibitor 5'-azacytidine (5'-Aza) hampered both callus formation and shoot regeneration from the leaf explant. We further showed that 5'-Aza down-regulated the genes involved in cell wall integrity, such as expansin, pectin lyase and pectin methylesterase genes, suggesting an essential role of cell wall metabolism during callus formation. This study reveals the contribution of DNA methylation in callus formation capacity and will provide a basis for developing a strategy to improve shoot regeneration for basic and applied research applications.
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Affiliation(s)
- Decai Liu
- State Key Laboratory of Plant Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Qin Mu
- State Key Laboratory of Plant Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Xianyang Li
- State Key Laboratory of Plant Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Sheng Xu
- State Key Laboratory of Plant Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yi Li
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT 06269, USA
| | - Tingting Gu
- State Key Laboratory of Plant Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
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8
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Khalilzadeh M, Weber KC, Dutt M, El-Mohtar CA, Levy A. Comparative transcriptome analysis of Citrus macrophylla tree infected with Citrus tristeza virus stem pitting mutants provides new insight into the role of phloem regeneration in stem pitting disease. FRONTIERS IN PLANT SCIENCE 2022; 13:987831. [PMID: 36267951 PMCID: PMC9577373 DOI: 10.3389/fpls.2022.987831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/24/2022] [Indexed: 05/21/2023]
Abstract
Stem pitting is a complex and economically important virus-associated disease of perennial woody plants. Molecular mechanisms and pathways occurring during virus-plant interaction that result in this phenomenon are still obscure. Previous studies indicated that different Citrus tristeza virus (CTV) mutants induce defined stem pitting phenotypes ranging from mild (CTVΔp13) to severe (CTVΔp33) in Citrus macrophylla trees. In this study, we conducted comparative transcriptome analyses of C. macrophylla trees infected with CTV mutants (CTVΔp13 and CTVΔp33) and a full-length virus in comparison to healthy plants as control. The mild CTV stem pitting mutant had very few differentially expressed genes (DEGs) related to plant defense mechanism and plant growth and development. In contrast, substantial gene expression changes were observed in plants infected with the severe mutant and the full-length virus, indicating that both the p13 and p33 proteins of CTV acted as a regulator of symptom production by activating and modulating plant responses, respectively. The analysis of transcriptome data for CTVΔp33 and the full-length virus suggested that xylem specification has been blocked by detecting several genes encoding xylem, cell wall and lignin degradation, and cell wall loosening enzymes. Furthermore, stem pitting was accompanied by downregulation of transcription factors involved in regulation of xylem differentiation and downregulation of some genes involved in lignin biosynthesis, showing that the xylem differentiation and specification program has been shut off. Upregulation of genes encoding transcription factors associated with phloem and cambium development indicated the activation of this program in stem pitting disease. Furthermore, we detected the induction of several DEGs encoding proteins associated with cell cycle re-entry such as chromatin remodeling factors and cyclin, and histone modification. This kind of expression pattern of genes related to xylem differentiation and specification, phloem and cambium development, and cell cycle re-entry is demonstrated during secondary vascular tissue (SVT) regeneration. The microscopy analysis confirmed that the regeneration of new phloem is associated with stem pitting phenotypes. The findings of this study, thus, provide evidence for the association between stem pitting phenotypes and SVT regeneration, suggesting that the expression of these genes might play important roles in development of stem pitting symptoms. Overall, our findings suggest that phloem regeneration contributes to development of stem pitting symptoms.
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Affiliation(s)
- Maryam Khalilzadeh
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
| | - Kyle Clark Weber
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
| | - Manjul Dutt
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
| | - Choaa Amine El-Mohtar
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
| | - Amit Levy
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
- *Correspondence: Amit Levy
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Dalakouras A, Vlachostergios D. Epigenetic approaches to crop breeding: current status and perspectives. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5356-5371. [PMID: 34017985 DOI: 10.1093/jxb/erab227] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/18/2021] [Indexed: 05/10/2023]
Abstract
In order to tackle the cumulative adverse effects of global climate change, reduced farmland, and heightened needs of an ever-increasing world population, modern agriculture is in urgent search of solutions that can ensure world food security and sustainable development. Classical crop breeding is still a powerful method to obtain crops with valued agronomical traits, but its potential is gradually being compromised by the menacing decline of genetic variation. Resorting to the epigenome as a source of variation could serve as a promising alternative. Here, we discuss current status of epigenetics-mediated crop breeding (epibreeding), highlight its advances and limitations, outline currently available methodologies, and propose novel RNA-based strategies to modify the epigenome in a gene-specific and transgene-free manner.
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Affiliation(s)
- Athanasios Dalakouras
- Institute of Industrial and Forage Crops, HAO-DEMETER, 41335 Larissa, Greece
- Institute of Plant Breeding and Genetic Resources, HAO-DEMETER, 57001 Thessaloniki, Greece
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10
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Azizi P, Hanafi MM, Sahebi M, Harikrishna JA, Taheri S, Yassoralipour A, Nasehi A. Epigenetic changes and their relationship to somaclonal variation: a need to monitor the micropropagation of plantation crops. FUNCTIONAL PLANT BIOLOGY : FPB 2020; 47:508-523. [PMID: 32349860 DOI: 10.1071/fp19077] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 02/23/2020] [Indexed: 06/11/2023]
Abstract
Chromatin modulation plays important roles in gene expression regulation and genome activities. In plants, epigenetic changes, including variations in histone modification and DNA methylation, are linked to alterations in gene expression. Despite the significance and potential of in vitro cell and tissue culture systems in fundamental research and marketable applications, these systems threaten the genetic and epigenetic networks of intact plant organs and tissues. Cell and tissue culture applications can lead to DNA variations, methylation alterations, transposon activation, and finally, somaclonal variations. In this review, we discuss the status of the current understanding of epigenomic changes that occur under in vitro conditions in plantation crops, including coconut, oil palm, rubber, cotton, coffee and tea. It is hoped that comprehensive knowledge of the molecular basis of these epigenomic variations will help researchers develop strategies to enhance the totipotent and embryogenic capabilities of tissue culture systems for plantation crops.
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Affiliation(s)
- Parisa Azizi
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; and Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Mohamed M Hanafi
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; and Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; and Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; and Corresponding author.
| | - Mahbod Sahebi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Jennifer A Harikrishna
- Centre of Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Sima Taheri
- Centre of Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Ali Yassoralipour
- Department of Agricultural and Food Science, Faculty of Science (Kampar Campus), Universiti Tunku Abdul Rahman (UTAR), Jalan Universiti, Bandar Barat, 31900 Kampar, Perak, Malaysia
| | - Abbas Nasehi
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
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Pei L, Zhang L, Li J, Shen C, Qiu P, Tu L, Zhang X, Wang M. Tracing the origin and evolution history of methylation-related genes in plants. BMC PLANT BIOLOGY 2019; 19:307. [PMID: 31299897 PMCID: PMC6624907 DOI: 10.1186/s12870-019-1923-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 07/03/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND DNA methylation is a crucial epigenetic modification, which is involved in many biological processes, including gene expression regulation, embryonic development, cell differentiation and genomic imprinting etc. And it also involves many key regulatory genes in eukaryotes. By tracing the evolutionary history of methylation-related genes, we can understand the origin and expansion time of these genes, which helps to understand the evolutionary history of plants, and we can also understand the changes of DNA methylation patterns in different species. However, most studies on the evolution of methylation-related genes failed to be carried out for the whole DNA methylation pathway. RESULTS In this study, we conducted a comprehensive identification of 33 methylation-related genes in 77 species, and investigated gene origin and evolution throughout the plant kingdom. We found that the origin of genes responsible for methylation maintenance and demethylation evolved early, while most de novo methylation-related genes appeared late. The methylation-related genes were expanded by whole genome duplication and tandem replication, but were also accompanied by a large number of gene absence events in different species. The gene length and intron length varied a lot in different species, but exon structure and functional domains were relatively conserved. The phylogenetic relationships of methylation-related genes were traced to reveal the evolution history of DNA methylation in different species. The expression patterns of methylation-related genes have changed during the evolution of species, and the expression patterns of these genes in different species can be clustered into four categories. CONCLUSIONS The study describes a global characterization of DNA methylation-related genes in the plant kingdom. The similarities and differences in origin time, gene structure and phylogenetic relationship of these genes lead us to understand the evolutionary conservation and dynamics of DNA methylation in plants.
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Affiliation(s)
- Liuling Pei
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Lin Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Jianying Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Chao Shen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Ping Qiu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Lili Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 Hubei China
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12
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Plant stem cells: what we know and what is anticipated. Mol Biol Rep 2018; 45:2897-2905. [PMID: 30196455 DOI: 10.1007/s11033-018-4344-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 08/30/2018] [Indexed: 01/08/2023]
Abstract
Plant stem cell research is of interest due to stem cells ability of unlimited division, therapeutic potential and steady supply to provide precursor cells. Their isolation and culture provides the important source for the production of homogenous lines of active constituents that allow large-scale production of various metabolites. The process of dedifferentiation and reversal to pluripotent cells involves the various pathways genes related to the stem cells and are associated to each other for maintaining a specific niche. Domains such as niche dynamics and maintenance signaling can be used for the identification of genes for stem cell niche. Significant findings have been achieved in the past on plant stem cells however our understanding towards mechanisms underlying some specific phenomenon like dedifferentiation, regulation, niche dynamics is still in infancy. The present review is based on the past research efforts and also pave a way forward for the future anticipation in the field of development of cell cultures for the production of active metabolites on large scale and undertanding transcriptional regulation of stem cell genes involved in niche signaling.
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Sováková PP, Magdolenová A, Konečná K, Rájecká V, Fajkus J, Fojtová M. Telomere elongation upon transfer to callus culture reflects the reprogramming of telomere stability control in Arabidopsis. PLANT MOLECULAR BIOLOGY 2018; 98:81-99. [PMID: 30128721 DOI: 10.1007/s11103-018-0765-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 08/12/2018] [Indexed: 05/23/2023]
Abstract
KEY MESSAGE Standard pathways involved in the regulation of telomere stability do not contribute to gradual telomere elongation observed in the course of A. thaliana calli propagation. Genetic and epigenetic changes accompanying the culturing of plant cells have frequently been reported. Here we aimed to characterize the telomere homeostasis during long term callus propagation. While in Arabidopsis thaliana calli gradual telomere elongation was observed, telomeres were stable in Nicotiana tabacum and N. sylvestris cultures. Telomere elongation during callus propagation is thus not a general feature of plant cells. The long telomere phenotype in Arabidopsis calli was correlated neither with changes in telomerase activity nor with activation of alternative mechanisms of telomere elongation. The dynamics of telomere length changes was maintained in mutant calli with loss of function of important epigenetic modifiers but compromised in the presence of epigenetically active drug zebularine. To examine whether the cell culture-induced disruption of telomere homeostasis is associated with the modulated structure of chromosome ends, epigenetic properties of telomere chromatin were analysed. Albeit distinct changes in epigenetic modifications of telomere histones were observed, these were broadly stochastic. Our results show that contrary to animal cells, the structure and function of plant telomeres is not determined significantly by the epigenetic character of telomere chromatin. Set of differentially transcribed genes was identified in calli, but considering the known telomere- or telomerase-related functions of respective proteins, none of these changes per se was apparently related to the elongated telomere phenotype. Based on our data, we propose that the disruption in telomere homeostasis in Arabidopsis calli arises from the interplay of multiple factors, as a part of reprogramming of plant cells to long-term culture conditions.
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Affiliation(s)
- Pavla Polanská Sováková
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, 625 00, Brno, Czech Republic
| | - Alžbeta Magdolenová
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, 625 00, Brno, Czech Republic
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic v.v.i., Prague, Czech Republic
| | - Klára Konečná
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, 625 00, Brno, Czech Republic
| | - Veronika Rájecká
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, 625 00, Brno, Czech Republic
| | - Jiří Fajkus
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, 625 00, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., 612 65, Brno, Czech Republic
| | - Miloslava Fojtová
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, 625 00, Brno, Czech Republic.
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic.
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Moon SH, Pandurangan M, Kim DH, Venkatesh J, Patel RV, Mistry BM. A rich source of potential bioactive compounds with anticancer activities by Catharanthus roseus cambium meristematic stem cell cultures. JOURNAL OF ETHNOPHARMACOLOGY 2018; 217:107-117. [PMID: 29452141 DOI: 10.1016/j.jep.2018.02.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 02/08/2018] [Accepted: 02/12/2018] [Indexed: 06/08/2023]
Abstract
ETHNOPHARMACOLOGICAL IMPORTANCE Catharanthus roseus (L.) G. Don. is an important medicinal plant with rich sources of remarkable health benefits consisting more than 100 alkaloids and significant amounts of bioactive compounds, which have been widely used as a folk medicine for treatment of several pathologies. THE AIM OF THE STUDY In the present study, we isolated and cultured innately undifferentiated cambium meristematic cells (CMCs), which were observed stable cell growth, enhancement of bioactive compounds from C.roseus. MATERIALS AND METHODS We attempted to determine the effect of association between time-course growth rates, bioactive compounds and terpenoids indole alkaloid (TIA) contents as well as antioxidant and anticancer efficacies of C. roseus CMC suspension culture treated by UV-C. RESULTS The bioactive compounds, vincristine contents, and antioxidant power were noticed significantly higher in 60 min exposure at 5 cm distances and with the directly collected sample (T7). A similar trend has also been noticed from the anticancer activity. Demonstration of TIA accumulation was found higher at 5 min exposure, at 20 cm distances and 48 h of incubation (T21) and the result of TIA contents had the highest correlation effects of anticancer activities. CONCLUSION In the current study, we demonstrated that UV-C light could enhance the production of the essential compounds and bioactivities in the CMCs of C. roseus, and thus, C. roseus CMCs have the potential to serve as an industrial platform for the production of bioactive alkaloids and antioxidant, anticancer activity. Moreover, additional efforts should be made to irradiate CMC suspension cultures from C. roseus with UV-C to achieve better pharmacological profiles.
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Affiliation(s)
- So Hyun Moon
- Department of Bioresources and Food Sciences, College of Life and Environmental Sciences, Konkuk University, Seoul, Republic of Korea; Natural Medicine Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 30 Yeongudanji-ro, Ochang-eup, Cheong-ju, Chungbuk 363-883, Republic of Korea
| | - Muthuraman Pandurangan
- Department of Bioresources and Food Sciences, College of Life and Environmental Sciences, Konkuk University, Seoul, Republic of Korea
| | - Doo Hwan Kim
- Department of Bioresources and Food Sciences, College of Life and Environmental Sciences, Konkuk University, Seoul, Republic of Korea
| | - Jelli Venkatesh
- Department of Plant Science and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Rahul V Patel
- Department of Food Science and Biotechnology, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do 410-820, Republic of Korea
| | - Bhupendra M Mistry
- Department of Food Science and Biotechnology, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do 410-820, Republic of Korea.
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15
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Lee K, Seo PJ. Dynamic Epigenetic Changes during Plant Regeneration. TRENDS IN PLANT SCIENCE 2018; 23:235-247. [PMID: 29338924 DOI: 10.1016/j.tplants.2017.11.009] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 11/28/2017] [Accepted: 11/29/2017] [Indexed: 05/18/2023]
Abstract
Plants have the remarkable ability to drive cellular dedifferentiation and regeneration. Changes in epigenetic landscapes accompany the cell fate transition. Notably, modifications of chromatin structure occur primarily during callus formation via an in vitro tissue culture process and, thus, pluripotent callus cells have unique epigenetic signatures. Here, we highlight the latest progress in epigenetic regulation of callus formation in plants, which addresses fundamental questions related to cell fate changes and pluripotency establishment. Global and local modifications of chromatin structure underlie callus formation, and the combination and sequence of epigenetic modifications further shape intricate cell fate changes. This review illustrates how a series of chromatin marks change dynamically during callus formation and their biological relevance in plant regeneration.
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Affiliation(s)
- Kyounghee Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Pil Joon Seo
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea.
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16
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Rosspopoff O, Chelysheva L, Saffar J, Lecorgne L, Gey D, Caillieux E, Colot V, Roudier F, Hilson P, Berthomé R, Da Costa M, Rech P. Direct conversion of root primordium into shoot meristem relies on timing of stem cell niche development. Development 2017; 144:1187-1200. [PMID: 28174250 DOI: 10.1242/dev.142570] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 01/26/2017] [Indexed: 02/01/2023]
Abstract
To understand how the identity of an organ can be switched, we studied the transformation of lateral root primordia (LRP) into shoot meristems in Arabidopsis root segments. In this system, the cytokinin-induced conversion does not involve the formation of callus-like structures. Detailed analysis showed that the conversion sequence starts with a mitotic pause and is concomitant with the differential expression of regulators of root and shoot development. The conversion requires the presence of apical stem cells, and only LRP at stages VI or VII can be switched. It is engaged as soon as cell divisions resume because their position and orientation differ in the converting organ compared with the undisturbed emerging LRP. By alternating auxin and cytokinin treatments, we showed that the root and shoot organogenetic programs are remarkably plastic, as the status of the same plant stem cell niche can be reversed repeatedly within a set developmental window. Thus, the networks at play in the meristem of a root can morph in the span of a couple of cell division cycles into those of a shoot, and back, through transdifferentiation.
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Affiliation(s)
- Olga Rosspopoff
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles 78000, France.,Sorbonne Universités, UPCM Université Paris 06, UFR 927, Paris F-75005, France
| | - Liudmila Chelysheva
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles 78000, France
| | - Julie Saffar
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles 78000, France.,Université Paris-Diderot, Sorbonne Paris Cité, Paris F-75205, France
| | - Lena Lecorgne
- Sorbonne Universités, UPCM Université Paris 06, UFR 927, Paris F-75005, France
| | - Delphine Gey
- Muséum d'Histoire Naturelle, UMS 2700, OMSI, Paris F-75231, France
| | - Erwann Caillieux
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, Paris F-75005, France
| | - Vincent Colot
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, Paris F-75005, France
| | - François Roudier
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, Paris F-75005, France
| | - Pierre Hilson
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles 78000, France
| | - Richard Berthomé
- LIPM, Université de Toulouse, INRA, CNRS, INPT, Castanet-Tolosan F-31126, France.,CNRS, Laboratoire des Interactions Plantes-Microorganismes, UMR2594, Castanet-Tolosan 31326, France.,Plant Genomics Research Unit, UMR INRA 1165 - CNRS 8114 - UEVE, 2, CP5708, Evry Cedex 91057, France
| | - Marco Da Costa
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles 78000, France .,Sorbonne Universités, UPCM Université Paris 06, UFR 927, Paris F-75005, France
| | - Philippe Rech
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles 78000, France .,Sorbonne Universités, UPCM Université Paris 06, UFR 927, Paris F-75005, France
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17
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18
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Lebedeva MA, Tvorogova VE, Tikhodeyev ON. Epigenetic mechanisms and their role in plant development. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795417090083] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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19
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Zhao L, Shao Z, Shanks JV. Anticancer Drugs. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807833.ch8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Le Zhao
- Iowa State University; Department of Chemical and Biological Engineering; 4140 Biorenewables Research Laboratory, 617 Bissell Road Ames 50011 IA USA
| | - Zengyi Shao
- Iowa State University; Department of Chemical and Biological Engineering; 4140 Biorenewables Research Laboratory, 617 Bissell Road Ames 50011 IA USA
| | - Jacqueline V Shanks
- Iowa State University; Department of Chemical and Biological Engineering; 4140 Biorenewables Research Laboratory, 617 Bissell Road Ames 50011 IA USA
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20
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Khan A, Yadav NS, Morgenstern Y, Zemach A, Grafi G. Activation of Tag1 transposable elements in Arabidopsis dedifferentiating cells and their regulation by CHROMOMETHYLASE 3-mediated CHG methylation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:1289-98. [PMID: 27475038 DOI: 10.1016/j.bbagrm.2016.07.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 07/13/2016] [Accepted: 07/25/2016] [Indexed: 12/11/2022]
Abstract
Dedifferentiation, that is, the acquisition of stem cell-like state, commonly induced by stress (e.g., protoplasting), is characterized by open chromatin conformation, a chromatin state that could lead to activation of transposable elements (TEs). Here, we studied the activation of the Arabidopsis class II TE Tag1, in which two copies, situated close to each other (near genes) on chromosome 1 are found in Landsberg erecta (Ler) but not in Columbia (Col). We first transformed protoplasts with a construct in which a truncated Tag1 (ΔTag1 non-autonomous) blocks the expression of a reporter gene AtMBD5-GFP and found a relatively high ectopic excision of ΔTag1 accompanied by expression of AtMBD5-GFP in protoplasts derived from Ler compared to Col; further increase was observed in ddm1 (decrease in DNA methylation1) protoplasts (Ler background). Ectopic excision was associated with transcription of the endogenous Tag1 and changes in histone H3 methylation at the promoter region. Focusing on the endogenous Tag1 elements we found low level of excision in Ler protoplasts, which was slightly and strongly enhanced in ddm1 and cmt3 (chromomethylase3) protoplasts, respectively, concomitantly with reduction in Tag1 gene body (GB) CHG methylation and increased Tag1 transcription; strong activation of Tag1 was also observed in cmt3 leaves. Notably, in cmt3, but not in ddm1, Tag1 elements were excised out from their original sites and transposed elsewhere in the genome. Our results suggest that dedifferentiation is associated with Tag1 activation and that CMT3 rather than DDM1 plays a central role in restraining Tag1 activation via inducing GB CHG methylation.
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Affiliation(s)
- Asif Khan
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben Gurion 84990, Israel
| | - Narendra Singh Yadav
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben Gurion 84990, Israel
| | - Yaakov Morgenstern
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben Gurion 84990, Israel
| | - Assaf Zemach
- Department of Molecular Biology and Ecology of Plants, Tel-Aviv University, 69978 Tel Aviv, Israel
| | - Gideon Grafi
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben Gurion 84990, Israel.
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21
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Lee WK, Cho MH. Telomere-binding protein regulates the chromosome ends through the interaction with histone deacetylases in Arabidopsis thaliana. Nucleic Acids Res 2016; 44:4610-24. [PMID: 26857545 PMCID: PMC4889915 DOI: 10.1093/nar/gkw067] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 01/20/2016] [Accepted: 01/28/2016] [Indexed: 01/13/2023] Open
Abstract
Telomeres are nucleoprotein complexes at the end of eukaryotic chromosomes. Many telomere-binding proteins bind to telomeric repeat sequences and further generate T-loops in animals. However, it is not clear if they regulate telomere organization using epigenetic mechanisms and how the epigenetic molecules are involved in regulating the telomeres. Here, we show direct interactions between the telomere-binding protein, AtTRB2 and histone deacetylases, HDT4 and HDA6, in vitro and in vivo AtTRB2 mediates the associations of HDT4 and HDA6 with telomeric repeats. Telomere elongation is found in AtTRB2, HDT4 and HDA6 mutants over generations, but also in met1 and cmt3 DNA methyltransferases mutants. We also characterized HDT4 as an Arabidopsis H3K27 histone deacetylase. HDT4 binds to acetylated peptides at residue K27 of histone H3 in vitro, and deacetylates this residue in vivo Our results suggest that AtTRB2 also has a role in the regulation of telomeric chromatin as a possible scaffold protein for recruiting the epigenetic regulators in Arabidopsis, in addition to its telomere binding and length regulation activity. Our data provide evidences that epigenetic molecules associate with telomeres by direct physical interaction with telomere-binding proteins and further regulate homeostasis of telomeres in Arabidopsis thaliana.
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Affiliation(s)
- Won Kyung Lee
- Department of Systems Biology, Yonsei University, Seoul 03722, Republic of Korea
| | - Myeon Haeng Cho
- Department of Systems Biology, Yonsei University, Seoul 03722, Republic of Korea
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22
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Wang M, Zi J, Zhu J, Chen S, Wang P, Song L, Yu R. Artemisinic Acid Serves as a Novel ORCA3 Inducer to Enhance Biosynthesis of Terpenoid Indole Alkaloids in Catharanthus roseus Cambial Meristematic Cells. Nat Prod Commun 2016. [DOI: 10.1177/1934578x1601100604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
To investigate the effect of artemisinic acid (AA) on improving the production of terpenoid indole alkaloids (TIAs) of Catharanthus roseus cambial meristematic cells (CMCs), feeding AA to C. roseus CMCs caused 2.35-fold and 2.51-fold increases in the production of vindoline and catharanthine, respectively, compared with those of the untreated CMCs. qRT-PCR experiments showed that AA resulted in a 1.36-8.52 fold increase in the transcript levels of several related genes, including octadecanoid-derivative responsive Catharanthus AP2-domain protein 3 (ORCA3), tryptophan decarboxylase (TDC), strictosidine synthase (STR) and desacetoxyvindoline 4-hydroxylase (D4H). However, no effect was observed on the concentration of either jasmonic acid (JA), or the octadecanoid-pathway inhibitors block TIA accumulation caused by AA. The results indicated that AA might serve as a novel ORCA3 inducer to manipulate biosynthesis of TIAs in C. roseus CMCs via an unknown mechanism.
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Affiliation(s)
- Mingxuan Wang
- Biotechnological Institute of Chinese Materia Medica, Jinan University, Guangzhou 510632, China
| | - Jiachen Zi
- Department of Natural Products Chemistry, College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Jianhua Zhu
- Biotechnological Institute of Chinese Materia Medica, Jinan University, Guangzhou 510632, China
| | - Shan Chen
- Department of Natural Products Chemistry, College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Pu Wang
- Biotechnological Institute of Chinese Materia Medica, Jinan University, Guangzhou 510632, China
| | - Liyan Song
- Department of Natural Products Chemistry, College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Rongmin Yu
- Biotechnological Institute of Chinese Materia Medica, Jinan University, Guangzhou 510632, China
- Department of Natural Products Chemistry, College of Pharmacy, Jinan University, Guangzhou 510632, China
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Abstract
AbstractPlant tissue culture techniques have become an integral part of progress in plant science research due to the opportunity offered for close study of detailed plant development with applications in food production through crop improvement, secondary metabolites production and conservation of species. Because the techniques involve growing plants under controlled conditions different from their natural outdoor environment, the plants need adjustments in physiology, anatomy and metabolism for successfulin vitropropagation. Therefore, the protocol has to be optimized for a given species or genotype due to the variability in physiological and growth requirement. Developing the protocol is hampered by several physiological and developmental aberrations in the anatomy and physiology of the plantlets, attributed toin vitroculture conditions of high humidity, low light levels and hetero- or mixotrophic conditions. Some of the culture-induced anomalies become genetic, and the phenotype is inherited by clonal progenies while others are temporary and can be corrected at a later stage of protocol development through changes in anatomy, physiology and metabolism. The success of protocols relies on the transfer of plantlets to field conditions which has been achieved with many species through stages of acclimatization, while with others it remains a challenging task. This review discusses various adjustments in nutrition, physiology and anatomy of micro-propagated plants and field grown ones, as well as anomalies induced by thein vitroculture conditions.
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Villacorta-Martín C, Sánchez-García AB, Villanova J, Cano A, van de Rhee M, de Haan J, Acosta M, Passarinho P, Pérez-Pérez JM. Gene expression profiling during adventitious root formation in carnation stem cuttings. BMC Genomics 2015; 16:789. [PMID: 26467528 PMCID: PMC4606512 DOI: 10.1186/s12864-015-2003-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 10/03/2015] [Indexed: 12/29/2022] Open
Abstract
Background Adventitious root (AR) formation is a critical step in vegetative propagation of most ornamental plants, such as carnation. AR formation from stem cuttings is usually divided into several stages according to physiological and metabolic markers. Auxin is often applied exogenously to promote the development of ARs on stem cuttings of difficult-to-root genotypes. Results By whole transcriptome sequencing, we identified the genes involved in AR formation in carnation cuttings and in response to exogenous auxin. Their expression profiles have been analysed through RNA-Seq during a time-course experiment in the stem cutting base of two cultivars with contrasting efficiencies of AR formation. We explored the kinetics of root primordia formation in these two cultivars and in response to exogenously-applied auxin through detailed histological and physiological analyses. Conclusions Our results provide, for the first time, a number of molecular, histological and physiological markers that characterize the different stages of AR formation in this species and that could be used to monitor adventitious rooting on a wide collection of carnation germplasm with the aim to identify the best-rooting cultivars for breeding purposes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2003-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Joan Villanova
- Instituto de Bioingeniería, Universidad Miguel Hernández, 03202, Elche, Alicante, Spain.
| | - Antonio Cano
- Departamento de Biología Vegetal (Fisiología Vegetal), Universidad de Murcia, Murcia, Spain.
| | - Miranda van de Rhee
- Genetwister Technologies B.V., P.O. Box 193, NL6700 AD, Wageningen, The Netherlands.
| | - Jorn de Haan
- Genetwister Technologies B.V., P.O. Box 193, NL6700 AD, Wageningen, The Netherlands.
| | - Manuel Acosta
- Departamento de Biología Vegetal (Fisiología Vegetal), Universidad de Murcia, Murcia, Spain.
| | - Paul Passarinho
- Genetwister Technologies B.V., P.O. Box 193, NL6700 AD, Wageningen, The Netherlands.
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Moon SH, Venkatesh J, Yu JW, Park SW. Differential induction of meristematic stem cells of Catharanthus roseus and their characterization. C R Biol 2015; 338:745-56. [PMID: 26298518 DOI: 10.1016/j.crvi.2015.05.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 05/24/2015] [Accepted: 05/25/2015] [Indexed: 12/22/2022]
Abstract
Plant cell culture technology has been introduced for the mass production of the many useful components. A variety of plant-derived compounds is being used in various fields, such as pharmaceuticals, foods, and cosmetics. Plant cell cultures are believed to be derived from the dedifferentiation process. In the present study, an undifferentiated cambial meristematic cell (CMCs) of Catharanthus is isolated using histological and genetic methods, and compared with dedifferentiation-derived callus (DDCs) cultures. Furthermore, differential culture conditions for both DDCs- and CMCs-derived cell lines were established. A suitable media for the increased accumulation of terpenoid indole alkaloids (TIAs) was also standardized. Compared with DDCs, CMCs showed marked accumulation of TIAs in cell lines grown on media with 1.5 mg·mL(-1) of NAA and 0.5 mg·mL(-1) of kinetin. CMCs-derived cultures of Catharanthus, as a source of key anticancer drugs (viblastine and vincristine), would overcome the obstacles usually associated with the production of natural metabolites through the use of DDCs. Cell culture systems that are derived from CMCs may also provide a cost-effective and eco-friendly basis for the sustainable production of a number of important plant natural products.
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Affiliation(s)
- So Hyun Moon
- Department of Bioresource and Food Science, Konkuk University, 1, Hwayang-dong, Gwangjin-gu, Seoul, Republic of Korea
| | - Jelli Venkatesh
- Department of Bioresource and Food Science, Konkuk University, 1, Hwayang-dong, Gwangjin-gu, Seoul, Republic of Korea
| | - Jae-Woong Yu
- Department of Bioresource and Food Science, Konkuk University, 1, Hwayang-dong, Gwangjin-gu, Seoul, Republic of Korea
| | - Se Won Park
- Department of Bioresource and Food Science, Konkuk University, 1, Hwayang-dong, Gwangjin-gu, Seoul, Republic of Korea.
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26
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Effects of β-cyclodextrin and methyl jasmonate on the production of vindoline, catharanthine, and ajmalicine in Catharanthus roseus cambial meristematic cell cultures. Appl Microbiol Biotechnol 2015; 99:7035-45. [PMID: 25981997 DOI: 10.1007/s00253-015-6651-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 04/19/2015] [Accepted: 04/22/2015] [Indexed: 10/23/2022]
Abstract
Long-term stable cell growth and production of vindoline, catharanthine, and ajmalicine of cambial meristematic cells (CMCs) from Catharanthus roseus were observed after 2 years of culture. C. roseus CMCs were treated with β-cyclodextrin (β-CD) and methyl jasmonate (MeJA) individually or in combination and were cultured both in conventional Erlenmeyer flasks (100, 250, and 500 mL) and in a 5-L stirred hybrid airlift bioreactor. CMCs of C. roseus cultured in the bioreactor showed higher yields of vindoline, catharanthine, and ajmalicine than those cultured in flasks. CMCs of C. roseus cultured in the bioreactor and treated with 10 mM β-CD and 150 μM MeJA gave the highest yields of vindoline (7.45 mg/L), catharanthine (1.76 mg/L), and ajmalicine (58.98 mg/L), concentrations that were 799, 654, and 426 % higher, respectively, than yields of CMCs cultured in 100-mL flasks without elicitors. Quantitative reverse transcription (RT)-PCR showed that β-CD and MeJA upregulated transcription levels of genes related to the biosynthesis of terpenoid indole alkaloids (TIAs). This is the first study to report that β-CD induced the generation of NO, which plays an important role in mediating the production of TIAs in C. roseus CMCs. These results suggest that β-CD and MeJA can enhance the production of TIAs in CMCs of C. roseus, and thus, CMCs of C. roseus have significant potential to be an industrial platform for production of bioactive alkaloids.
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27
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Sugiyama M. Historical review of research on plant cell dedifferentiation. JOURNAL OF PLANT RESEARCH 2015; 128:349-59. [PMID: 25725626 DOI: 10.1007/s10265-015-0706-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 01/20/2015] [Indexed: 05/23/2023]
Abstract
Plant cell dedifferentiation has long attracted interest as a key process for understanding the plasticity of plant development. In early studies, typical examples of plant cell dedifferentiation were described as physiological and cytological changes associated with wound healing or regenerative development. Subsequently, plant tissue and cell culture techniques, in which exciting progress was achieved after discovery of the hormonal control of cell proliferation and organogenesis in vitro in the 1950s, have been used extensively to study dedifferentiation. The pioneer studies of plant tissue/cell culture led to the hypothesis that many mature plant cells retain totipotency and related dedifferentiation to the initial step of the expression of totipotency. Plant tissue/cell cultures have provided experimental systems not only for physiological analysis, but also for genetic and molecular biological analysis, of dedifferentiation. More recently, proteomic, transcriptomic, and epigenetic analyses have been applied to the study of plant cell dedifferentiation. All of these works have expanded our knowledge of plant cell dedifferentiation, and current research is contributing to unraveling the molecular mechanisms. The present article provides a brief overview of the history of research on plant cell dedifferentiation.
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Affiliation(s)
- Munetaka Sugiyama
- Botanical Gardens, Graduate School of Science, The University of Tokyo, 3-7-1 Hakusan, Bunkyo-ku, Tokyo, 112-0001, Japan,
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28
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Dełeńko K, Niedojadło J, Łabędzka A, Wiśniewska E, Bednarska-Kozakiewicz E. Dedifferentiation of Arabidopsis thaliana cells is accompanied by a strong decrease in RNA polymerase II transcription activity and poly(A+) RNA and 25S rRNA eradication from the cytoplasm. PROTOPLASMA 2015; 252:537-46. [PMID: 25248757 PMCID: PMC4335095 DOI: 10.1007/s00709-014-0700-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 09/09/2014] [Indexed: 05/09/2023]
Abstract
The mechanisms of plant cell dedifferentiation and the acquisition of totipotency are poorly understood. One of the methods to induce the dedifferentiation process in plant cells is simple and requires the removal of the cell wall. After cell wall removal in protoplasts, large-scale chromatin decondensation is observed (Tessadori et al. in J Cell Sci 120:1200-1208, 2007). Here, we show that in Arabidopsis thaliana protoplasts, despite chromatin decondensation, RNA polymerase II transcriptional activity is reduced. The subsequent investigated stages displayed a clear decrease in the quantity of 25S ribosomal RNA (rRNA) first and then poly(A+) RNA, particularly in the cytoplasm. Therefore, the reduced transcription activity and the removal of these RNA transcripts from the cytoplasm is a crucial process in obtaining totipotency in plant cells. After the cytoplasm cleaning of transcripts derived from mesophyll cells, we observed the resynthesis of these RNAs. An increase in the amount of examined molecules to a level similar to that in differentiated mesophyll cells precedes the divisions of already undifferentiated cells. In this work, we show changes in RNA polymerase II transcription dynamics and the quantity of poly(A+) RNA and 25S rRNA during dedifferentiation and re-entry into the cell cycle.
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Affiliation(s)
- Konrad Dełeńko
- Department of Cell Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, Gagarina 9, 87-100 Toruń, Poland
| | - Janusz Niedojadło
- Department of Cell Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, Gagarina 9, 87-100 Toruń, Poland
| | - Agata Łabędzka
- Department of Cell Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, Gagarina 9, 87-100 Toruń, Poland
| | - Ewa Wiśniewska
- Department of Clinical Pathomorphology, Ludwik Rydygier Collegium Medium Bydgoszcz, Nicolaus Copernicus University in Toruń, Skłodowskiej-Curie 9, 85-094 Bydgoszcz, Poland
| | - Elżbieta Bednarska-Kozakiewicz
- Department of Cell Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, Gagarina 9, 87-100 Toruń, Poland
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Ochoa-Villarreal M, Howat S, Jang MO, Kim IS, Jin YW, Lee EK, Loake GJ. Cambial meristematic cells: a platform for the production of plant natural products. N Biotechnol 2015; 32:581-7. [PMID: 25686717 DOI: 10.1016/j.nbt.2015.02.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 01/23/2015] [Accepted: 02/08/2015] [Indexed: 01/18/2023]
Abstract
Plant cell culture constitutes a sustainable, controllable and environmentally friendly tool to produce natural products for the pharmaceutical, cosmetic and industrial biotechnology industries. However, there are significant obstacles to the commercial synthesis of high value chemicals from plant culture including low yields, performance instability, slow plant cell growth, industrial scale-up and downstream processing. Cambial meristematic cells constitute a platform to ameliorate many of these potential problems enabling the commercial production of high value chemicals.
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Affiliation(s)
- Marisol Ochoa-Villarreal
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, King's Buildings, Edinburgh EH9 3BF, UK
| | - Susan Howat
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, King's Buildings, Edinburgh EH9 3BF, UK
| | - Mi Ok Jang
- Unhwa Corp., Wooah-Dong, Dukjin-gu, Jeonju, South Korea
| | - Il Suk Kim
- Unhwa Corp., Wooah-Dong, Dukjin-gu, Jeonju, South Korea
| | - Young-Woo Jin
- Unhwa Corp., Wooah-Dong, Dukjin-gu, Jeonju, South Korea
| | - Eun-Kyong Lee
- Unhwa Corp., Wooah-Dong, Dukjin-gu, Jeonju, South Korea
| | - Gary J Loake
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, King's Buildings, Edinburgh EH9 3BF, UK.
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30
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Jiang F, Feng Z, Liu H, Zhu J. Involvement of Plant Stem Cells or Stem Cell-Like Cells in Dedifferentiation. FRONTIERS IN PLANT SCIENCE 2015; 6:1028. [PMID: 26635851 PMCID: PMC4649052 DOI: 10.3389/fpls.2015.01028] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 11/05/2015] [Indexed: 05/02/2023]
Abstract
Dedifferentiation is the transformation of cells from a given differentiated state to a less differentiated or stem cell-like state. Stem cell-related genes play important roles in dedifferentiation, which exhibits similar histone modification and DNA methylation features to stem cell maintenance. Hence, stem cell-related factors possibly synergistically function to provide a specific niche beneficial to dedifferentiation. During callus formation in Arabidopsis petioles, cells adjacent to procambium cells (stem cell-like cells) are dedifferentiated and survive more easily than other cell types. This finding indicates that stem cells or stem cell-like cells may influence the dedifferentiating niche. In this paper, we provide a brief overview of stem cell maintenance and dedifferentiation regulation. We also summarize current knowledge of genetic and epigenetic mechanisms underlying the balance between differentiation and dedifferentiation. Furthermore, we discuss the correlation of stem cells or stem cell-like cells with dedifferentiation.
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Affiliation(s)
- Fangwei Jiang
- Department of Molecular and Cell Biology, School of Life Science and Technology, Tongji University, Shanghai, China
| | - Zhenhua Feng
- Department of Molecular and Cell Biology, School of Life Science and Technology, Tongji University, Shanghai, China
| | - Hailiang Liu
- Translational Center for Stem Cell Research, Tongji University School of Medicine, Tongji Hospital, Shanghai, China
- *Correspondence: Hailiang Liu, ; Jian Zhu,
| | - Jian Zhu
- Department of Molecular and Cell Biology, School of Life Science and Technology, Tongji University, Shanghai, China
- *Correspondence: Hailiang Liu, ; Jian Zhu,
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31
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Somatic embryogenesis - Stress-induced remodeling of plant cell fate. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1849:385-402. [PMID: 25038583 DOI: 10.1016/j.bbagrm.2014.07.005] [Citation(s) in RCA: 211] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 07/08/2014] [Accepted: 07/10/2014] [Indexed: 01/13/2023]
Abstract
Plants as sessile organisms have remarkable developmental plasticity ensuring heir continuous adaptation to the environment. An extreme example is somatic embryogenesis, the initiation of autonomous embryo development in somatic cells in response to exogenous and/or endogenous signals. In this review I briefly overview the various pathways that can lead to embryo development in plants in addition to the fertilization of the egg cell and highlight the importance of the interaction of stress- and hormone-regulated pathways during the induction of somatic embryogenesis. Somatic embryogenesis can be initiated in planta or in vitro, directly or indirectly, and the requirement for dedifferentiation as well as the way to achieve developmental totipotency in the various systems is discussed in light of our present knowledge. The initiation of all forms of the stress/hormone-induced in vitro as well as the genetically provoked in planta somatic embryogenesis requires extensive and coordinated genetic reprogramming that has to take place at the chromatin level, as the embryogenic program is under strong epigenetic repression in vegetative plant cells. Our present knowledge on chromatin-based mechanisms potentially involved in the somatic-to-embryogenic developmental transition is summarized emphasizing the potential role of the chromatin to integrate stress, hormonal, and developmental pathways leading to the activation of the embryogenic program. The role of stress-related chromatin reorganization in the genetic instability of in vitro cultures is also discussed. This article is part of a Special Issue entitled: Stress as a fundamental theme in cell plasticity.
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32
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Jiang F, Zhu J, Liu HL. Protoplasts: a useful research system for plant cell biology, especially dedifferentiation. PROTOPLASMA 2013; 250:1231-8. [PMID: 23719716 DOI: 10.1007/s00709-013-0513-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 05/16/2013] [Indexed: 05/03/2023]
Abstract
As protoplasts have the characteristics of no cell walls, rapid population growth, and synchronicity, they are useful tools for research in many fields, especially cellular biology (Table 1). This article is an overview that focuses on the application of protoplasts to investigate the mechanisms of dedifferentiation, including changes in hormone signals, epigenetic changes, and organelle distribution during the dedifferentiation process. The article also emphasizes the wide range of uses for protoplasts in studying protein positions and signaling during different stresses. The examples provided help to show that protoplast systems, for example the mesophyll protoplast system of Arabidopsis, represent promising tools for studying developmental biology. Meanwhile, specific analysis of protoplast, which comes from different tissue, has specific advantages and limitations (Table 2), and it can provide recommendations to use this system.
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Affiliation(s)
- Fangwei Jiang
- School of Life Science and Technology, Tongji University, Shanghai, 200092, China
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33
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Nic-Can GI, López-Torres A, Barredo-Pool F, Wrobel K, Loyola-Vargas VM, Rojas-Herrera R, De-la-Peña C. New insights into somatic embryogenesis: leafy cotyledon1, baby boom1 and WUSCHEL-related homeobox4 are epigenetically regulated in Coffea canephora. PLoS One 2013; 8:e72160. [PMID: 23977240 PMCID: PMC3748027 DOI: 10.1371/journal.pone.0072160] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 07/07/2013] [Indexed: 01/09/2023] Open
Abstract
Plant cells have the capacity to generate a new plant without egg fertilization by a process known as somatic embryogenesis (SE), in which differentiated somatic cells can form somatic embryos able to generate a functional plant. Although there have been advances in understanding the genetic basis of SE, the epigenetic mechanism that regulates this process is still unknown. Here, we show that the embryogenic development of Coffea canephora proceeds through a crosstalk between DNA methylation and histone modifications during the earliest embryogenic stages of SE. We found that low levels of DNA methylation, histone H3 lysine 9 dimethylation (H3K9me2) and H3K27me3 change according to embryo development. Moreover, the expression of LEAFY cotyledon1 (LEC1) and BABY BOOM1 (BBM1) are only observed after SE induction, whereas WUSCHEL-related homeobox4 (WOX4) decreases its expression during embryo maturation. Using a pharmacological approach, it was found that 5-Azacytidine strongly inhibits the embryogenic response by decreasing both DNA methylation and gene expression of LEC1 and BBM1. Therefore, in order to know whether these genes were epigenetically regulated, we used Chromatin Immunoprecipitation (ChIP) assays. It was found that WOX4 is regulated by the repressive mark H3K9me2, while LEC1 and BBM1 are epigenetically regulated by H3K27me3. We conclude that epigenetic regulation plays an important role during somatic embryogenic development, and a molecular mechanism for SE is proposed.
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Affiliation(s)
- Geovanny I. Nic-Can
- Campus de Ciencias Exactas e Ingeniería, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | | | - Felipe Barredo-Pool
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
| | - Kazimierz Wrobel
- Facultad de Química, Universidad de Guanajuato, Guanajuato, México
| | - Víctor M. Loyola-Vargas
- Centro de Investigación Científica de Yucatán, Unidad de Bioquímica y Biología Molecular de Plantas, Mérida, Yucatán, México
| | - Rafael Rojas-Herrera
- Campus de Ciencias Exactas e Ingeniería, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | - Clelia De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
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Vining K, Pomraning KR, Wilhelm LJ, Ma C, Pellegrini M, Di Y, Mockler TC, Freitag M, Strauss SH. Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa. BMC PLANT BIOLOGY 2013; 13:92. [PMID: 23799904 PMCID: PMC3728041 DOI: 10.1186/1471-2229-13-92] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 06/12/2013] [Indexed: 05/22/2023]
Abstract
BACKGROUND Cytosine DNA methylation (5mC) is an epigenetic modification that is important to genome stability and regulation of gene expression. Perturbations of 5mC have been implicated as a cause of phenotypic variation among plants regenerated through in vitro culture systems. However, the pattern of change in 5mC and its functional role with respect to gene expression, are poorly understood at the genome scale. A fuller understanding of how 5mC changes during in vitro manipulation may aid the development of methods for reducing or amplifying the mutagenic and epigenetic effects of in vitro culture and plant transformation. RESULTS We investigated the in vitro methylome of the model tree species Populus trichocarpa in a system that mimics routine methods for regeneration and plant transformation in the genus Populus (poplar). Using methylated DNA immunoprecipitation followed by high-throughput sequencing (MeDIP-seq), we compared the methylomes of internode stem segments from micropropagated explants, dedifferentiated calli, and internodes from regenerated plants. We found that more than half (56%) of the methylated portion of the genome appeared to be differentially methylated among the three tissue types. Surprisingly, gene promoter methylation varied little among tissues, however, the percentage of body-methylated genes increased from 9% to 14% between explants and callus tissue, then decreased to 8% in regenerated internodes. Forty-five percent of differentially-methylated genes underwent transient methylation, becoming methylated in calli, and demethylated in regenerants. These genes were more frequent in chromosomal regions with higher gene density. Comparisons with an expression microarray dataset showed that genes methylated at both promoters and gene bodies had lower expression than genes that were unmethylated or only promoter-methylated in all three tissues. Four types of abundant transposable elements showed their highest levels of 5mC in regenerated internodes. CONCLUSIONS DNA methylation varies in a highly gene- and chromosome-differential manner during in vitro differentiation and regeneration. 5mC in redifferentiated tissues was not reset to that in original explants during the study period. Hypermethylation of gene bodies in dedifferentiated cells did not interfere with transcription, and may serve a protective role against activation of abundant transposable elements.
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Affiliation(s)
- Kelly Vining
- Department of Forest Ecosystems and Society, 321 Richardson Hall, Corvallis, OR, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA
| | - Kyle R Pomraning
- Molecular and Cellular Biology Program, Corvallis, OR 97331, USA
- Department of Biochemistry and Biophysics, Corvallis, OR 97331, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA
| | | | - Cathleen Ma
- Department of Forest Ecosystems and Society, 321 Richardson Hall, Corvallis, OR, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Yanming Di
- Statistics Department, Oregon State University, Corvallis, Oregon, USA
| | - Todd C Mockler
- The Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Michael Freitag
- Molecular and Cellular Biology Program, Corvallis, OR 97331, USA
- Department of Biochemistry and Biophysics, Corvallis, OR 97331, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA
| | - Steven H Strauss
- Department of Forest Ecosystems and Society, 321 Richardson Hall, Corvallis, OR, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA
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35
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Benoit M, Layat E, Tourmente S, Probst AV. Heterochromatin dynamics during developmental transitions in Arabidopsis - a focus on ribosomal DNA loci. Gene 2013; 526:39-45. [PMID: 23410919 DOI: 10.1016/j.gene.2013.01.060] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 01/16/2013] [Accepted: 01/23/2013] [Indexed: 01/01/2023]
Abstract
The Arabidopsis chromosomes contain conspicuous heterochromatin domains comprising the repetitive 45S and 5S ribosomal DNA loci as well as centromeric and pericentromeric repeats that organize into chromocenters during interphase. During developmental phase transitions such as seed maturation, germination, seedling growth and flowering that require large-scale reprogramming of gene expression patterns, the organization of repetitive sequences into chromocenters dynamically changes. Here we illustrate recent studies that shed light on the heterochromatin dynamics in cotyledons, the first aerial tissues preformed in the embryo, and in true leaves. We will summarize available data for the 5S rDNA repeat loci, in particular their chromatin organization and expression dynamics during the first days of post-germination development, and discuss how the plant accommodates 5S rRNA transcription during large-scale chromatin reorganization events.
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Affiliation(s)
- Matthias Benoit
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, 24 Avenue des Landais, BP 80026, 63171 Aubière Cedex, France.
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Wang QM, Wang L. An evolutionary view of plant tissue culture: somaclonal variation and selection. PLANT CELL REPORTS 2012; 31:1535-47. [PMID: 22610486 DOI: 10.1007/s00299-012-1281-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 04/30/2012] [Accepted: 04/30/2012] [Indexed: 05/20/2023]
Abstract
Plants regenerated from in vitro cultures possess an array of genetic and epigenetic changes. This phenomenon is known as 'somaclonal variation' and the frequency of somaclonal variation (SV) is usually elevated far beyond that expected in nature. Initially, the relationship between time in culture and detected SV was found to support the widespread belief that SV accumulates with culture age. However, a few studies indicated that older cultures yielded regenerants with less SV. What leads to this seemed contradiction? In this article, we have proposed a novel in vitro callus selection hypothesis, differentiation bottleneck (D-bottleneck) and dedifferentiation bottleneck (Dd-bottleneck), which consider natural selection theory to be fit for cell population in vitro. The results of multiplication races between the cells with the true-to-type phenotype and the deleterious cells determine the increase/decrease of SV frequencies in calli or regenerants as in vitro culture time goes on. The possibility of interpreting the complex situation of time-related SV by the evolutionary theory is discussed in this paper. In addition, the SV threshold, space-determined hypothesis and D-bottleneck are proposed to interpret the loss of the regenerability through a long period of plant tissue culture (PTC).
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Affiliation(s)
- Qin-Mei Wang
- Institute of Genetics and Cytology, Northeast Normal University, Changchun, 130024, People's Republic of China.
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Yun UW, Yan Z, Amir R, Hong S, Jin YW, Lee EK, Loake GJ. Plant natural products: history, limitations and the potential of cambial meristematic cells. Biotechnol Genet Eng Rev 2012; 28:47-59. [PMID: 22616481 DOI: 10.5661/bger-28-47] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Humans have utilised plant derived natural products as medicines for millenia. Moreover, many contemporary pharmaceuticals are also natural products or derivatives thereof. However, the full potential of these compounds remains to be exploited because often they are: complex and difficult to synthesise; found in low quantities; produced by undomesticated and sometimes rare plants; and, their synthesis is routinely influenced by weather conditions. Potentially, the in vitro culture of cells from the corresponding plant species could circumvent some of these problems but the growth of plant cells on an industrial scale is also problematic. The recent isolation and culture of cambial meristematic cells (CMCs), stem cells which ordinarily generate the plant vasculature, may now provide a key platform technology to help realise the full potential of plant natural products.
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Affiliation(s)
- Ung-Wook Yun
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, King's Buildings, Edinburgh EH9 3JR, UK
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Xu K, Liu J, Fan M, Xin W, Hu Y, Xu C. A genome-wide transcriptome profiling reveals the early molecular events during callus initiation in Arabidopsis multiple organs. Genomics 2012; 100:116-24. [PMID: 22664253 DOI: 10.1016/j.ygeno.2012.05.013] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 05/24/2012] [Accepted: 05/24/2012] [Indexed: 12/21/2022]
Abstract
Induction of a pluripotent cell mass termed callus is the first step in an in vitro plant regeneration system, which is required for subsequent regeneration of new organs or whole plants. However, the early molecular mechanism underlying callus initiation is largely elusive. Here, we analyzed the dynamic transcriptome profiling of callus initiation in Arabidopsis aerial and root explants and identified 1342 differentially expressed genes in both explants after incubation on callus-inducing medium. Detailed categorization revealed that the differentially expressed genes were mainly related to hormone homeostasis and signaling, transcriptional and post transcriptional regulations, protein phosphorelay cascades and DNA- or chromatin-modification. Further characterization showed that overexpression of two transcription factors, HB52 or CRF3, resulted in the callus formation in transgenic plants without exogenous auxin. Therefore, our comprehensive analyses provide some insight into the early molecular regulations during callus initiation and are useful for further identification of the regulators governing callus formation.
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Affiliation(s)
- Ke Xu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
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39
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Choi JI, Jee MK, Im YB, Kang SK. Novel GSK-3β inhibitors and CBM-1078 guide hATSCs' deaging via Oct4 and β-catenin activation. Antioxid Redox Signal 2012. [PMID: 22364277 DOI: 10.1089/ars.2011.4422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
UNLABELLED Abstract Aims: The fate decision of adult stem cells is determined by the activation of specific intracellular signaling pathways after exposure to specific stimuli. In this study, we demonstrated specific functions of a novel small molecule, CBM-1078, that induced cell self-renewal via Oct4- and canonical Wnt/β-catenin-mediated deaging in cultured human adipose tissue-derived stem cells (hATSCs). RESULTS As a potential glycogen synthase kinase-3β (GSK-3β) inhibitor, CBM-1078 primarily activated β-catenin and Oct4 expression after inhibition of GSK-3β. Treatment of hATSCs with CBM-1078 led to transdifferentiation toward a neural precursor cell fate after transient self-renewal, and the cells were capable of differentiation into gamma-Aminobutyric acid (GABA)-secreting neuronal cells with pain-modulating functions in an animal model of neuropathic pain. During cell self-renewal, CBM-1078 directs the translocalization of β-catenin and Oct4 into the nucleus, an event that is crucial for the cooperative activation of hATSC neurogenesis via Oct4 and Wnt/β-catenin. Nuclear-localized β-catenin and Oct4 act together to regulate the expression of Oct4, Nanog, Sox2, β-catenin, c-Myc, and STAT3 after binding to the regulatory regions of these genes. Nuclear Oct4 and Wnt3a/β-catenin also control cell growth by binding to the promoters of STAT3, Gli3, and c-Myc after complex formation and direct interaction. CBM-1078 actively enhanced the DNA-binding affinity of Oct4 and β-catenin to functional genes and activated the Wnt/β-catenin pathway to promote hATSC reprogramming. INNOVATION AND CONCLUSION This study revealed the value of a single small molecule, CBM-1078, showing a definitive cell reprogramming mechanism. Finally, we confirmed the therapeutic potential of GABA-hATSCs for treatment of neuropathic pain, which could be used for therapeutic purposes in humans. Antioxid. Redox Signal. 00, 000-000.
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Affiliation(s)
- Jee-In Choi
- Laboratory of Stem Cell Biology, Department of Biotechnology, College of Veterinary Medicine, Seoul National University , Seoul, Republic of Korea
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40
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Neelakandan AK, Wang K. Recent progress in the understanding of tissue culture-induced genome level changes in plants and potential applications. PLANT CELL REPORTS 2012; 31:597-620. [PMID: 22179259 DOI: 10.1007/s00299-011-1202-z] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 11/30/2011] [Accepted: 12/01/2011] [Indexed: 05/23/2023]
Abstract
In vitro cell and tissue-based systems have tremendous potential in fundamental research and for commercial applications such as clonal propagation, genetic engineering and production of valuable metabolites. Since the invention of plant cell and tissue culture techniques more than half a century ago, scientists have been trying to understand the morphological, physiological, biochemical and molecular changes associated with tissue culture responses. Establishment of de novo developmental cell fate in vitro is governed by factors such as genetic make-up, stress and plant growth regulators. In vitro culture is believed to destabilize the genetic and epigenetic program of intact plant tissue and can lead to chromosomal and DNA sequence variations, methylation changes, transposon activation, and generation of somaclonal variants. In this review, we discuss the current status of understanding the genomic and epigenomic changes that take place under in vitro conditions. It is hoped that a precise and comprehensive knowledge of the molecular basis of these variations and acquisition of developmental cell fate would help to devise strategies to improve the totipotency and embryogenic capability in recalcitrant species and genotypes, and to address bottlenecks associated with clonal propagation.
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41
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Jang SH, Lee EK, Lim MJ, Hong NJ, Oh IS, Jin YW, Jeong HS, Jeong YS, Lee JC, Jang YS. Suppression of lipopolysaccharide-induced expression of inflammatory indicators in RAW 264.7 macrophage cells by extract prepared from Ginkgo biloba cambial meristematic cells. PHARMACEUTICAL BIOLOGY 2012; 50:420-428. [PMID: 22129367 DOI: 10.3109/13880209.2011.610805] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
CONTEXT Ginkgo biloba L. (Ginkgoaceae) leaves have been used as an herbal medicine that has a complex range of biological activities. However, when we consider that biological activity of plant extracts is highly variable according to the source, location, and harvest season, technology to obtain the natural products with homogeneity is extremely important. OBJECTIVE We established the technology to obtain the cambial meristematic cells (CMCs) of Ginkgo biloba, which were expanded in vitro with homogeneity through a suspension culture and then determined the anti-inflammatory activity of fractionated samples prepared from the ethanol extract of CMCs. MATERIALS AND METHODS We determined the anti-inflammatory activity of samples using lipopolysaccharide (LPS)-stimulated RAW 264.7 macrophage cells. Especially, influence of sample treatment on the expression of various indicators, such as nitric oxide (NO), inducible nitric oxide synthase (iNOS), cyclooxygenase (COX)-2, mitogen-activated protein (MAP) kinases, transcription factor, and cytokines, involved in inflammatory activity was assessed. RESULTS A fractionated sample demonstrated 53.4% inhibition of LPS-induced NO production from the cells. Additionally, when fractionated samples were treated, iNOS and COX-2 expressions were almost completely suppressed. Fractionated samples also inhibited the phosphorylation of LPS-induced extracellular signal-regulated (ERK) and p38 MAP kinases more than 60%. IκB phosphorylation and subsequent nuclear factor (NF)-κB activation were also suppressed by fractionated samples. The expression of pro-inflammatory cytokines, IL-6 and tumor necrosis factor (TNF)-α, was significantly inhibited by the sample treatment. DISCUSSION AND CONCLUSION Fractionated samples from the ethanol extract of Ginkgo biloba CMCs could potentially be the source of a powerful anti-inflammatory substance.
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Affiliation(s)
- Sun-Hee Jang
- Department of Molecular Biology and the Institute for Molecular Biology and Genetics, Chonbuk National University, Jeonju, Korea
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Zhang J, Gao G, Chen JJ, Taylor G, Cui KM, He XQ. Molecular features of secondary vascular tissue regeneration after bark girdling in Populus. THE NEW PHYTOLOGIST 2011; 192:869-884. [PMID: 21883236 DOI: 10.1111/j.1469-8137.2011.03855.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Regeneration is a common strategy for plants to repair damage to their tissue after attacks from other organisms or physical assaults. However, how differentiating cells acquire regenerative competence and rebuild the pattern of new tissues remains largely unknown. Using anatomical observation and microarray analysis, we investigated the morphological process and molecular features of secondary vascular tissue regeneration after bark girdling in trees. After bark girdling, new phloem and cambium regenerate from differentiating xylem cells and rebuild secondary vascular tissue pattern within 1 month. Differentiating xylem cells acquire regenerative competence through epigenetic regulation and cell cycle re-entry. The xylem developmental program was blocked, whereas the phloem or cambium program was activated, resulting in the secondary vascular tissue pattern re-establishment. Phytohormones play important roles in vascular tissue regeneration. We propose a model describing the molecular features of secondary vascular tissue regeneration after bark girdling in trees. It provides information for understanding mechanisms of tissue regeneration and pattern formation of the secondary vascular tissues in plants.
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Affiliation(s)
- Jing Zhang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Ge Gao
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Jia-Jia Chen
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Gail Taylor
- School of Biological Sciences, University of Southampton SO16 7PX, UK
| | - Ke-Ming Cui
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Xin-Qiang He
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
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43
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Seed maturation in Arabidopsis thaliana is characterized by nuclear size reduction and increased chromatin condensation. Proc Natl Acad Sci U S A 2011; 108:20219-24. [PMID: 22123962 DOI: 10.1073/pnas.1117726108] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Most plant species rely on seeds for their dispersal and survival under unfavorable environmental conditions. Seeds are characterized by their low moisture content and significantly reduced metabolic activities. During the maturation phase, seeds accumulate storage reserves and become desiccation-tolerant and dormant. Growth is resumed after release of dormancy and the occurrence of favorable environmental conditions. Here we show that embryonic cotyledon nuclei of Arabidopsis thaliana seeds have a significantly reduced nuclear size, which is established at the beginning of seed maturation. In addition, the chromatin of embryonic cotyledon nuclei from mature seeds is highly condensed. Nuclei regain their size and chromatin condensation level during germination. The reduction in nuclear size is controlled by the seed maturation regulator ABSCISIC ACID-INSENSITIVE 3, and the increase during germination requires two predicted nuclear matrix proteins, LITTLE NUCLEI 1 and LITTLE NUCLEI 2. Our results suggest that the specific properties of nuclei in ripe seeds are an adaptation to desiccation, independent of dormancy. We conclude that the changes in nuclear size and chromatin condensation in seeds are independent, developmentally controlled processes.
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44
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Grafi G, Florentin A, Ransbotyn V, Morgenstern Y. The stem cell state in plant development and in response to stress. FRONTIERS IN PLANT SCIENCE 2011; 2:53. [PMID: 22645540 PMCID: PMC3355748 DOI: 10.3389/fpls.2011.00053] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 09/03/2011] [Indexed: 05/18/2023]
Abstract
Stem cells are commonly defined by their developmental capabilities, namely, self-renewal and multitype differentiation, yet the biology of stem cells and their inherent features both in plants and animals are only beginning to be elucidated. In this review article we highlight the stem cell state in plants with reference to animals and the plastic nature of plant somatic cells often referred to as totipotency as well as the essence of cellular dedifferentiation. Based on recent published data, we illustrate the picture of stem cells with emphasis on their open chromatin conformation. We discuss the process of dedifferentiation and highlight its transient nature, its distinction from re-entry into the cell cycle and its activation following exposure to stress. We also discuss the potential hazard that can be brought about by stress-induced dedifferentiation and its major impact on the genome, which can undergo stochastic, abnormal reorganization leading to genetic variation by means of DNA transposition and/or DNA recombination.
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Affiliation(s)
- Gideon Grafi
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev Midreshet Ben-Gurion, Israel
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45
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Vaquero-Sedas MI, Vega-Palas MA. On the chromatin structure of eukaryotic telomeres. Epigenetics 2011; 6:1055-8. [PMID: 21822057 PMCID: PMC3225743 DOI: 10.4161/epi.6.9.16845] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 07/05/2011] [Indexed: 01/12/2023] Open
Abstract
Telomeres prevent chromosome fusions and degradation by exonucleases and are implicated in DNA repair, homologous recombination, chromosome pairing and segregation. All these functions of telomeres require the integrity of their chromatin structure, which has been traditionally considered as heterochromatic. In agreement with this idea, different studies have reported that telomeres associate with heterochromatic marks. However, these studies addressed simultaneously the chromatin structures of telomeres and subtelomeric regions or the chromatin structure of telomeres and Interstitial Telomeric Sequences (ITSs). The independent analysis of Arabidopsis telomeres, subtelomeric regions and ITSs has allowed the discovery of euchromatic telomeres. In Arabidopsis, whereas subtelomeric regions and ITSs associate with heterochromatic marks, telomeres exhibit euchromatic features. We think that this scenario could be found in other model systems if the chromatin organizations of telomeres, subtelomeric regions and ITSs are independently analyzed.
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Affiliation(s)
- María I Vaquero-Sedas
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-CSIC, Seville, Spain
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46
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Li W, Liu H, Cheng ZJ, Su YH, Han HN, Zhang Y, Zhang XS. DNA methylation and histone modifications regulate de novo shoot regeneration in Arabidopsis by modulating WUSCHEL expression and auxin signaling. PLoS Genet 2011; 7:e1002243. [PMID: 21876682 PMCID: PMC3158056 DOI: 10.1371/journal.pgen.1002243] [Citation(s) in RCA: 159] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Accepted: 07/06/2011] [Indexed: 12/11/2022] Open
Abstract
Plants have a profound capacity to regenerate organs from differentiated somatic tissues, based on which propagating plants in vitro was made possible. Beside its use in biotechnology, in vitro shoot regeneration is also an important system to study de novo organogenesis. Phytohormones and transcription factor WUSCHEL (WUS) play critical roles in this process but whether and how epigenetic modifications are involved is unknown. Here, we report that epigenetic marks of DNA methylation and histone modifications regulate de novo shoot regeneration of Arabidopsis through modulating WUS expression and auxin signaling. First, functional loss of key epigenetic genes—including METHYLTRANSFERASE1 (MET1) encoding for DNA methyltransferase, KRYPTONITE (KYP) for the histone 3 lysine 9 (H3K9) methyltransferase, JMJ14 for the histone 3 lysine 4 (H3K4) demethylase, and HAC1 for the histone acetyltransferase—resulted in altered WUS expression and developmental rates of regenerated shoots in vitro. Second, we showed that regulatory regions of WUS were developmentally regulated by both DNA methylation and histone modifications through bisulfite sequencing and chromatin immunoprecipitation. Third, DNA methylation in the regulatory regions of WUS was lost in the met1 mutant, thus leading to increased WUS expression and its localization. Fourth, we did a genome-wide transcriptional analysis and found out that some of differentially expressed genes between wild type and met1 were involved in signal transduction of the phytohormone auxin. We verified that the increased expression of AUXIN RESPONSE FACTOR3 (ARF3) in met1 indeed was due to DNA demethylation, suggesting DNA methylation regulates de novo shoot regeneration by modulating auxin signaling. We propose that DNA methylation and histone modifications regulate de novo shoot regeneration by modulating WUS expression and auxin signaling. The study demonstrates that, although molecular components involved in organogenesis are divergently evolved in plants and animals, epigenetic modifications play an evolutionarily convergent role in this process. Plants have a strong ability to generate organs from differentiated somatic tissues. Due to this feature, shoot regeneration in vitro has been used as an important way for producing whole plants in agriculture and biotechnology. Phytohormones and the transcription factor WUSCHEL (WUS) are essential for reprogramming during de novo shoot regeneration. Epigenetic modifications are also critical for mammalian cell differentiation and organogenesis. Here, we show that epigenetic modifications mediate the de novo shoot regeneration in Arabidopsis. Mutations of key epigenetic genes resulted in altered WUS expression and developmental rates of regenerated shoots in vitro. Bisulfite sequencing and chromatin immunoprecipitation revealed that the regulatory regions of WUS were developmentally regulated by both DNA methylation and histone modifications. By transcriptome analysis, we identified that some differentially expressed genes between wild type and met1 are involved in signal transduction of the phytohormone auxin. Our results suggest that DNA methylation and histone modifications regulate de novo shoot regeneration by modulating WUS expression and auxin signaling. The study demonstrates that, although molecular components involved in organogenesis are divergently evolved in plants and animals, epigenetic modifications play an evolutionarily convergent role during de novo organogenesis.
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Affiliation(s)
- Wei Li
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China
| | - Hui Liu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China
| | - Zhi Juan Cheng
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China
| | - Ying Hua Su
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China
| | - Hua Nan Han
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China
| | - Yan Zhang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China
| | - Xian Sheng Zhang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China
- * E-mail:
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47
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Miguel C, Marum L. An epigenetic view of plant cells cultured in vitro: somaclonal variation and beyond. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:3713-25. [PMID: 21617249 DOI: 10.1093/jxb/err155] [Citation(s) in RCA: 152] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Epigenetic mechanisms are highly dynamic events that modulate gene expression. As more accurate and powerful tools for epigenetic analysis become available for application in a broader range of plant species, analysis of the epigenetic landscape of plant cell cultures may turn out to be crucial for understanding variant phenotypes. In vitro plant cell and tissue culture methodologies are important for many ongoing plant propagation and breeding programmes as well as for cutting-edge research in several plant model species. Although it has long been known that in vitro conditions induce variation at several levels, most studies using such conditions rely on the assumption that in vitro cultured plant cells/tissues mostly conform genotypically and phenotypically. However, when large-scale clonal propagation is the aim, there has been a concern in confirming true-to-typeness using molecular markers for evaluating stability. While in most reports genetic variation has been found to occur at relatively modest frequencies, variation in DNA methylation patterns seems to be much more frequent and in some cases it has been directly implicated in phenotypic variation. Recent advances in the field of epigenetics have uncovered highly dynamic mechanisms of chromatin remodelling occurring during cell dedifferentiation and differentiation processes on which in vitro adventitious plant regeneration systems are based. Here, an overview of recent findings related to developmental switches occurring during in vitro culture is presented. Additionally, an update on the detection of epigenetic variation in plant cell cultures will be provided and discussed in the light of recent progress in the plant epigenetics field.
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Affiliation(s)
- Célia Miguel
- Instituto de Tecnologia Química e Biológica-Universidade Nova de Lisboa, Oeiras, Portugal.
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48
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Costas C, Desvoyes B, Gutierrez C. A chromatin perspective of plant cell cycle progression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1809:379-87. [PMID: 21453801 DOI: 10.1016/j.bbagrm.2011.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 03/18/2011] [Accepted: 03/23/2011] [Indexed: 12/27/2022]
Abstract
The finely regulated series of events that span from the birth of a cell to the production of two new born cells encompass the cell cycle. Cell cycle progression occurs in a unidirectional manner and requires passing through a number of stages in response to cellular, developmental and environmental cues. In addition to these signaling cascades, transcriptional regulation plays a major role and acts coordinately with genome duplication during S-phase and chromosome segregation during mitosis. In this context, chromatin is revealing as a highly dynamic and major player in cell cycle regulation not only owing to the changes that occur as a consequence of cell cycle progression but also because some specific chromatin modifications are crucial to move across the cell cycle. These are particularly relevant for controlling transcriptional activation and repression as well as initiation of DNA replication and chromosome compaction. As a consequence the epigenetic landscape of a proliferating cell is very complex throughout the cell cycle. These aspects of chromatin dynamics together with the impact of epigenetic modifications on cell proliferation will be discussed in this article. This article is part of a Special Issue entitled: Epigenetic Control of cellular and developmental processes in plants.
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Affiliation(s)
- Celina Costas
- Centro de Biologia Molecukar Severo Ochoa, Madrid, Spain
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49
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Abstract
While adult stem cells can be induced to transdifferentiate into multiple lineages of cells or tissues, their plasticity and utility for human therapy remains controversial. In this chapter, we describe methods for the transdifferentiation of human adipose tissue-derived stem cells (ASCs) along neural lineages using in vitro and in vivo systems. The in vitro neural differentiation of ASCs has been reported by several groups using serum-free cytokine induction, butylated hydroxyanisole (BHA) chemical induction, and neurosphere formation in combination with the cytokines, such as brain-derived neurotrophic factor (BDNF) and basic fibroblast growth factor (bFGF). For in vivo neurogenic induction, ASCs are treated with BDNF and bFGF to form neurospheres in vitro and then delivered directly to the brain. In this chapter, several detailed protocols for the effective neurogenic induction of ASCs in vitro and in vivo are described. The protocols described herein can be applied to further molecular and mechanistic studies of neurogenic induction and differentiation of ASCs. In addition, these methods can be useful for differentiating ASCs for therapeutic intervention in central nervous system disorders.
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Affiliation(s)
- Ji Min Yu
- Division of Regenerative Medicine, Tulane National Primate Research Center, Covington, LA, USA
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50
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van Zanten M, Tessadori F, Bossen L, Peeters AJM, Fransz P. Large-scale chromatin de-compaction induced by low light is not accompanied by nucleosomal displacement. PLANT SIGNALING & BEHAVIOR 2010; 5:1677-8. [PMID: 21139439 PMCID: PMC3115134 DOI: 10.4161/psb.5.12.14039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Accepted: 10/28/2010] [Indexed: 05/22/2023]
Abstract
Arabidopsis thaliana is widely used as model to study chromatin compaction dynamics during development and in response to the environment. Signals such as prolonged heat treatment, low light and pathogen infestation are known to induce large-scale de-condensation of nuclear chromatin. Here we demonstrate that the response to different environments varies at the nucleosomal level. Our results show that in contrast to previous reports on heat and biotic infestation, low light intensity signaling does not alter nucleosomal occupancy, despite the marked effects of low light on global chromatin compaction.
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Affiliation(s)
- Martijn van Zanten
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands.
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