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Li J, Zhang Q, Wang Z, Liu Q. The roles of epigenetic regulators in plant regeneration: Exploring patterns amidst complex conditions. PLANT PHYSIOLOGY 2024; 194:2022-2038. [PMID: 38290051 PMCID: PMC10980418 DOI: 10.1093/plphys/kiae042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/06/2023] [Accepted: 12/17/2023] [Indexed: 02/01/2024]
Abstract
Plants possess remarkable capability to regenerate upon tissue damage or optimal environmental stimuli. This ability not only serves as a crucial strategy for immobile plants to survive through harsh environments, but also made numerous modern plant improvements techniques possible. At the cellular level, this biological process involves dynamic changes in gene expression that redirect cell fate transitions. It is increasingly recognized that chromatin epigenetic modifications, both activating and repressive, intricately interact to regulate this process. Moreover, the outcomes of epigenetic regulation on regeneration are influenced by factors such as the differences in regenerative plant species and donor tissue types, as well as the concentration and timing of hormone treatments. In this review, we focus on several well-characterized epigenetic modifications and their regulatory roles in the expression of widely studied morphogenic regulators, aiming to enhance our understanding of the mechanisms by which epigenetic modifications govern plant regeneration.
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Affiliation(s)
- Jiawen Li
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Qiyan Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Zejia Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Qikun Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
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2
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Liu J, Ke M, Sun Y, Niu S, Zhang W, Li Y. Epigenetic regulation and epigenetic memory resetting during plant rejuvenation. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:733-745. [PMID: 37930766 DOI: 10.1093/jxb/erad435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/29/2023] [Indexed: 11/07/2023]
Abstract
Reversal of plant developmental status from the mature to the juvenile phase, thus leading to the restoration of the developmental potential, is referred to as plant rejuvenation. It involves multilayer regulation, including resetting gene expression patterns, chromatin remodeling, and histone modifications, eventually resulting in the restoration of juvenile characteristics. Although plants can be successfully rejuvenated using some forestry practices to restore juvenile morphology, physiology, and reproductive capabilities, studies on the epigenetic mechanisms underlying this process are in the nascent stage. This review provides an overview of the plant rejuvenation process and discusses the key epigenetic mechanisms involved in DNA methylation, histone modification, and chromatin remodeling in the process of rejuvenation, as well as the roles of small RNAs in this process. Additionally, we present new inquiries regarding the epigenetic regulation of plant rejuvenation, aiming to advance our understanding of rejuvenation in sexually and asexually propagated plants. Overall, we highlight the importance of epigenetic mechanisms in the regulation of plant rejuvenation, providing valuable insights into the complexity of this process.
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Affiliation(s)
- Jie Liu
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, PR China
| | - Meng Ke
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, PR China
| | - Yuhan Sun
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, PR China
| | - Shihui Niu
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, PR China
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, PR China
| | - Yun Li
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, PR China
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3
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Grin IR, Petrova DV, Endutkin AV, Ma C, Yu B, Li H, Zharkov DO. Base Excision DNA Repair in Plants: Arabidopsis and Beyond. Int J Mol Sci 2023; 24:14746. [PMID: 37834194 PMCID: PMC10573277 DOI: 10.3390/ijms241914746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
Base excision DNA repair (BER) is a key pathway safeguarding the genome of all living organisms from damage caused by both intrinsic and environmental factors. Most present knowledge about BER comes from studies of human cells, E. coli, and yeast. Plants may be under an even heavier DNA damage threat from abiotic stress, reactive oxygen species leaking from the photosynthetic system, and reactive secondary metabolites. In general, BER in plant species is similar to that in humans and model organisms, but several important details are specific to plants. Here, we review the current state of knowledge about BER in plants, with special attention paid to its unique features, such as the existence of active epigenetic demethylation based on the BER machinery, the unexplained diversity of alkylation damage repair enzymes, and the differences in the processing of abasic sites that appear either spontaneously or are generated as BER intermediates. Understanding the biochemistry of plant DNA repair, especially in species other than the Arabidopsis model, is important for future efforts to develop new crop varieties.
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Affiliation(s)
- Inga R. Grin
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia; (D.V.P.); (A.V.E.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia
| | - Daria V. Petrova
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia; (D.V.P.); (A.V.E.)
| | - Anton V. Endutkin
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia; (D.V.P.); (A.V.E.)
| | - Chunquan Ma
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Harbin 150080, China; (C.M.); (B.Y.); (H.L.)
- Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region, Harbin 150080, China
- School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Bing Yu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Harbin 150080, China; (C.M.); (B.Y.); (H.L.)
- Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region, Harbin 150080, China
- School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Haiying Li
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Harbin 150080, China; (C.M.); (B.Y.); (H.L.)
- Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region, Harbin 150080, China
- School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Dmitry O. Zharkov
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia; (D.V.P.); (A.V.E.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia
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Chmielarz P, Kotlarski S, Kalemba EM, Martins JPR, Michalak M. Successful In Vitro Shoot Multiplication of Quercus robur L. Trees Aged up to 800 Years. PLANTS (BASEL, SWITZERLAND) 2023; 12:2230. [PMID: 37375856 DOI: 10.3390/plants12122230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023]
Abstract
The conservation of the genetic resources of old trees is crucial to their ecological role but is extremely difficult, especially for oak species (Quercus spp.) displaying recalcitrance in seed and vegetative propagation methods. Our study aimed to assess the regenerative potential of Quercus robur trees of different ages (up to 800 years) during micropropagation. We also aimed to determine how in vitro conditions can influence in vitro regeneration responses. Lignified branches collected from 67 selected trees were cultivated ex vitro in culture pots at 25 °C to obtain epicormic shoots (explant sources). The explants were cultivated on an agar medium supplemented with 0.8 mg L-1 6-benzylaminopurine (BAP) for at least 21 months. In a second experiment, two different shoot multiplication conditions (temporary immersion-RITA® bioreactor and agar medium) and two culture medium formulations (Woody Plant Medium and modified Quoirin and Lepoivre medium) were tested. The results showed that the mean length of the epicormic shoots obtained in a pot culture was a function of donor age and was similar among the group of younger trees (ca. 20-200 years), and varied between older trees (ca. 300-800 years). The efficiency of in vitro shoot multiplication strictly depended on the genotype. A sustainable in vitro culture (defined as survival after 6 months) was only possible for half of the tested old donor trees, even when they survived the first month of in vitro growth. A continuous monthly increase in the number of in vitro cultured shoots was reported in younger oaks and in some old oaks. We found a significant effect of the culture system and the macro- and micronutrient composition on in vitro shoot growth. This is the first report demonstrating that the in vitro culture can be successfully applied to the propagation of even 800-year-old pedunculate oak trees.
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Affiliation(s)
- Paweł Chmielarz
- Institute of Dendrology Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
| | - Szymon Kotlarski
- Institute of Dendrology Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
- PPHU ASKIK Co., Ltd., Bukowy Las 20, 63-014 Murzynowo Kościelne, Poland
| | - Ewa Marzena Kalemba
- Institute of Dendrology Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
| | | | - Marcin Michalak
- Institute of Dendrology Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
- Department of Plant Physiology, Genetics and Biotechnology, University of Warmia and Mazury in Olsztyn, M. Oczapowskiego 1A, 10-721 Olsztyn, Poland
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Liu X, Zhu K, Xiao J. Recent advances in understanding of the epigenetic regulation of plant regeneration. ABIOTECH 2023; 4:31-46. [PMID: 37220541 PMCID: PMC10199984 DOI: 10.1007/s42994-022-00093-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/27/2022] [Indexed: 05/22/2023]
Abstract
Ever since the concept of "plant cell totipotency" was first proposed in the early twentieth century, plant regeneration has been a major focus of study. Regeneration-mediated organogenesis and genetic transformation are important topics in both basic research and modern agriculture. Recent studies in the model plant Arabidopsis thaliana and other species have expanded our understanding of the molecular regulation of plant regeneration. The hierarchy of transcriptional regulation driven by phytohormone signaling during regeneration is associated with changes in chromatin dynamics and DNA methylation. Here, we summarize how various aspects of epigenetic regulation, including histone modifications and variants, chromatin accessibility dynamics, DNA methylation, and microRNAs, modulate plant regeneration. As the mechanisms of epigenetic regulation are conserved in many plants, research in this field has potential applications in boosting crop breeding, especially if coupled with emerging single-cell omics technologies.
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Affiliation(s)
- Xuemei Liu
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Kehui Zhu
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jun Xiao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
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6
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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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7
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Zhang Z, Liu J, Sun Y, Wang S, Xing X, Feng X, Pérez-Pérez JM, Li Y. Genome-wide high-resolution mapping of DNA methylation reveals epigenetic variation in the offspring of sexual and asexual propagation in Robinia pseudoacacia. PLANT CELL REPORTS 2021; 40:2435-2447. [PMID: 34524479 DOI: 10.1007/s00299-021-02787-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 09/07/2021] [Indexed: 06/13/2023]
Abstract
We detected the genome-wide pattern of DNA methylation and its association with gene expression in sexual and asexual progenies of mature Robinia pseudoacacia trees. DNA methylation plays an important role in plant reproduction and development. Although some studies on sexual reproduction have been carried out in model plants, little is known about the dynamic changes in DNA methylation and their effect on gene expression in sexual and asexual progeny of woody plants. Here, through whole-genome bisulfite sequencing, we revealed DNA methylation patterns in the sexual and asexual progenies of mature Robinia pseudoacacia to understand the regulation of gene expression by DNA methylation in juvenile seedlings. An average of 53% CG, 34% CHG and 5% CHH contexts was methylated in the leaves of mature and juvenile individuals. The CHH methylation level of asexually propagated seedlings was significantly lower than that of seed-derived seedlings and mature trees. The intergenic regions had the highest methylation level. Analysis of differentially methylated regions (DMRs) showed that most of them were hypermethylated and located in the gene upstream and introns. A total of 24, 108 and 162 differentially expressed genes containing DMRs were identified in root sprouts (RSs), root cuttings (RCs) and seed-derived seedlings (SSs), respectively, and a large proportion of them showed hypermethylation. In addition, DMRs were enriched within GO subcategories including catalytic activity, metabolic process and cellular process. The results reveal widespread DNA methylation changes between mature plants and their progenies through sexual/asexual reproduction, which provides novel insights into DNA methylation reprogramming and the regulation of gene expression in woody plants.
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Affiliation(s)
- Zijie Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Science and Technology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Jie Liu
- National Engineering Laboratory for Tree Breeding, College of Biological Science and Technology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Yuhan Sun
- National Engineering Laboratory for Tree Breeding, College of Biological Science and Technology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Shaoming Wang
- State-Owned Quanbaoshan Forestry Station in Luoning County of He'nan Province, Luoyang, 471717, People's Republic of China
| | - Xiuxia Xing
- Agricultural Service Center of Wangfan Hui Town in Luoning County of He'nan Province, Luoyang, 471700, People's Republic of China
| | - Xiaojing Feng
- State-Owned Lvcun Forestry Station in Luoning County of He'nan Province, Luoyang, 471700, People's Republic of China
| | | | - Yun Li
- National Engineering Laboratory for Tree Breeding, College of Biological Science and Technology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, 100083, People's Republic of China.
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Kruglova NN, Titova GE, Seldimirova OA, Zinatullina AE. Cytophysiological Features of the Cereal-Based Experimental System “Embryo In Vivo–Callus In Vitro”. Russ J Dev Biol 2021. [DOI: 10.1134/s1062360421040044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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DNA methylation-mediated modulation of rapid desiccation tolerance acquisition and dehydration stress memory in the resurrection plant Boea hygrometrica. PLoS Genet 2021; 17:e1009549. [PMID: 33930012 PMCID: PMC8115786 DOI: 10.1371/journal.pgen.1009549] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 05/12/2021] [Accepted: 04/14/2021] [Indexed: 12/02/2022] Open
Abstract
Pre-exposure of plants to various abiotic conditions confers improved tolerance to subsequent stress. Mild drought acclimation induces acquired rapid desiccation tolerance (RDT) in the resurrection plant Boea hygrometrica, but the mechanisms underlying the priming and memory processes remain unclear. In this study, we demonstrated that drought acclimation-induced RDT can be maintained for at least four weeks but was completely erased after 18 weeks based on a combination of the phenotypic and physiological parameters. Global transcriptome analysis identified several RDT-specific rapid dehydration-responsive genes related to cytokinin and phospholipid biosynthesis, nitrogen and carbon metabolism, and epidermal morphogenesis, most of which were pre-induced by drought acclimation. Comparison of whole-genome DNA methylation revealed dehydration stress-responsive hypomethylation in the CG, CHG, and CHH contexts and acclimation-induced hypermethylation in the CHH context of the B. hygrometrica genome, consistent with the transcriptional changes in methylation pathway genes. As expected, the global promoter and gene body methylation levels were negatively correlated with gene expression levels in both acclimated and dehydrated plants but showed no association with transcriptional divergence during the procedure. Nevertheless, the promoter methylation variations in the CG and CHG contexts were significantly associated with the differential expression of genes required for fundamental genetic processes of DNA conformation, RNA splicing, translation, and post-translational protein modification during acclimation, growth, and rapid dehydration stress response. It was also associated with the dehydration stress-induced upregulation of memory genes, including pre-mRNA-splicing factor 38A, vacuolar amino acid transporter 1-like, and UDP-sugar pyrophosphorylase, which may contribute directly or indirectly to the improvement of dehydration tolerance in B. hygrometrica plants. Altogether, our findings demonstrate the potential implications of DNA methylation in dehydration stress memory and, therefore, provide a molecular basis for enhanced dehydration tolerance in plants induced by drought acclimation. Drought is a major adverse environmental condition affecting plant growth and productivity. Although plants can be trained to improved tolerance to the subsequent drought stress, most land plants are unable to recover from severe dehydration when the relative water content in their vegetative tissues drops below 20–30%. However, a small group of angiosperms, termed resurrection plants, can survive extreme water deficiency of their vegetative tissues to an air-dried state and recovered upon rehydration. Understanding the biochemical and molecular basis of desiccation tolerance is valuable for extending our knowledge of the maximum ability of plants to deal with extreme water loss. Boea hygrometrica is a well-characterized resurrection plant that can not only tolerate slow dehydration but also extend its ability to survive rapid dehydration after a priming process of slow dehydration and rehydration. The rapid desiccation tolerance in primed plants can be maintained for at least four weeks. Here, we utilized this system of drought acclimation-induced RDT acquisition, maintenance, and erasing to explore plant phenotypic, physiological, and transcriptional changes, as well as DNA methylation dynamics. The analyses of the effect of DNA methylation on gene expression and promoter methylation changes with differential gene expression revealed the putative epigenetic control of dehydration stress memory in plants.
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Pasternak T, Lystvan K, Betekhtin A, Hasterok R. From Single Cell to Plants: Mesophyll Protoplasts as a Versatile System for Investigating Plant Cell Reprogramming. Int J Mol Sci 2020; 21:E4195. [PMID: 32545519 PMCID: PMC7348876 DOI: 10.3390/ijms21124195] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/07/2020] [Accepted: 06/10/2020] [Indexed: 01/24/2023] Open
Abstract
Plants are sessile organisms that have a remarkable developmental plasticity, which ensures their optimal adaptation to environmental stresses. Plant cell totipotency is an extreme example of such plasticity, whereby somatic cells have the potential to form plants via direct shoot organogenesis or somatic embryogenesis in response to various exogenous and/or endogenous signals. Protoplasts provide one of the most suitable systems for investigating molecular mechanisms of totipotency, because they are effectively single cell populations. In this review, we consider the current state of knowledge of the mechanisms that induce cell proliferation from individual, differentiated somatic plant cells. We highlight initial explant metabolic status, ploidy level and isolation procedure as determinants of successful cell reprogramming. We also discuss the importance of auxin signalling and its interaction with stress-regulated pathways in governing cell cycle induction and further stages of plant cell totipotency.
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Affiliation(s)
- Taras Pasternak
- Institute of Biology II/Molecular Plant Physiology, Centre for BioSystems Analysis, BIOSS Centre for Biological Signalling Studies University of Freiburg, 79104 Freiburg, Germany
| | - Kateryna Lystvan
- Institute of Cell Biology and Genetic Engineering of the National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine;
| | - Alexander Betekhtin
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 40-032 Katowice, Poland;
| | - Robert Hasterok
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 40-032 Katowice, Poland;
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11
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Sun RZ, Cheng G, Li Q, Zhu YR, Zhang X, Wang Y, He YN, Li SY, He L, Chen W, Pan QH, Duan CQ, Wang J. Comparative physiological, metabolomic, and transcriptomic analyses reveal developmental stage-dependent effects of cluster bagging on phenolic metabolism in Cabernet Sauvignon grape berries. BMC PLANT BIOLOGY 2019; 19:583. [PMID: 31878879 PMCID: PMC6933938 DOI: 10.1186/s12870-019-2186-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 12/05/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND Light conditions significantly influence grape berry ripening and the accumulation of phenolic compounds, but the underlying molecular basis remains partially understood. Here, we applied integrated transcriptomics and pathway-level metabolomics analyses to investigate the effect of cluster bagging during various developmental stages on phenolic metabolism in Cabernet Sauvignon grapes. RESULTS Bagging treatments had limited effects on berry quality attributes at harvest and did not consistently affect phenolic acid biosynthesis between seasons. Significantly elevated flavan-3-ol and flavonol contents were detected in re-exposed berries after bagging during early-developmental stages, while bagging after véraison markedly inhibited skin anthocyanin accumulation. Several anthocyanin derivatives and flavonol glycosides were identified as marker phenolic metabolites for distinguishing bagged and non-bagged grapes. Coordinated transcriptional changes in the light signaling components CRY2 and HY5/HYHs, transcription regulator MYBA1, and enzymes LAR, ANR, UFGT and FLS4, coincided well with light-responsive biosynthesis of the corresponding flavonoids. The activation of multiple hormone signaling pathways after both light exclusion and re-exposure treatments was inconsistent with the changes in phenolic accumulation, indicating a limited role of plant hormones in mediating light/darkness-regulated phenolic biosynthesis processes. Furthermore, gene-gene and gene-metabolite network analyses discovered that the light-responsive expression of genes encoding bHLH, MYB, WRKY, NAC, and MADS-box transcription factors, and proteins involved in genetic information processing and epigenetic regulation such as nucleosome assembly and histone acetylation, showed a high positive correlation with grape berry phenolic accumulation in response to different light regimes. CONCLUSIONS Altogether, our findings provide novel insights into the understanding of berry phenolic biosynthesis under light/darkness and practical guidance for improving grape features.
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Affiliation(s)
- Run-Ze Sun
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Science, Beijing, 100093, China
| | - Guo Cheng
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
- Grape and Wine Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Qiang Li
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yan-Rong Zhu
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
- Nongfu Spring Co. Ltd., Hangzhou, 310000, China
| | - Xue Zhang
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
- Ruifeng Oseis (Yantai) Wine Manor Co. Ltd., Yantai, 264010, China
| | - Yu Wang
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing, 100083, China
| | - Yan-Nan He
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
- College of Bioscience & Bioengineering, Hebei University of Science and Technology, Shijiazhuang, 050018, China
| | - Si-Yu Li
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing, 100083, China
| | - Lei He
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing, 100083, China
| | - Wu Chen
- CITIC Guoan Wine Co. Ltd., Xinjiang, 832200, Manasi, China
| | - Qiu-Hong Pan
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing, 100083, China
| | - Chang-Qing Duan
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing, 100083, China
| | - Jun Wang
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing, 100083, China.
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