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Haider S, Farrona S. Decoding histone 3 lysine methylation: Insights into seed germination and flowering. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102598. [PMID: 38986392 DOI: 10.1016/j.pbi.2024.102598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 06/01/2024] [Accepted: 06/12/2024] [Indexed: 07/12/2024]
Abstract
Histone lysine methylation is a highly conserved epigenetic modification across eukaryotes that contributes to creating different dynamic chromatin states, which may result in transcriptional changes. Over the years, an accumulated set of evidence has shown that histone methylation allows plants to align their development with their surroundings, enabling them to respond and memorize past events due to changes in the environment. In this review, we discuss the molecular mechanisms of histone methylation in plants. Writers, readers, and erasers of Arabidopsis histone methylation marks are described with an emphasis on their role in two of the most important developmental transition phases in plants, seed germination and flowering. Further, the crosstalk between different methylation marks is also discussed. An overview of the mechanisms of histone methylation modifications and their biological outcomes will shed light on existing research gaps and may provide novel perspectives to increase crop yield and resistance in the era of global climate change.
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Affiliation(s)
- Saqlain Haider
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, Galway H91 TK33, Ireland
| | - Sara Farrona
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, Galway H91 TK33, Ireland.
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2
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Marquez-Molins J, Cheng J, Corell-Sierra J, Juarez-Gonzalez VT, Villalba-Bermell P, Annacondia ML, Gomez G, Martinez G. Hop stunt viroid infection induces heterochromatin reorganization. THE NEW PHYTOLOGIST 2024; 243:2351-2367. [PMID: 39030826 DOI: 10.1111/nph.19986] [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: 03/02/2024] [Accepted: 06/26/2024] [Indexed: 07/22/2024]
Abstract
Viroids are pathogenic noncoding RNAs that completely rely on their host molecular machinery to accomplish their life cycle. Several interactions between viroids and their host molecular machinery have been identified, including interference with epigenetic mechanisms such as DNA methylation. Despite this, whether viroids influence changes in other epigenetic marks such as histone modifications remained unknown. Epigenetic regulation is particularly important during pathogenesis processes because it might be a key regulator of the dynamism of the defense response. Here we have analyzed the changes taking place in Cucumis sativus (cucumber) facultative and constitutive heterochromatin during hop stunt viroid (HSVd) infection using chromatin immunoprecipitation (ChIP) of the two main heterochromatic marks: H3K9me2 and H3K27me3. We find that HSVd infection is associated with changes in both H3K27me3 and H3K9me2, with a tendency to decrease the levels of repressive epigenetic marks through infection progression. These epigenetic changes are connected to the transcriptional regulation of their expected targets, genes, and transposable elements. Indeed, several genes related to the defense response are targets of both epigenetic marks. Our results highlight another host regulatory mechanism affected by viroid infection, providing further information about the complexity of the multiple layers of interactions between pathogens/viroids and hosts/plants.
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Affiliation(s)
- Joan Marquez-Molins
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, 75007, Sweden
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC), University of Valencia (UV), Paterna, 46980, Spain
| | - Jinping Cheng
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, 75007, Sweden
| | - Julia Corell-Sierra
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC), University of Valencia (UV), Paterna, 46980, Spain
| | - Vasti Thamara Juarez-Gonzalez
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, 75007, Sweden
| | - Pascual Villalba-Bermell
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC), University of Valencia (UV), Paterna, 46980, Spain
| | - Maria Luz Annacondia
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, 75007, Sweden
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, 1871, Denmark
| | - Gustavo Gomez
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC), University of Valencia (UV), Paterna, 46980, Spain
| | - German Martinez
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, 75007, Sweden
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Wang Y, Sun X, Peng J, Li F, Ali F, Wang Z. Regulation of seed germination: ROS, epigenetic, and hormonal aspects. J Adv Res 2024:S2090-1232(24)00225-X. [PMID: 38838783 DOI: 10.1016/j.jare.2024.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/31/2024] [Accepted: 06/01/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND The whole life of a plant is regulated by complex environmental or hormonal signaling networks that control genomic stability, environmental signal transduction, and gene expression affecting plant development and viability. Seed germination, responsible for the transformation from seed to seedling, is a key initiation step in plant growth and is controlled by unique physiological and biochemical processes. It is continuously modulated by various factors including epigenetic modifications, hormone transport, ROS signaling, and interaction among them. ROS showed versatile crucial functions in seed germination including various physiological oxidations to nucleic acid, protein, lipid, or chromatin in the cytoplasm, cell wall, and nucleus. AIM of review: This review intends to provide novel insights into underlying mechanisms of seed germination especially associated with the ROS, and considers how these versatile regulatory mechanisms can be developed as useful tools for crop improvement. KEY SCIENTIFIC CONCEPTS OF REVIEW We have summarized the generation and elimination of ROS during seed germination, with a specific focus on uncovering and understanding the mechanisms of seed germination at the level of phytohormones, ROS, and epigenetic switches, as well as the close connections between them. The findings exhibit that ROS plays multiple roles in regulating the ethylene, ABA, and GA homeostasis as well as the Ca2+ signaling, NO signaling, and MAPK cascade in seed germination via either the signal trigger or the oxidative modifier agent. Further, ROS shows the potential in the nuclear genome remodeling and some epigenetic modifiers function, although the detailed mechanisms are unclear in seed germination. We propose that ROS functions as a hub in the complex network regulating seed germination.
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Affiliation(s)
- Yakong Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China; State Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xiangyang Sun
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Jun Peng
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, Hainan, China; State Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Fuguang Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, Hainan, China
| | - Faiza Ali
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China.
| | - Zhi Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, Hainan, China; State Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
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Sajeev N, Koornneef M, Bentsink L. A commitment for life: Decades of unraveling the molecular mechanisms behind seed dormancy and germination. THE PLANT CELL 2024; 36:1358-1376. [PMID: 38215009 PMCID: PMC11062444 DOI: 10.1093/plcell/koad328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/19/2023] [Indexed: 01/14/2024]
Abstract
Seeds are unique time capsules that can switch between 2 complex and highly interlinked stages: seed dormancy and germination. Dormancy contributes to the survival of plants because it allows to delay germination to optimal conditions. The switch between dormancy and germination occurs in response to developmental and environmental cues. In this review we provide a comprehensive overview of studies that have helped to unravel the molecular mechanisms underlying dormancy and germination over the last decades. Genetic and physiological studies provided a strong foundation for this field of research and revealed the critical role of the plant hormones abscisic acid and gibberellins in the regulation of dormancy and germination, and later natural variation studies together with quantitative genetics identified previously unknown genetic components that control these processes. Omics technologies like transcriptome, proteome, and translatomics analysis allowed us to mechanistically dissect these processes and identify new components in the regulation of seed dormancy and germination.
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Affiliation(s)
- Nikita Sajeev
- Wageningen Seed Science Centre, Laboratory of Plant Physiology, Wageningen University, 6708PB Wageningen, the Netherlands
| | - Maarten Koornneef
- Laboratory of Genetics, Wageningen University, 6708PB Wageningen, the Netherlands
- Max Planck Institute for Plant Breeding Research, Former Department of Plant Breeding and Genetics, Koeln 50829, Germany
| | - Leónie Bentsink
- Wageningen Seed Science Centre, Laboratory of Plant Physiology, Wageningen University, 6708PB Wageningen, the Netherlands
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Tognacca RS, Ljung K, Botto JF. Unveiling Molecular Signatures in Light-Induced Seed Germination: Insights from PIN3, PIN7, and AUX1 in Arabidopsis thaliana. PLANTS (BASEL, SWITZERLAND) 2024; 13:408. [PMID: 38337941 PMCID: PMC10856848 DOI: 10.3390/plants13030408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024]
Abstract
Light provides seeds with information that is essential for the adjustment of their germination to the conditions that are most favorable for the successful establishment of the future seedling. The promotion of germination depends mainly on environmental factors, like temperature and light, as well as internal factors associated with the hormonal balance between gibberellins (GA) and abscisic acid (ABA), although other hormones such as auxins may act secondarily. While transcriptomic studies of light-germinating Arabidopsis thaliana seeds suggest that auxins and auxin transporters are necessary, there are still no functional studies connecting the activity of the auxin transporters in light-induced seed germination. In this study, we investigated the roles of two auxin efflux carrier (PIN3 and PIN7) proteins and one auxin influx (AUX1) carrier protein during Arabidopsis thaliana seed germination. By using next-generation sequencing (RNAseq), gene expression analyses, hormonal sensitivity assays, and the quantification of indole-3-acetic acid (IAA) levels, we assessed the functional roles of PIN3, PIN7, and AUX1 during light-induced seed germination. We showed that auxin levels are increased 24 h after a red-pulse (Rp). Additionally, we evaluated the germination responses of pin3, pin7, and aux1 mutant seeds and showed that PIN3, PIN7, and AUX1 auxin carriers are important players in the regulation of seed germination. By using gene expression analysis in water, fluridone (F), and ABA+F treated seeds, we confirmed that Rp-induced seed germination is associated with auxin transport, and ABA controls the function of PIN3, PIN7, and AUX1 during this process. Overall, our results highlight the relevant and positive role of auxin transporters in germinating the seeds of Arabidopsis thaliana.
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Affiliation(s)
- Rocío Soledad Tognacca
- Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Agronomía, Universidad de Buenos Aires (UBA), Buenos Aires C1417DSE, Argentina
- Departamento de Fisiología, Biología, Molecular, y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina
| | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden;
| | - Javier Francisco Botto
- Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Agronomía, Universidad de Buenos Aires (UBA), Buenos Aires C1417DSE, Argentina
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Ma X, Feng L, Tao A, Zenda T, He Y, Zhang D, Duan H, Tao Y. Identification and validation of seed dormancy loci and candidate genes and construction of regulatory networks by WGCNA in maize introgression lines. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:259. [PMID: 38038768 DOI: 10.1007/s00122-023-04495-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/26/2023] [Indexed: 12/02/2023]
Abstract
KEY MESSAGE Seventeen PHS-QTLs and candidate genes were obtained, including eleven major loci, three under multiple environments and two with co-localization by the other mapping methods; The functions of three candidate genes were validated using mutants; nine target proteins and five networks were filtered by joint analysis of GWAS and WGCNA. Seed dormancy (SD) and pre-harvest sprouting (PHS) affect yield, as well as grain and hybrid quality in seed production. Therefore, identification of genetic and regulatory pathways underlying PHS and SD is key to gene function analysis, allelic variation mining and genetic improvement. In this study, 78,360 SNPs by SLAF-seq of 230 maize chromosome segment introgression lines (ILs), PHS under five environments were used to conduct GWAS (genome wide association study) (a threshold of 1/n), and seventeen unreported PHS QTLs were obtained, including eleven QTLs with PVE > 10% and three QTLs under multiple environments. Two QTL loci were co-located between the other two genetic mapping methods. Using differential gene expression analyses at two stages of grain development, gene functional analysis of Arabidopsis mutants, and gene functional analysis in the QTL region, seventeen PHS QTL-linked candidate genes were identified, and their five molecular regulatory networks constructed. Based on the Arabidopsis T-DNA mutations, three candidate genes were shown to regulate for SD and PHS. Meanwhile, using RNA-seq of grain development, the weighted correlation network analysis (WGCNA) was performed, deducing five regulatory pathways and target genes that regulate PHS and SD. Based on the conjoint analysis of GWAS and WGCNA, four pathways, nine target proteins and target genes were revealed, most of which regulate cell wall metabolism, cell proliferation and seed dehydration tolerance. This has important theoretical and practical significance for elucidating the genetic basis of maize PHS and SD, as well as mining of genetic resources and genetic improvement of traits.
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Affiliation(s)
- Xiaolin Ma
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
| | - Liqing Feng
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
| | - Anyan Tao
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
| | - Tinashe Zenda
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
| | - Yuan He
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
| | - Daxiao Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
| | - Huijun Duan
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China.
| | - Yongsheng Tao
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China.
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Seni S, Singh RK, Prasad M. Dynamics of epigenetic control in plants via SET domain containing proteins: Structural and functional insights. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194966. [PMID: 37532097 DOI: 10.1016/j.bbagrm.2023.194966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/25/2023] [Accepted: 07/28/2023] [Indexed: 08/04/2023]
Abstract
Plants control expression of their genes in a way that involves manipulating the chromatin structural dynamics in order to adapt to environmental changes and carry out developmental processes. Histone modifications like histone methylation are significant epigenetic marks which profoundly and globally modify chromatin, potentially affecting the expression of several genes. Methylation of histones is catalyzed by histone lysine methyltransferases (HKMTs), that features an evolutionary conserved domain known as SET [Su(var)3-9, E(Z), Trithorax]. This methylation is directed at particular lysine (K) residues on H3 or H4 histone. Plant SET domain group (SDG) proteins are categorized into different classes that have been conserved through evolution, and each class have specificity that influences how the chromatin structure operates. The domains discovered in plant SET domain proteins have typically been linked to protein-protein interactions, suggesting that majority of the SDGs function in complexes. Additionally, SDG-mediated histone mark deposition also affects alternative splicing events. In present review, we discussed the diversity of SDGs in plants including their structural properties. Additionally, we have provided comprehensive summary of the functions of the SDG-domain containing proteins in plant developmental processes and response to environmental stimuli have also been highlighted.
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Affiliation(s)
- Sushmita Seni
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Roshan Kumar Singh
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India; Department of Plant Sciences, University of Hyderabad, Hyderabad, Telangana 500046, India.
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8
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Han Y, Georgii E, Priego-Cubero S, Wurm CJ, Hüther P, Huber G, Koller R, Becker C, Durner J, Lindermayr C. Arabidopsis histone deacetylase HD2A and HD2B regulate seed dormancy by repressing DELAY OF GERMINATION 1. FRONTIERS IN PLANT SCIENCE 2023; 14:1124899. [PMID: 37313253 PMCID: PMC10258333 DOI: 10.3389/fpls.2023.1124899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 04/06/2023] [Indexed: 06/15/2023]
Abstract
Seed dormancy is a crucial developmental transition that affects the adaption and survival of plants. Arabidopsis DELAY OF GERMINATION 1 (DOG1) is known as a master regulator of seed dormancy. However, although several upstream factors of DOG1 have been reported, the exact regulation of DOG1 is not fully understood. Histone acetylation is an important regulatory layer, controlled by histone acetyltransferases and histone deacetylases. Histone acetylation strongly correlates with transcriptionally active chromatin, whereas heterochromatin is generally characterized by hypoacetylated histones. Here we describe that loss of function of two plant-specific histone deacetylases, HD2A and HD2B, resulted in enhanced seed dormancy in Arabidopsis. Interestingly, the silencing of HD2A and HD2B caused hyperacetylation of the DOG1 locus and promoted the expression of DOG1 during seed maturation and imbibition. Knockout of DOG1 could rescue the seed dormancy and partly rescue the disturbed development phenotype of hd2ahd2b. Transcriptomic analysis of the hd2ahd2b line shows that many genes involved in seed development were impaired. Moreover, we demonstrated that HSI2 and HSL1 interact with HD2A and HD2B. In sum, these results suggest that HSI2 and HSL1 might recruit HD2A and HD2B to DOG1 to negatively regulate DOG1 expression and to reduce seed dormancy, consequently, affecting seed development during seed maturation and promoting seed germination during imbibition.
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Affiliation(s)
- Yongtao Han
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, München, Germany
| | - Elisabeth Georgii
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, München, Germany
| | | | - Christoph J. Wurm
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, München, Germany
| | - Patrick Hüther
- Genetics, LMU Biocenter, Ludwig-Maximilians-Universität München, München, Germany
| | - Gregor Huber
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Robert Koller
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Claude Becker
- Genetics, LMU Biocenter, Ludwig-Maximilians-Universität München, München, Germany
| | - Jörg Durner
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, München, Germany
- Chair of Biochemical Plant Pathology, Technische Universität München, Freising, Germany
| | - Christian Lindermayr
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, München, Germany
- Institute of Lung Health and Immunity, Comprehensive Pneumology Center, Helmholtz Zentrum München, Member of the German Center for Lung Research, München, Germany
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9
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Pan J, Zhang H, Zhan Z, Zhao T, Jiang D. A REF6-dependent H3K27me3-depleted state facilitates gene activation during germination in Arabidopsis. J Genet Genomics 2023; 50:178-191. [PMID: 36113770 DOI: 10.1016/j.jgg.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 09/07/2022] [Indexed: 11/17/2022]
Abstract
Seed germination is a critical developmental switch from a quiescent state to active growth, which involves extensive changes in metabolism, gene expression, and cellular identity. However, our understanding of epigenetic and transcriptional reprogramming during this process is limited. The histone H3 lysine 27 trimethylation (H3K27me3) plays a key role in regulating gene repression and cell fate specification. Here, we profile H3K27me3 dynamics and dissect the function of H3K27 demethylation during germination in Arabidopsis. Our temporal genome-wide profiling of H3K27me3 and transcription reveals delayed H3K27me3 reprogramming compared with transcriptomic changes during germination, with H3K27me3 changes mainly occurring when the embryo is entering into vegetative development. RELATIVE OF EARLY FLOWERING 6 (REF6)-mediated H3K27 demethylation is necessary for robust germination but does not significantly contribute to H3K27me3 dynamics during germination, but rather stably establishes an H3K27me3-depleted state that facilitates the activation of hormone-related and expansin-coding genes important for germination. We also show that the REF6 chromatin occupancy is gradually established during germination to counteract increased Polycomb repressive complex 2 (PRC2). Our study provides key insights into the H3K27me3 dynamics during germination and suggests the function of H3K27me3 in facilitating cell fate switch. Furthermore, we reveal the importance of H3K27 demethylation-established transcriptional competence in gene activation during germination and likely other developmental processes.
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Affiliation(s)
- Jie Pan
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huairen Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhenping Zhan
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ting Zhao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Danhua Jiang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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10
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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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11
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Yang T, Wu X, Wang W, Wu Y. Regulation of seed storage protein synthesis in monocot and dicot plants: A comparative review. MOLECULAR PLANT 2023; 16:145-167. [PMID: 36495013 DOI: 10.1016/j.molp.2022.12.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/27/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
Seeds are a major source of nutrients for humans and animal livestock worldwide. With improved living standards, high nutritional quality has become one of the main targets for breeding. Storage protein content in seeds, which is highly variable depending on plant species, serves as a pivotal criterion of seed nutritional quality. In the last few decades, our understanding of the molecular genetics and regulatory mechanisms of storage protein synthesis has greatly advanced. Here, we systematically and comprehensively summarize breakthroughs on the conservation and divergence of storage protein synthesis in dicot and monocot plants. With regard to storage protein accumulation, we discuss evolutionary origins, developmental processes, characteristics of main storage protein fractions, regulatory networks, and genetic modifications. In addition, we discuss potential breeding strategies to improve storage protein accumulation and provide perspectives on some key unanswered problems that need to be addressed.
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Affiliation(s)
- Tao Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Xingguo Wu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200233, China
| | - Wenqin Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200233, China
| | - Yongrui Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
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12
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Morgan BL, Donohue K. Parental methylation mediates how progeny respond to environments of parents and of progeny themselves. ANNALS OF BOTANY 2022; 130:883-899. [PMID: 36201313 PMCID: PMC9758305 DOI: 10.1093/aob/mcac125] [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: 06/01/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND AND AIMS Environments experienced by both parents and offspring influence progeny traits, but the epigenetic mechanisms that regulate the balance of parental vs. progeny control of progeny phenotypes are not known. We tested whether DNA methylation in parents and/or progeny mediates responses to environmental cues experienced in both generations. METHODS Using Arabidopsis thaliana, we manipulated parental and progeny DNA methylation both chemically, via 5-azacytidine, and genetically, via mutants of methyltransferase genes, then measured progeny germination responses to simulated canopy shade in parental and progeny generations. KEY RESULTS We first found that germination of offspring responded to parental but not seed demethylation. We further found that parental demethylation reversed the parental effect of canopy in seeds with low (Cvi-1) to intermediate (Col) dormancy, but it obliterated the parental effect in seeds with high dormancy (Cvi-0). Demethylation did so by either suppressing germination of seeds matured under white-light (Cvi-1) or under canopy (Cvi-0), or by increasing the germination of seeds matured under canopy (Col). Disruption of parental methylation also prevented seeds from responding to their own light environment in one genotype (Cvi-0, most dormant), but it enabled seeds to respond to their own environment in another genotype (Cvi-1, least dormant). Using mutant genotypes, we found that both CG and non-CG DNA methylation were involved in parental effects on seed germination. CONCLUSIONS Parental methylation state influences seed germination more strongly than does the progeny's own methylation state, and it influences how seeds respond to environments of parents and progeny in a genotype-specific manner.
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Affiliation(s)
- Britany L Morgan
- University Program in Ecology Duke University, Durham, NC 27705, USA
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Kathleen Donohue
- University Program in Ecology Duke University, Durham, NC 27705, USA
- Biology Department, Duke University, Durham, NC 27705, USA
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13
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Sato H, Köhler C. Genomic imprinting regulates establishment and release of seed dormancy. CURRENT OPINION IN PLANT BIOLOGY 2022; 69:102264. [PMID: 35872392 DOI: 10.1016/j.pbi.2022.102264] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/12/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Seed dormancy enables plant seeds to time germination until environmental conditions become favorable for seedling survival. This trait has high adaptive value and is of great agricultural relevance. The endosperm is a reproductive tissue formed after fertilization that in addition to support embryo growth has major roles in establishing seed dormancy. Many genes adopt parent-of-origin specific expression patterns in the endosperm, a phenomenon that has been termed genomic imprinting. Imprinted genes are targeted by epigenetic mechanisms acting before and after fertilization. Recent studies revealed that imprinted genes are involved in establishing seed dormancy, highlighting a new mechanism of parental control over this adaptive trait. Here, we review the regulatory mechanisms establishing genomic imprinting and their effect on seed dormancy.
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Affiliation(s)
- Hikaru Sato
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala, Sweden; Department of Plant Reproductive Biology and Epigenetics, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
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14
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Bennett M, Piya S, Baum TJ, Hewezi T. miR778 mediates gene expression, histone modification, and DNA methylation during cyst nematode parasitism. PLANT PHYSIOLOGY 2022; 189:2432-2453. [PMID: 35579365 PMCID: PMC9342967 DOI: 10.1093/plphys/kiac228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/27/2022] [Indexed: 05/20/2023]
Abstract
Despite the known critical regulatory functions of microRNAs, histone modifications, and DNA methylation in reprograming plant epigenomes in response to pathogen infection, the molecular mechanisms underlying the tight coordination of these components remain poorly understood. Here, we show how Arabidopsis (Arabidopsis thaliana) miR778 coordinately modulates the root transcriptome, histone methylation, and DNA methylation via post-transcriptional regulation of the H3K9 methyltransferases SU(var)3-9 homolog 5 (SUVH5) and SUVH6 upon infection by the beet cyst nematode Heterodera schachtii. miR778 post-transcriptionally silences SUVH5 and SUVH6 upon nematode infection. Manipulation of the expression of miR778 and its two target genes significantly altered plant susceptibility to H. schachtii. RNA-seq analysis revealed a key role of SUVH5 and SUVH6 in reprograming the transcriptome of Arabidopsis roots upon H. schachtii infection. In addition, chromatin immunoprecipitation (ChIP)-seq analysis established SUVH5 and SUVH6 as the main enzymes mediating H3K9me2 deposition in Arabidopsis roots in response to nematode infection. ChIP-seq analysis also showed that these methyltransferases possess distinct DNA binding preferences in that they are targeting transposable elements under noninfected conditions and protein-coding genes in infected plants. Further analyses indicated that H3K9me2 deposition directed by SUVH5 and SUVH6 contributes to gene expression changes both in roots and in nematode feeding sites and preferentially associates with CG DNA methylation. Together, our results uncovered multi-layered epigenetic regulatory mechanisms coordinated by miR778 during Arabidopsis-H. schachtii interactions.
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Affiliation(s)
- Morgan Bennett
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Sarbottam Piya
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
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15
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Farooq MA, Ma W, Shen S, Gu A. Underlying Biochemical and Molecular Mechanisms for Seed Germination. Int J Mol Sci 2022; 23:ijms23158502. [PMID: 35955637 PMCID: PMC9369107 DOI: 10.3390/ijms23158502] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 07/24/2022] [Accepted: 07/29/2022] [Indexed: 02/01/2023] Open
Abstract
With the burgeoning population of the world, the successful germination of seeds to achieve maximum crop production is very important. Seed germination is a precise balance of phytohormones, light, and temperature that induces endosperm decay. Abscisic acid and gibberellins—mainly with auxins, ethylene, and jasmonic and salicylic acid through interdependent molecular pathways—lead to the rupture of the seed testa, after which the radicle protrudes out and the endosperm provides nutrients according to its growing energy demand. The incident light wavelength and low and supra-optimal temperature modulates phytohormone signaling pathways that induce the synthesis of ROS, which results in the maintenance of seed dormancy and germination. In this review, we have summarized in detail the biochemical and molecular processes occurring in the seed that lead to the germination of the seed. Moreover, an accurate explanation in chronological order of how phytohormones inside the seed act in accordance with the temperature and light signals from outside to degenerate the seed testa for the thriving seed’s germination has also been discussed.
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16
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Nemati I, Sedghi M, Hosseini Salekdeh G, Tavakkol Afshari R, Naghavi MR, Gholizadeh S. DELAY OF GERMINATION 1 ( DOG1) regulates dormancy in dimorphic seeds of Xanthium strumarium. FUNCTIONAL PLANT BIOLOGY : FPB 2022; 49:742-758. [PMID: 35569923 DOI: 10.1071/fp21315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 03/23/2022] [Indexed: 06/15/2023]
Abstract
Seed dormancy ensures plant survival but many mechanisms remain unclear. A high-throughput RNA-seq analysis investigated the mechanisms involved in the establishment of dormancy in dimorphic seeds of Xanthium strumarium (L.) developing in one single burr. Results showed that DOG1 , the main dormancy gene in Arabidopsis thaliana L., was over-represented in the dormant seed leading to the formation of two seeds with different cell wall properties. Less expression of DME /EMB1649 , UBP26 , EMF2, MOM, SNL2, and AGO4 in the non-dormant seed was observed, which function in the chromatin remodelling of dormancy-associated genes through DNA methylation. However, higher levels of ATXR7 /SDG25, ELF6 , and JMJ16/PKDM7D in the non-dormant seed that act at the level of histone demethylation and activate germination were found. Dramatically lower expression in the splicing factors SUA, PWI , and FY in non-dormant seed may indicate that variation in RNA splicing for ABA sensitivity and transcriptional elongation control of DOG1 is of importance for inducing seed dormancy. Seed size and germination may be influenced by respiratory factors, and alterations in ABA content and auxin distribution and responses. TOR (a serine/threonine-protein kinase) is likely at the centre of a regulatory hub controlling seed metabolism, maturation, and germination. Over-representation of the respiration-associated genes (ACO3 , PEPC3 , and D2HGDH ) was detected in non-dormant seed, suggesting differential energy supplies in the two seeds. Degradation of ABA biosynthesis and/or proper auxin signalling in the large seed may control germinability, and suppression of endoreduplication in the small seed may be a mechanism for cell differentiation and cell size determination.
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Affiliation(s)
- Iman Nemati
- Department of Plant Production and Genetics Engineering, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Mohammad Sedghi
- Department of Plant Production and Genetics Engineering, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; and Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Reza Tavakkol Afshari
- Department of Agronomy, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Somayeh Gholizadeh
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
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17
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Iwasaki M, Penfield S, Lopez-Molina L. Parental and Environmental Control of Seed Dormancy in Arabidopsis thaliana. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:355-378. [PMID: 35138879 DOI: 10.1146/annurev-arplant-102820-090750] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Seed dormancy-the absence of seed germination under favorable germination conditions-is a plant trait that evolved to enhance seedling survival by avoiding germination under unsuitable environmental conditions. In Arabidopsis, dormancy levels are influenced by the seed coat composition, while the endosperm is essential to repress seed germination of dormant seeds upon their imbibition. Recent research has shown that the mother plant modulates its progeny seed dormancy in response to seasonal temperature changes by changing specific aspects of seed coat and endosperm development. This process involves genomic imprinting by means of epigenetic marks deposited in the seed progeny and regulators previously known to regulate flowering time. This review discusses and summarizes these discoveries and provides an update on our present understanding of the role of DOG1 and abscisic acid, two key contributors to dormancy.
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Affiliation(s)
- Mayumi Iwasaki
- Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland;
| | - Steven Penfield
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Luis Lopez-Molina
- Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland;
- Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
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18
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Identification of the Wheat (Triticum aestivum) IQD Gene Family and an Expression Analysis of Candidate Genes Associated with Seed Dormancy and Germination. Int J Mol Sci 2022; 23:ijms23084093. [PMID: 35456910 PMCID: PMC9025732 DOI: 10.3390/ijms23084093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/01/2022] [Accepted: 04/05/2022] [Indexed: 02/04/2023] Open
Abstract
The IQ67 Domain (IQD) gene family plays important roles in plant developmental processes and stress responses. Although IQDs have been characterized in model plants, little is known about their functions in wheat (Triticum aestivum), especially their roles in the regulation of seed dormancy and germination. Here, we identified 73 members of the IQD gene family from the wheat genome and phylogenetically separated them into six major groups. Gene structure and conserved domain analyses suggested that most members of each group had similar structures. A chromosome positional analysis showed that TaIQDs were unevenly located on 18 wheat chromosomes. A synteny analysis indicated that segmental duplications played significant roles in TaIQD expansion, and that the IQD gene family underwent strong purifying selection during evolution. Furthermore, a large number of hormone, light, and abiotic stress response elements were discovered in the promoters of TaIQDs, implying their functional diversity. Microarray data for 50 TaIQDs showed different expression levels in 13 wheat tissues. Transcriptome data and a quantitative real-time PCR analysis of wheat varieties with contrasting seed dormancy and germination phenotypes further revealed that seven genes (TaIQD4/-28/-32/-58/-64/-69/-71) likely participated in seed dormancy and germination through the abscisic acid-signaling pathway. The study results provide valuable information for cloning and a functional investigation of candidate genes controlling wheat seed dormancy and germination; consequently, they increase our understanding of the complex regulatory networks affecting these two traits.
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19
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Wang Z, Cao H, Zhang C, Chen F, Liu Y. The SNF5-type protein BUSHY regulates seed germination via the gibberellin pathway and is dependent on HUB1 in Arabidopsis. PLANTA 2022; 255:34. [PMID: 35006338 DOI: 10.1007/s00425-021-03767-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 10/21/2021] [Indexed: 06/14/2023]
Abstract
The SNF5-type protein BUSHY plays a role in the regulation of seed germination via the gibberellin pathway dependent on HUB1 in Arabidopsis thaliana. SWITCH/SUCROSE NONFERMENTING (SWI/SNF) complexes play diverse roles in plant development. Some components have roles in embryo development and seed maturation, however, whether the SNF5-type protein BUSHY (BSH), one of the components, plays a role in Arabidopsis seed related traits is presently unclear. In our study, we show that a loss-of-function mutation in BSH causes increased seed germination in Arabidopsis. BSH transcription was induced by the gibberellin (GA) inhibitor paclobutrazol (PAC) in the seed, and BSH regulates the expression of GA pathway genes, such as Gibberellin 3-Oxidase 1 (GA3OX1), Gibberellic Acid-Stimulated Arabidopsis 4 (GASA4), and GASA6 during seed germination. A genetic analysis showed that seed germination was distinctly improved in the bshga3ox1ga3ox2 triple mutant, indicating that BSH acts partially downstream of GA3OX1 and GA3OX2. Moreover, the regulation of seed germination by BSH in response to PAC is dependent on HUB1. These results provide new insights and clues to understand the mechanisms of phytohormones in the regulation of seed germination.
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Affiliation(s)
- Zhi Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Hong Cao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Cun Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fengying Chen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongxiu Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
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20
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Ding X, Jia X, Xiang Y, Jiang W. Histone Modification and Chromatin Remodeling During the Seed Life Cycle. FRONTIERS IN PLANT SCIENCE 2022; 13:865361. [PMID: 35548305 PMCID: PMC9083068 DOI: 10.3389/fpls.2022.865361] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/21/2022] [Indexed: 05/16/2023]
Abstract
Seeds are essential for the reproduction and dispersion of spermatophytes. The seed life cycle from seed development to seedling establishment proceeds through a series of defined stages regulated by distinctive physiological and biochemical mechanisms. The role of histone modification and chromatin remodeling in seed behavior has been intensively studied in recent years. In this review, we summarize progress in elucidating the regulatory network of these two kinds of epigenetic regulation during the seed life cycle, especially in two model plants, rice and Arabidopsis. Particular emphasis is placed on epigenetic effects on primary tissue formation (e.g., the organized development of embryo and endosperm), pivotal downstream gene expression (e.g., transcription of DOG1 in seed dormancy and repression of seed maturation genes in seed-to-seedling transition), and environmental responses (e.g., seed germination in response to different environmental cues). Future prospects for understanding of intricate interplay of epigenetic pathways and the epigenetic mechanisms in other commercial species are also proposed.
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Affiliation(s)
- Xiali Ding
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Xuhui Jia
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
- College of Life Science and Technology, Guangxi University, Nanning, China
| | - Yong Xiang
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Wenhui Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
- *Correspondence: Wenhui Jiang,
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21
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Dhariwal R, Hiebert CW, Sorrells ME, Spaner D, Graf RJ, Singh J, Randhawa HS. Mapping pre-harvest sprouting resistance loci in AAC Innova × AAC Tenacious spring wheat population. BMC Genomics 2021; 22:900. [PMID: 34911435 PMCID: PMC8675488 DOI: 10.1186/s12864-021-08209-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 11/11/2021] [Indexed: 11/30/2022] Open
Abstract
Background Pre-harvest sprouting (PHS) is a major problem for wheat production due to its direct detrimental effects on wheat yield, end-use quality and seed viability. Annually, PHS is estimated to cause > 1.0 billion USD in losses worldwide. Therefore, identifying PHS resistance quantitative trait loci (QTLs) is crucial to aid molecular breeding efforts to minimize losses. Thus, a doubled haploid mapping population derived from a cross between white-grained PHS susceptible cv AAC Innova and red-grained resistant cv AAC Tenacious was screened for PHS resistance in four environments and utilized for QTL mapping. Results Twenty-one PHS resistance QTLs, including seven major loci (on chromosomes 1A, 2B, 3A, 3B, 3D, and 7D), each explaining ≥10% phenotypic variation for PHS resistance, were identified. In every environment, at least one major QTL was identified. PHS resistance at most of these loci was contributed by AAC Tenacious except at two loci on chromosomes 3D and 7D where it was contributed by AAC Innova. Thirteen of the total twenty-one identified loci were located to chromosome positions where at least one QTL have been previously identified in other wheat genotype(s). The remaining eight QTLs are new which have been identified for the first time in this study. Pedigree analysis traced several known donors of PHS resistance in AAC Tenacious genealogy. Comparative analyses of the genetic intervals of identified QTLs with that of already identified and cloned PHS resistance gene intervals using IWGSC RefSeq v2.0 identified MFT-A1b (in QTL interval QPhs.lrdc-3A.1) and AGO802A (in QTL interval QPhs.lrdc-3A.2) on chromosome 3A, MFT-3B-1 (in QTL interval QPhs.lrdc-3B.1) on chromosome 3B, and AGO802D, HUB1, TaVp1-D1 (in QTL interval QPhs.lrdc-3D.1) and TaMyb10-D1 (in QTL interval QPhs.lrdc-3D.2) on chromosome 3D. These candidate genes are involved in embryo- and seed coat-imposed dormancy as well as in epigenetic control of dormancy. Conclusions Our results revealed the complex PHS resistance genetics of AAC Tenacious and AAC Innova. AAC Tenacious possesses a great reservoir of important PHS resistance QTLs/genes supposed to be derived from different resources. The tracing of pedigrees of AAC Tenacious and other sources complements the validation of QTL analysis results. Finally, comparing our results with previous PHS studies in wheat, we have confirmed the position of several major PHS resistance QTLs and candidate genes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08209-6.
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Affiliation(s)
- Raman Dhariwal
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 1st Avenue South, Lethbridge, AB, T1J 4B1, Canada
| | - Colin W Hiebert
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, R6M 1Y5, Canada
| | - Mark E Sorrells
- School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, 240 Emerson Hall, Ithaca, NY, 14853, USA
| | - Dean Spaner
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Robert J Graf
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 1st Avenue South, Lethbridge, AB, T1J 4B1, Canada
| | - Jaswinder Singh
- Department of Plant Science, McGill University, Ste-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Harpinder S Randhawa
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 1st Avenue South, Lethbridge, AB, T1J 4B1, Canada.
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22
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Arabidopsis LSH8 Positively Regulates ABA Signaling by Changing the Expression Pattern of ABA-Responsive Proteins. Int J Mol Sci 2021; 22:ijms221910314. [PMID: 34638657 PMCID: PMC8508927 DOI: 10.3390/ijms221910314] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/19/2021] [Accepted: 09/23/2021] [Indexed: 01/17/2023] Open
Abstract
Phytohormone ABA regulates the expression of numerous genes to significantly affect seed dormancy, seed germination and early seedling responses to biotic and abiotic stresses. However, the function of many ABA-responsive genes remains largely unknown. In order to improve the ABA-related signaling network, we conducted a large-scale ABA phenotype screening. LSH, an important transcription factor family, extensively participates in seedling development and floral organogenesis in plants, but whether its family genes are involved in the ABA signaling pathway has not been reported. Here we describe a new function of the transcription factor LSH8 in an ABA signaling pathway. In this study, we found that LSH8 was localized in the nucleus, and the expression level of LSH8 was significantly induced by exogenous ABA at the transcription level and protein level. Meanwhile, seed germination and root length measurements revealed that lsh8 mutant lines were ABA insensitive, whereas LSH8 overexpression lines showed an ABA-hypersensitive phenotype. With further TMT labeling quantitative proteomic analysis, we found that under ABA treatment, ABA-responsive proteins (ARPs) in the lsh8 mutant presented different changing patterns with those in wild-type Col4. Additionally, the number of ARPs contained in the lsh8 mutant was 397, six times the number in wild-type Col4. In addition, qPCR analysis found that under ABA treatment, LSH8 positively mediated the expression of downstream ABA-related genes of ABI3, ABI5, RD29B and RAB18. These results indicate that in Arabidopsis, LSH8 is a novel ABA regulator that could specifically change the expression pattern of APRs to positively mediate ABA responses.
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23
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Sato H, Santos-González J, Köhler C. Combinations of maternal-specific repressive epigenetic marks in the endosperm control seed dormancy. eLife 2021; 10:e64593. [PMID: 34427186 PMCID: PMC8456740 DOI: 10.7554/elife.64593] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 08/23/2021] [Indexed: 12/20/2022] Open
Abstract
Polycomb Repressive Complex 2 (PRC2)-mediated trimethylation of histone H3 on lysine 27 (H3K27me3) and methylation of histone 3 on lysine 9 (H3K9me) are two repressive epigenetic modifications that are typically localized in distinct regions of the genome. For reasons unknown, however, they co-occur in some organisms and special tissue types. In this study, we show that maternal alleles marked by H3K27me3 in the Arabidopsis endosperm were targeted by the H3K27me3 demethylase REF6 and became activated during germination. In contrast, maternal alleles marked by H3K27me3, H3K9me2, and CHG methylation (CHGm) are likely to be protected from REF6 targeting and remained silenced. Our study unveils that combinations of different repressive epigenetic modifications time a key adaptive trait by modulating access of REF6.
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Affiliation(s)
- Hikaru Sato
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant BiologyUppsalaSweden
| | - Juan Santos-González
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant BiologyUppsalaSweden
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant BiologyUppsalaSweden
- Max Planck Institute of Molecular Plant PhysiologyPotsdam-GolmGermany
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Tognacca RS, Botto JF. Post-transcriptional regulation of seed dormancy and germination: Current understanding and future directions. PLANT COMMUNICATIONS 2021; 2:100169. [PMID: 34327318 PMCID: PMC8299061 DOI: 10.1016/j.xplc.2021.100169] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/26/2021] [Accepted: 02/13/2021] [Indexed: 05/06/2023]
Abstract
Seed dormancy is a developmental checkpoint that prevents mature seeds from germinating under conditions that are otherwise favorable for germination. Temperature and light are the most relevant environmental factors that regulate seed dormancy and germination. These environmental cues can trigger molecular and physiological responses including hormone signaling, particularly that of abscisic acid and gibberellin. The balance between the content and sensitivity of these hormones is the key to the regulation of seed dormancy. Temperature and light tightly regulate the transcription of thousands of genes, as well as other aspects of gene expression such as mRNA splicing, translation, and stability. Chromatin remodeling determines specific transcriptional outputs, and alternative splicing leads to different outcomes and produces transcripts that encode proteins with altered or lost functions. Proper regulation of chromatin remodeling and alternative splicing may be highly relevant to seed germination. Moreover, microRNAs are also critical for the control of gene expression in seeds. This review aims to discuss recent updates on post-transcriptional regulation during seed maturation, dormancy, germination, and post-germination events. We propose future prospects for understanding how different post-transcriptional processes in crop seeds can contribute to the design of genotypes with better performance and higher productivity.
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Affiliation(s)
- Rocío Soledad Tognacca
- Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Facultad de Ciencias Exactas y Naturales, CP1428 Buenos Aires, Argentina
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Facultad de Agronomía, CP1417 Buenos Aires, Argentina
| | - Javier Francisco Botto
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Facultad de Agronomía, CP1417 Buenos Aires, Argentina
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25
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Yang Q, Gao Y, Wu X, Moriguchi T, Bai S, Teng Y. Bud endodormancy in deciduous fruit trees: advances and prospects. HORTICULTURE RESEARCH 2021; 8:139. [PMID: 34078882 PMCID: PMC8172858 DOI: 10.1038/s41438-021-00575-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/23/2021] [Accepted: 04/19/2021] [Indexed: 05/12/2023]
Abstract
Bud endodormancy is a complex physiological process that is indispensable for the survival, growth, and development of deciduous perennial plants. The timely release of endodormancy is essential for flowering and fruit production of deciduous fruit trees. A better understanding of the mechanism of endodormancy will be of great help in the artificial regulation of endodormancy to cope with climate change and in creating new cultivars with different chilling requirements. Studies in poplar have clarified the mechanism of vegetative bud endodormancy, but the endodormancy of floral buds in fruit trees needs further study. In this review, we focus on the molecular regulation of endodormancy induction, maintenance and release in floral buds of deciduous fruit trees. We also describe recent advances in quantitative trait loci analysis of chilling requirements in fruit trees. We discuss phytohormones, epigenetic regulation, and the detailed molecular network controlling endodormancy, centered on SHORT VEGETATIVE PHASE (SVP) and Dormancy-associated MADS-box (DAM) genes during endodormancy maintenance and release. Combining previous studies and our observations, we propose a regulatory model for bud endodormancy and offer some perspectives for the future.
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Affiliation(s)
- Qinsong Yang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Key Laboratory for Silviculture and Conservation, Ministry of Education, Beijing Forestry University, Haidian District, Beijing, 100083, China
| | - Yuhao Gao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Xinyue Wu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Takaya Moriguchi
- Shizuoka Professional University of Agriculture, Iwata, Shizuoka, 438-0803, Japan
| | - Songling Bai
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Yuanwen Teng
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Hainan Institute of Zhejiang University, Sanya, Hainan, 572000, China
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26
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Layat E, Bourcy M, Cotterell S, Zdzieszyńska J, Desset S, Duc C, Tatout C, Bailly C, Probst AV. The Histone Chaperone HIRA Is a Positive Regulator of Seed Germination. Int J Mol Sci 2021; 22:ijms22084031. [PMID: 33919775 PMCID: PMC8070706 DOI: 10.3390/ijms22084031] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/05/2021] [Accepted: 04/12/2021] [Indexed: 11/18/2022] Open
Abstract
Histone chaperones regulate the flow and dynamics of histone variants and ensure their assembly into nucleosomal structures, thereby contributing to the repertoire of histone variants in specialized cells or tissues. To date, not much is known on the distribution of histone variants and their modifications in the dry seed embryo. Here, we bring evidence that genes encoding the replacement histone variant H3.3 are expressed in Arabidopsis dry seeds and that embryo chromatin is characterized by a low H3.1/H3.3 ratio. Loss of HISTONE REGULATOR A (HIRA), a histone chaperone responsible for H3.3 deposition, reduces cellular H3 levels and increases chromatin accessibility in dry seeds. These molecular differences are accompanied by increased seed dormancy in hira-1 mutant seeds. The loss of HIRA negatively affects seed germination even in the absence of HISTONE MONOUBIQUITINATION 1 or TRANSCRIPTION ELONGATION FACTOR II S, known to be required for seed dormancy. Finally, hira-1 mutant seeds show lower germination efficiency when aged under controlled deterioration conditions or when facing unfavorable environmental conditions such as high salinity. Altogether, our results reveal a dependency of dry seed chromatin organization on the replication-independent histone deposition pathway and show that HIRA contributes to modulating seed dormancy and vigor.
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Affiliation(s)
- Elodie Layat
- IBPS, UMR 7622 Biologie du Développement, CNRS, Sorbonne Université, 75005 Paris, France; (E.L.); (M.B.); (C.B.)
| | - Marie Bourcy
- IBPS, UMR 7622 Biologie du Développement, CNRS, Sorbonne Université, 75005 Paris, France; (E.L.); (M.B.); (C.B.)
| | - Sylviane Cotterell
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (S.C.); (S.D.); (C.T.)
| | - Julia Zdzieszyńska
- Department of Plant Physiology, Institute of Biology, Warsaw University of Life Sciences–SGGW, 02-776 Warsaw, Poland;
| | - Sophie Desset
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (S.C.); (S.D.); (C.T.)
| | - Céline Duc
- UFIP UMR-CNRS 6286, Épigénétique et Dynamique de la Chromatine, Université de Nantes, 2 rue de la Houssinière, 44322 Nantes, France;
| | - Christophe Tatout
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (S.C.); (S.D.); (C.T.)
| | - Christophe Bailly
- IBPS, UMR 7622 Biologie du Développement, CNRS, Sorbonne Université, 75005 Paris, France; (E.L.); (M.B.); (C.B.)
| | - Aline V. Probst
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (S.C.); (S.D.); (C.T.)
- Correspondence:
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27
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Luján-Soto E, Dinkova TD. Time to Wake Up: Epigenetic and Small-RNA-Mediated Regulation during Seed Germination. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10020236. [PMID: 33530470 PMCID: PMC7911344 DOI: 10.3390/plants10020236] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/22/2021] [Accepted: 01/22/2021] [Indexed: 05/03/2023]
Abstract
Plants make decisions throughout their lifetime based on complex networks. Phase transitions during seed growth are not an exception. From embryo development through seedling growth, several molecular pathways control genome stability, environmental signal transduction and the transcriptional landscape. Particularly, epigenetic modifications and small non-coding RNAs (sRNAs) have been extensively studied as significant handlers of these processes in plants. Here, we review key epigenetic (histone modifications and methylation patterns) and sRNA-mediated regulatory networks involved in the progression from seed maturation to germination, their relationship with seed traits and crosstalk with environmental inputs.
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28
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Zhang Z, Pei X, Zhang R, Lu Y, Zheng J, Zheng Y. Molecular characterization and expression analysis of small heat shock protein 17.3 gene from Sorbus pohuashanensis (Hance) Hedl. in response to abiotic stress. Mol Biol Rep 2020; 47:9325-9335. [PMID: 33242181 DOI: 10.1007/s11033-020-06020-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/19/2020] [Indexed: 02/07/2023]
Abstract
Sorbus pohuashanensis, a native tree species in China that is distributed at high altitudes. However, the problem of adaptability when introducing S. pohuashanensis to low altitude areas has not been solved. sHSPs can respond and play an essential role when exposing to abiotic stresses for plants. In this study, we aimed to investigate the expression patterns underlying the abiotic stress response of the small heat shock protein 17.3 gene from S. pohuashanensis (SpHSP17.3) at growing low altitude. 1 to 4 years old seedlings of S. pohuashanensis were used as materials for the gene cloning, the tissue-specific expression and the expression analysis underlying the response to abiotic stress using the transgentic methods and qPCR. We identified the open reading frame (ORF) sequence of SpHSP17.3 of 471 bp, which encodes a 17.3 kD protein of 156 amino acids that is located in cytoplasmic. We found that SpHSP17.3 had the highest expression in the stem, followed sequentially by fruit, root, and flower. The expression level of SpHSP17.3 in the leaves was significantly induced by the high temperature (42 °C), NaCl salt and drought stress of S. pohuashanensis. Notably, the same SpHSP17.3 expression trend was detected in the SpHSP17.3-overexpressing homozygous transgenic Arabidopsis underlying the high temperature, NaCl salt and drought stress, and the SpHSP17.3-overexpressing homozygous transgenic Arabidopsis also showed higher seed germination rates under the NaCl salt stress conditions. Our results suggested that SpHSP17.3 is involved in the response to high temperature, Nacl salt, and drought stress which would play a certain effect in the adaptability of introduction and domestication of S. pohuashanensis.
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Affiliation(s)
- Ze Zhang
- School of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
| | - Xin Pei
- School of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
| | - Ruili Zhang
- School of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
| | - Yizeng Lu
- Shandong Provincial Center of Forest Tree Germplasm Resources, Jinan, 250102, Shandong Province, China
| | - Jian Zheng
- School of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China.
| | - Yongqi Zheng
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
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29
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Zhou Y, Yang P, Zhang F, Luo X, Xie J. Histone deacetylase HDA19 interacts with histone methyltransferase SUVH5 to regulate seed dormancy in Arabidopsis. PLANT BIOLOGY (STUTTGART, GERMANY) 2020; 22:1062-1071. [PMID: 32643178 DOI: 10.1111/plb.13158] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 05/10/2020] [Accepted: 06/30/2020] [Indexed: 05/22/2023]
Abstract
Seed dormancy controls the timing of germination and plays a significant role in adaptation and evolution of seed plants. In this study, a yeast two-hybrid, pull-down assay and co-immunoprecipitation assay were used to ascertain the protein relationship of SUVH5 and HDA19. Both qRT-PCR and ChIP-qPCR were used to examine the molecular mechanism of how HDA19 and SUVH5 regulate seed dormancy. The results demonstrated that histone methyltransferase SUVH5 interacted with histone deacetylase HDA19 in vivo and in vitro. In addition, they showed that mutants of HDA19 could deepen seed dormancy, and that SUVH5 had the same effect. The hda19 suvh5 double mutant displayed a higher level of seed dormancy than the single mutants hda19 or suvh5. Moreover, the expression of seed dormancy-related genes increased in hda19, suvh5 and in hda19 suvh5 double mutant plants, which was associated with increased histone H3 acetylation (H3ac), but decreased histone H3 Lys 9 dimethylation (H3K9me2). ChIP assays proved that HDA19 could directly integrate into the chromatin of genes regulating seed dormancy. Taken together, our results show that HDA19 and SUVH5 work together and have a negative role in seed dormancy.
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Affiliation(s)
- Y Zhou
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - P Yang
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - F Zhang
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - X Luo
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - J Xie
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
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30
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Epigenetics and epigenomics: underlying mechanisms, relevance, and implications in crop improvement. Funct Integr Genomics 2020; 20:739-761. [PMID: 33089419 DOI: 10.1007/s10142-020-00756-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 01/21/2023]
Abstract
Epigenetics is defined as changes in gene expression that are not associated with changes in DNA sequence but due to the result of methylation of DNA and post-translational modifications to the histones. These epigenetic modifications are known to regulate gene expression by bringing changes in the chromatin state, which underlies plant development and shapes phenotypic plasticity in responses to the environment and internal cues. This review articulates the role of histone modifications and DNA methylation in modulating biotic and abiotic stresses, as well as crop improvement. It also highlights the possibility of engineering epigenomes and epigenome-based predictive models for improving agronomic traits.
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31
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Lou L, Ding L, Wang T, Xiang Y. Emerging Roles of RNA-Binding Proteins in Seed Development and Performance. Int J Mol Sci 2020; 21:ijms21186822. [PMID: 32957608 PMCID: PMC7555721 DOI: 10.3390/ijms21186822] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/10/2020] [Accepted: 09/10/2020] [Indexed: 02/01/2023] Open
Abstract
Seed development, dormancy, and germination are key physiological events that are not only important for seed generation, survival, and dispersal, but also contribute to agricultural production. RNA-binding proteins (RBPs) directly interact with target mRNAs and fine-tune mRNA metabolism by governing post-transcriptional regulation, including RNA processing, intron splicing, nuclear export, trafficking, stability/decay, and translational control. Recent studies have functionally characterized increasing numbers of diverse RBPs and shown that they participate in seed development and performance, providing significant insight into the role of RBP-mRNA interactions in seed processes. In this review, we discuss recent research progress on newly defined RBPs that have crucial roles in RNA metabolism and affect seed development, dormancy, and germination.
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Katsuya-Gaviria K, Caro E, Carrillo-Barral N, Iglesias-Fernández R. Reactive Oxygen Species (ROS) and Nucleic Acid Modifications During Seed Dormancy. PLANTS (BASEL, SWITZERLAND) 2020; 9:E679. [PMID: 32471221 PMCID: PMC7356579 DOI: 10.3390/plants9060679] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/24/2020] [Accepted: 05/26/2020] [Indexed: 12/15/2022]
Abstract
The seed is the propagule of higher plants and allows its dissemination and the survival of the species. Seed dormancy prevents premature germination under favourable conditions. Dormant seeds are only able to germinate in a narrow range of conditions. During after-ripening (AR), a mechanism of dormancy release, seeds gradually lose dormancy through a period of dry storage. This review is mainly focused on how chemical modifications of mRNA and genomic DNA, such as oxidation and methylation, affect gene expression during late stages of seed development, especially during dormancy. The oxidation of specific nucleotides produced by reactive oxygen species (ROS) alters the stability of the seed stored mRNAs, being finally degraded or translated into non-functional proteins. DNA methylation is a well-known epigenetic mechanism of controlling gene expression. In Arabidopsis thaliana, while there is a global increase in CHH-context methylation through embryogenesis, global DNA methylation levels remain stable during seed dormancy, decreasing when germination occurs. The biological significance of nucleic acid oxidation and methylation upon seed development is discussed.
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Affiliation(s)
- Kai Katsuya-Gaviria
- Centro de Biotecnología y Genómica de Plantas-Severo Ochoa (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223-Pozuelo de Alarcón, Spain; (K.K.-G.); (E.C.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM, 28040-Madrid, Spain
| | - Elena Caro
- Centro de Biotecnología y Genómica de Plantas-Severo Ochoa (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223-Pozuelo de Alarcón, Spain; (K.K.-G.); (E.C.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM, 28040-Madrid, Spain
| | - Néstor Carrillo-Barral
- Departamento de Fisiología Vegetal, Facultad de Ciencias, Universidad da Coruña (UdC), 15008-A Coruña, Spain;
| | - Raquel Iglesias-Fernández
- Centro de Biotecnología y Genómica de Plantas-Severo Ochoa (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223-Pozuelo de Alarcón, Spain; (K.K.-G.); (E.C.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM, 28040-Madrid, Spain
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33
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Xu L, Jiang H. Writing and Reading Histone H3 Lysine 9 Methylation in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2020; 11:452. [PMID: 32435252 PMCID: PMC7218100 DOI: 10.3389/fpls.2020.00452] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/27/2020] [Indexed: 05/05/2023]
Abstract
In eukaryotes, histone H3 lysine 9 methylation (H3K9me) mediates the silencing of invasive and repetitive sequences by preventing the expression of aberrant gene products and the activation of transposition. In Arabidopsis, while it is well known that dimethylation of histone H3 at lysine 9 (H3K9me2) is maintained through a feedback loop between H3K9me2 and DNA methylation, the details of the H3K9me2-dependent silencing pathway have not been fully elucidated. Recently, the regulation and the function of H3K9 methylation have been extensively characterized. In this review, we summarize work from the recent studies regarding the regulation of H3K9me2, emphasizing the process of deposition and reading and the biological significance of H3K9me2 in Arabidopsis.
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Affiliation(s)
| | - Hua Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
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34
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Carrillo-Barral N, Rodríguez-Gacio MDC, Matilla AJ. Delay of Germination-1 (DOG1): A Key to Understanding Seed Dormancy. PLANTS 2020; 9:plants9040480. [PMID: 32283717 PMCID: PMC7238029 DOI: 10.3390/plants9040480] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 01/19/2023]
Abstract
DELAY OF GERMINATION-1 (DOG1), is a master regulator of primary dormancy (PD) that acts in concert with ABA to delay germination. The ABA and DOG1 signaling pathways converge since DOG1 requires protein phosphatase 2C (PP2C) to control PD. DOG1 enhances ABA signaling through its binding to PP2C ABA HYPERSENSITIVE GERMINATION (AHG1/AHG3). DOG1 suppresses the AHG1 action to enhance ABA sensitivity and impose PD. To carry out this suppression, the formation of DOG1-heme complex is essential. The binding of DOG1-AHG1 to DOG1-Heme is an independent processes but essential for DOG1 function. The quantity of active DOG1 in mature and viable seeds is correlated with the extent of PD. Thus, dog1 mutant seeds, which have scarce endogenous ABA and high gibberellin (GAs) content, exhibit a non-dormancy phenotype. Despite being studied extensively in recent years, little is known about the molecular mechanism underlying the transcriptional regulation of DOG1. However, it is well-known that the physiological function of DOG1 is tightly regulated by a complex array of transformations that include alternative splicing, alternative polyadenylation, histone modifications, and a cis-acting antisense non-coding transcript (asDOG1). The DOG1 becomes modified (i.e., inactivated) during seed after-ripening (AR), and its levels in viable seeds do not correlate with germination potential. Interestingly, it was recently found that the transcription factor (TF) bZIP67 binds to the DOG1 promoter. This is required to activate DOG1 expression leading to enhanced seed dormancy. On the other hand, seed development under low-temperature conditions triggers DOG1 expression by increasing the expression and abundance of bZIP67. Together, current data indicate that DOG1 function is not strictly limited to PD process, but that it is also required for other facets of seed maturation, in part by also interfering with the ethylene signaling components. Otherwise, since DOG1 also affects other processes such us flowering and drought tolerance, the approaches to understanding its mechanism of action and control are, at this time, still inconclusive.
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Affiliation(s)
- Néstor Carrillo-Barral
- Departamento de Biología, Facultad de Ciencias, Universidad de A Coruña, Campus Zapateira, 15071-A Coruña, Spain;
| | - María del Carmen Rodríguez-Gacio
- Departamento de Biología Funcional (Área Fisiología Vegetal), Facultad de Farmacia, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain;
| | - Angel Jesús Matilla
- Departamento de Biología Funcional (Área Fisiología Vegetal), Facultad de Farmacia, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain;
- Correspondence: ; Tel.: +34-981-563-100
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35
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Zha P, Liu S, Li Y, Ma T, Yang L, Jing Y, Lin R. The Evening Complex and the Chromatin-Remodeling Factor PICKLE Coordinately Control Seed Dormancy by Directly Repressing DOG1 in Arabidopsis. PLANT COMMUNICATIONS 2020; 1:100011. [PMID: 33404551 PMCID: PMC7748002 DOI: 10.1016/j.xplc.2019.100011] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 11/23/2019] [Accepted: 11/28/2019] [Indexed: 05/22/2023]
Abstract
Primary seed dormancy is acquired during seed development and maturation, which is important for plant fitness and survival. DELAY OF GERMINATION1 (DOG1) plays a critical role in inducing seed dormancy. DOG1 expression increases rapidly during seed development, but the precise mechanism underlying this process remains elusive. In this study, we showed that mutants with a loss or reduced function of the chromatin-remodeling factor PICKLE (PKL) exhibit increased seed dormancy. PKL associates with DOG1 chromatin and inhibits its transcription. We found that PKL physically interacts with LUX ARRHYTHMO (LUX), a member of the evening complex (EC) of the circadian clock. Furthermore, LUX directly binds to a specific coding sequence of DOG1, and DOG1 acts genetically downstream of PKL and LUX. Mutations in either LUX or EARLY FLOWERING3 (ELF3) encoding another member of the EC led to increased DOG1 expression and enhanced seed dormancy. Surprisingly, these phenotypes were abolished when the parent plants were grown under continuous light. In addition, we observed that loss of function of either PKL or LUX decreased H3K27me3 levels at the DOG1 locus. Taken together, our study reveals a regulatory mechanism in which EC proteins coordinate with PKL to transmit circadian signals for directly regulating DOG1 expression and seed dormancy during seed development.
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Affiliation(s)
- Ping Zha
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Shuangrong Liu
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Li
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tingting Ma
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Liwen Yang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yanjun Jing
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Rongcheng Lin
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- Corresponding author
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Gupta MK, Lenka SK, Gupta S, Rawal RK. Agonist, antagonist and signaling modulators of ABA receptor for agronomic and post-harvest management. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 148:10-25. [PMID: 31923734 DOI: 10.1016/j.plaphy.2019.12.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 12/18/2019] [Accepted: 12/18/2019] [Indexed: 05/18/2023]
Abstract
Abscisic acid (ABA) is a ubiquitous phytohormone, plays important roles in several physiological processes, including stress adaptation, flowering, seed germination, fruit ripening, and leaf senescence etc. ABA binds with START domain proteins called Pyrabactin Resistance1 (PYR1)/PYR1-like (PYL)/Regulatory Components of ABA Receptors (RCARs) and controls the activity of PP2C phosphatase proteins and in turn the ABA-dependent signaling pathway. Fourteen ABA receptors have been identified in the model plant Arabidopsis thaliana and have shown to be involved in various biological functions. Under field conditions, exogenous application of ABA produces inadequate physiological response due to its rapid conversion into the biologically inactive metabolites. ABA shows selective binding preferences to PYL receptor subtypes and hence produces pleiotropic physiological and phenotypic effects which limit the usage of ABA in agriculture. An agrochemical meant for ameliorating the undesirable physiological effect of the plant should ideally have positive biological attributes without affecting the normal growth, development, and yield. Therefore, to overcome the limitations of ABA for its usage in various agricultural applications, several types of ABA-mimicking agents have been developed. Many compounds have been identified as having significant ABA-agonist/antagonist activity and can be employed to reverse the excessive/moderate ABA action. The present review highlights the potential usage of ABA signaling modulators for managing agronomic and postharvest traits. Besides, designing, development and versatile usage of ABA-mimicking compounds displaying ABA agonists and antagonist activities are discussed in detail.
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Affiliation(s)
- Manish K Gupta
- TERI-Deakin Nanobiotechnology Centre, The Energy and Resources Institute (TERI), Gurugram, HR, India.
| | - Sangram K Lenka
- TERI-Deakin Nanobiotechnology Centre, The Energy and Resources Institute (TERI), Gurugram, HR, India
| | - Swati Gupta
- Amity Institute of Pharmacy, Amity University, Sector 125, Noida, UP, India
| | - Ravindra K Rawal
- Department of Chemistry, Maharishi Markandeshwar (Deemed to be University), Mullana, HR, India
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Cheng K, Xu Y, Yang C, Ouellette L, Niu L, Zhou X, Chu L, Zhuang F, Liu J, Wu H, Charron JB, Luo M. Histone tales: lysine methylation, a protagonist in Arabidopsis development. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:793-807. [PMID: 31560751 DOI: 10.1093/jxb/erz435] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 09/17/2019] [Indexed: 05/20/2023]
Abstract
Histone methylation plays a fundamental role in the epigenetic regulation of gene expression driven by developmental and environmental cues in plants, including Arabidopsis. Histone methyltransferases and demethylases act as 'writers' and 'erasers' of methylation at lysine and/or arginine residues of core histones, respectively. A third group of proteins, the 'readers', recognize and interpret the methylation marks. Emerging evidence confirms the crucial roles of histone methylation in multiple biological processes throughout the plant life cycle. In this review, we summarize the regulatory mechanisms of lysine methylation, especially at histone H3 tails, and focus on the recent advances regarding the roles of lysine methylation in Arabidopsis development, from seed performance to reproductive development, and in callus formation.
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Affiliation(s)
- Kai Cheng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Yingchao Xu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chao Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Luc Ouellette
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Longjian Niu
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Xiaochen Zhou
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Liutian Chu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Feng Zhuang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jin Liu
- Institute for Food and Bioresource Engineering, Department of Energy and Resources Engineering and BIC-ESAT, College of Engineering, Peking University, Beijing, China
| | - Hualing Wu
- Tea Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Tea Plant Resources Innovation & Utilization, Guangzhou, Guangdong, China
| | - Jean-Benoit Charron
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
| | - Ming Luo
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
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Grasser KD. The FACT Histone Chaperone: Tuning Gene Transcription in the Chromatin Context to Modulate Plant Growth and Development. FRONTIERS IN PLANT SCIENCE 2020; 11:85. [PMID: 32140163 PMCID: PMC7042381 DOI: 10.3389/fpls.2020.00085] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 01/21/2020] [Indexed: 05/20/2023]
Abstract
FACT is a heterodimeric histone chaperone consisting of the SSRP1 and SPT16 proteins and is conserved among eukaryotes. It interacts with the histones H2A-H2B and H3-H4 as well as with DNA. Based on in vitro and in vivo studies mainly in yeast and mammalian cells, FACT can mediate nucleosome disassembly and reassembly and thus facilitates in the chromatin context DNA-dependent processes including transcription, replication and repair. In plants, primarily the role of FACT related to RNA polymerase II transcription has been examined. FACT was found to associate with elongating Arabidopsis RNA polymerase II (RNAPII) as part of the transcript elongation complex and it was identified as repressor of aberrant intragenic transcriptional initiation. Arabidopsis mutants depleted in FACT subunits exhibit various defects in vegetative and reproductive development. Strikingly, FACT modulates important developmental transitions by promoting expression of key repressors of these processes. Thus, FACT facilitates expression of DOG1 and FLC adjusting the switch from seed dormancy to germination and from vegetative to reproductive development, respectively. In the central cell of the female gametophyte, FACT can facilitate DNA demethylation especially within heterochromatin, and thereby contributes to gene imprinting during Arabidopsis reproduction. This review discusses results particularly from the plant perspective about the contribution of FACT to processes that involve reorganisation of nucleosomes with a main focus on RNAPII transcription and its implications for diverse areas of plant biology.
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Zhao T, Zhan Z, Jiang D. Histone modifications and their regulatory roles in plant development and environmental memory. J Genet Genomics 2019; 46:467-476. [PMID: 31813758 DOI: 10.1016/j.jgg.2019.09.005] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/23/2019] [Accepted: 09/29/2019] [Indexed: 11/24/2022]
Abstract
Plants grow in dynamic environments where they receive diverse environmental signals. Swift and precise control of gene expression is essential for plants to align their development and metabolism with fluctuating surroundings. Modifications on histones serve as "histone code" to specify chromatin and gene activities. Different modifications execute distinct functions on the chromatin, promoting either active transcription or gene silencing. Histone writers, erasers, and readers mediate the regulation of histone modifications by catalyzing, removing, and recognizing modifications, respectively. Growing evidence indicates the important function of histone modifications in plant development and environmental responses. Histone modifications also serve as environmental memory for plants to adapt to environmental changes. Here we review recent progress on the regulation of histone modifications in plants, the impact of histone modifications on environment-controlled developmental transitions including germination and flowering, and the role of histone modifications in environmental memory.
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Affiliation(s)
- Ting Zhao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhenping Zhan
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Danhua Jiang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100101, China.
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40
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Michl-Holzinger P, Mortensen SA, Grasser KD. The SSRP1 subunit of the histone chaperone FACT is required for seed dormancy in Arabidopsis. JOURNAL OF PLANT PHYSIOLOGY 2019; 236:105-108. [PMID: 30947026 DOI: 10.1016/j.jplph.2019.03.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 03/15/2019] [Accepted: 03/15/2019] [Indexed: 05/06/2023]
Abstract
SSRP1 is a subunit of the histone chaperone FACT that associates with elongating RNA polymerase II (RNAPII) along the transcribed region of genes. FACT facilitates transcriptional elongation by destabilising nucleosomes in the path of RNAPII, assisting efficient transcription of chromatin templates. In contrast to wild type seeds, freshly harvested seeds of the Arabidopsis ssrp1 mutant germinate efficiently, exhibiting reduced seed dormancy. In line with this phenotype, the ssrp1 seeds have decreased transcript levels of the DOG1 gene, which is a known quantitative trait locus (QTL) for seed dormancy. Analysis of ssrp1 plants harbouring an additional copy of DOG1 show increased levels of DOG1 transcript and consistently more robust seed dormancy. Therefore, our findings indicate that SSRP1 is a novel factor required for the efficient expression of DOG1 and hence a modulator of seed dormancy in Arabidopsis.
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Affiliation(s)
- Philipp Michl-Holzinger
- Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Simon A Mortensen
- Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Klaus D Grasser
- Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany.
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41
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Gu D, Ji R, He C, Peng T, Zhang M, Duan J, Xiong C, Liu X. Arabidopsis Histone Methyltransferase SUVH5 Is a Positive Regulator of Light-Mediated Seed Germination. FRONTIERS IN PLANT SCIENCE 2019; 10:841. [PMID: 31316539 PMCID: PMC6610342 DOI: 10.3389/fpls.2019.00841] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 06/12/2019] [Indexed: 05/20/2023]
Abstract
Plant lifecycle starts from seed germination, which is regulated by various environmental cues and endogenous hormones. Light promotes seed germination mainly by phytochrome B (PHYB) during the initial phase of imbibition, which involves genome-wide light-responsive transcription changes. Recent studies indicated an involvement of multiple epigenetic factors in the control of seed germination. However, few studies have been reported about the role of a histone methyltransferase in light-mediated seed germination process. Here, we identified SUVH5, a histone H3 lysine 9 methyltransferase, as a positive regulator in light-mediated seed germination in Arabidopsis. Loss of function of SUVH5 leads to decreased PHYB-dependent seed germination. RNA-sequencing analysis displayed that SUVH5 regulates 24.6% of light-responsive transcriptome in imbibed seeds, which mainly related to hormonal signaling pathways and developmental processes. Furthermore, SUVH5 represses the transcription of ABA biosynthesis and signal transduction-related genes, as well as a family of DELAY OF GERMINATION (DOG) genes via dimethylation of histone H3 at lysine 9 (H3K9me2) in imbibed seeds. Taken together, our findings revealed that SUVH5 is a novel positive regulator of light-mediated seed germination in Arabidopsis.
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Affiliation(s)
- Dachuan Gu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Core Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Rujun Ji
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Core Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Chunmei He
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Core Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Tao Peng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Core Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Mingyong Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Core Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Jun Duan
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Core Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Changyun Xiong
- College of Tropical Crops, Yunnan Agricultural University, Pu’er, China
- *Correspondence: Changyun Xiong,
| | - Xuncheng Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Core Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Xuncheng Liu,
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Lepiniec L, Devic M, Roscoe TJ, Bouyer D, Zhou DX, Boulard C, Baud S, Dubreucq B. Molecular and epigenetic regulations and functions of the LAFL transcriptional regulators that control seed development. PLANT REPRODUCTION 2018; 31:291-307. [PMID: 29797091 DOI: 10.1007/s00497-018-0337-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 05/10/2018] [Indexed: 05/20/2023]
Abstract
The LAFL (i.e. LEC1, ABI3, FUS3, and LEC2) master transcriptional regulators interact to form different complexes that induce embryo development and maturation, and inhibit seed germination and vegetative growth in Arabidopsis. Orthologous genes involved in similar regulatory processes have been described in various angiosperms including important crop species. Consistent with a prominent role of the LAFL regulators in triggering and maintaining embryonic cell fate, their expression appears finely tuned in different tissues during seed development and tightly repressed in vegetative tissues by a surprisingly high number of genetic and epigenetic factors. Partial functional redundancies and intricate feedback regulations of the LAFL have hampered the elucidation of the underpinning molecular mechanisms. Nevertheless, genetic, genomic, cellular, molecular, and biochemical analyses implemented during the last years have greatly improved our knowledge of the LALF network. Here we summarize and discuss recent progress, together with current issues required to gain a comprehensive insight into the network, including the emerging function of LEC1 and possibly LEC2 as pioneer transcription factors.
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Affiliation(s)
- L Lepiniec
- IJPB (Institut Jean-Pierre Bourgin), INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles, France.
| | - M Devic
- Régulations Epigénétiques et Développement de la Graine, ERL 5300 CNRS-IRD UMR DIADE, IRD centre de Montpellier, 911 Avenue Agropolis, BP 64501, 34394, Montpellier, France
- Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, Sorbonne Universités, Université Pierre et Marie Curie (Paris 06) & Centre National pour la Recherche Scientifique CNRS UMR 7621, 66650, Banyuls-sur-Mer, France
| | - T J Roscoe
- Régulations Epigénétiques et Développement de la Graine, ERL 5300 CNRS-IRD UMR DIADE, IRD centre de Montpellier, 911 Avenue Agropolis, BP 64501, 34394, Montpellier, France
- Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, Sorbonne Universités, Université Pierre et Marie Curie (Paris 06) & Centre National pour la Recherche Scientifique CNRS UMR 7621, 66650, Banyuls-sur-Mer, France
| | - D Bouyer
- Institut de Biologie de l'ENS, CNRS UMR8197, Ecole Normale Supérieure, 46 rue d'Ulm, 75230, Paris Cedex 05, France
| | - D-X Zhou
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Sud 11, Université Paris-Saclay, 91405, Orsay, France
| | - C Boulard
- IJPB (Institut Jean-Pierre Bourgin), INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles, France
| | - S Baud
- IJPB (Institut Jean-Pierre Bourgin), INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles, France
| | - B Dubreucq
- IJPB (Institut Jean-Pierre Bourgin), INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles, France
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Jia Y, Li R, Yang W, Chen Z, Hu X. Carbon monoxide signal regulates light-initiated seed germination by suppressing SOM expression. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 272:88-98. [PMID: 29807609 DOI: 10.1016/j.plantsci.2018.04.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 03/28/2018] [Accepted: 04/11/2018] [Indexed: 05/09/2023]
Abstract
Light is a critical external signal for seed germination. The photoreceptor phytochrome B (PHYB) perceives light stimulation and promotes seed germination during the early phase after imbibition. SOM is a CCH-type zinc finger protein and negatively regulates PHYB-mediated seed germination by controlling downstream gibberellic acid (GA) and abscisic acid (ABA) metabolism. As a small molecular signal, carbon monoxide (CO) has been reported to regulate seed germination under environmental stress, but the underlying mechanism remains unclear. In this study, we first found that CO enhanced PHYB-dependent seed germination, and red light irradiation increased the transcriptional level of gene encoding Heme oxygenase 1(HY1) for CO production, this process required PHYB. Pharmacological and genetic analyses revealed that CO signals repressed the transcriptional level of SOM to alter downstream GA/ABA metabolism related genes expression, ultimately relieving the inhibitory effect of SOM on seed germination. Furthermore, CO signals possibly recruited histone deacetylase 6 (HDA6) to the promoter region of SOM to decrease its expression by diminishing histone H3 acetylation levels at this locus. Taken together, our results propose a novel mechanism for CO signals in promoting light-initiated seed germination via recruiting HDA6 to epigenetically regulate SOM expression.
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Affiliation(s)
- Yujie Jia
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Ruijing Li
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Wenjuan Yang
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Zhen Chen
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Xiangyang Hu
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, 200444, China.
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Mizuno Y, Yamanouchi U, Hoshino T, Nonoue Y, Nagata K, Fukuoka S, Ando T, Yano M, Sugimoto K. Genetic dissection of pre-harvest sprouting resistance in an upland rice cultivar. BREEDING SCIENCE 2018; 68:200-209. [PMID: 29875603 PMCID: PMC5982176 DOI: 10.1270/jsbbs.17062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 11/06/2017] [Indexed: 05/04/2023]
Abstract
Seed dormancy is important in rice breeding because it confers resistance to pre-harvest sprouting (PHS). To detect quantitative trait loci (QTLs) for pre-harvest sprouting resistance, we used chromosome segment substitution lines (CSSLs) derived from a cross between the Japanese upland rice cultivar 'Owarihatamochi' and the lowland rice cultivar 'Koshihikari'. In the CSSLs, several chromosomal regions were associated with PHS resistance. Among these, the chromosome 9 segment from 'Owarihatamochi' had the greatest association with increased PHS resistance. Further QTL analysis using an advanced backcross population (BC4F2) derived from a 'Koshihikari' × 'Owarihatamochi' cross revealed two putative QTLs, here designated qSDR9.1 (Seed dormancy 9.1) and qSDR9.2, on chromosome 9. The 'Owarihatamochi' alleles of the two QTLs reduced germination. Further fine mapping revealed that qSDR9.1 and qSDR9.2 were located within 4.1-Mb and 2.3-Mb intervals (based on the 'Nipponbare' reference genome sequence) defined by the simple sequence repeat marker loci RM24039 and RM24260 and Indel_2 and RM24540, respectively. We thus identified two QTLs for PHS resistance in 'Owarihatamochi', even though resistance levels are relatively low in this cultivar. This unexpected finding suggests the advantages of using CSSLs for QTL detection.
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Affiliation(s)
- Yosuke Mizuno
- Tsukuba University,
1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577,
Japan
| | - Utako Yamanouchi
- Institute of Crop Sciences, NARO,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Tomoki Hoshino
- Institute of Crop Sciences, NARO,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Yasunori Nonoue
- Institute of Crop Sciences, NARO,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Kazufumi Nagata
- Institute of Crop Sciences, NARO,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Shuichi Fukuoka
- Institute of Crop Sciences, NARO,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Tsuyu Ando
- Institute of Crop Sciences, NARO,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Masahiro Yano
- Tsukuba University,
1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577,
Japan
- Institute of Crop Sciences, NARO,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Kazuhiko Sugimoto
- Institute of Crop Sciences, NARO,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
- Corresponding author (e-mail: )
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Vishal B, Kumar PP. Regulation of Seed Germination and Abiotic Stresses by Gibberellins and Abscisic Acid. FRONTIERS IN PLANT SCIENCE 2018; 9:838. [PMID: 29973944 PMCID: PMC6019495 DOI: 10.3389/fpls.2018.00838] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/30/2018] [Indexed: 05/19/2023]
Abstract
Overall growth and development of a plant is regulated by complex interactions among various hormones, which is critical at different developmental stages. Some of the key aspects of plant growth include seed development, germination and plant survival under unfavorable conditions. Two of the key phytohormones regulating the associated physiological processes are gibberellins (GA) and abscisic acid (ABA). GAs participate in numerous developmental processes, including, seed development and seed germination, seedling growth, root proliferation, determination of leaf size and shape, flower induction and development, pollination and fruit expansion. Despite the association with abiotic stresses, ABA is essential for normal plant growth and development. It plays a critical role in different abiotic stresses by regulating various downstream ABA-dependent stress responses. Plants maintain a balance between GA and ABA levels constantly throughout the developmental processes at different tissues and organs, including under unfavorable environmental or physiological conditions. Here, we will review the literature on how GA and ABA control different stages of plant development, with focus on seed germination and selected abiotic stresses. The possible crosstalk of ABA and GA in specific events of the above processes will also be discussed, with emphasis on downstream stress signaling components, kinases and transcription factors (TFs). The importance of several key ABA and GA signaling intermediates will be illustrated. The knowledge gained from such studies will also help to establish a solid foundation to develop future crop improvement strategies.
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Inácio V, Martins MT, Graça J, Morais-Cecílio L. Cork Oak Young and Traumatic Periderms Show PCD Typical Chromatin Patterns but Different Chromatin-Modifying Genes Expression. FRONTIERS IN PLANT SCIENCE 2018; 9:1194. [PMID: 30210513 PMCID: PMC6120546 DOI: 10.3389/fpls.2018.01194] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/25/2018] [Indexed: 05/20/2023]
Abstract
Plants are subjected to adverse conditions being outer protective tissues fundamental to their survival. Tree stems are enveloped by a periderm made of cork cells, resulting from the activity of the meristem phellogen. DNA methylation and histone modifications have important roles in the regulation of plant cell differentiation. However, studies on its involvement in cork differentiation are scarce despite periderm importance. Cork oak periderm development was used as a model to study the formation and differentiation of secondary protective tissues, and their behavior after traumatic wounding (traumatic periderm). Nuclei structural changes, dynamics of DNA methylation, and posttranslational histone modifications were assessed in young and traumatic periderms, after cork harvesting. Lenticular phellogen producing atypical non-suberized cells that disaggregate and form pores was also studied, due to high impact for cork industrial uses. Immunolocalization of active and repressive marks, transcription analysis of the corresponding genes, and correlations between gene expression and cork porosity were investigated. During young periderm development, a reduction in nuclei area along with high levels of DNA methylation occurred throughout epidermis disruption. As cork cells became more differentiated, whole nuclei progressive chromatin condensation with accumulation in the nuclear periphery and increasing DNA methylation was observed. Lenticular cells nuclei were highly fragmented with faint 5-mC labeling. Phellogen nuclei were less methylated than in cork cells, and in lenticular phellogen were even lower. No significant differences were detected in H3K4me3 and H3K18ac signals between cork cells layers, although an increase in H3K4me3 signals was found from the phellogen to cork cells. Distinct gene expression patterns in young and traumatic periderms suggest that cork differentiation might be under specific silencing regulatory pathways. Significant correlations were found between QsMET1, QsMET2, and QsSUVH4 gene expression and cork porosity. This work evidences that DNA methylation and histone modifications play a role in cork differentiation and epidermis induced tension-stress. It also provides the first insights into chromatin dynamics during cork and lenticular cells differentiation pointing to a distinct type of remodeling associated with cell death.
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Affiliation(s)
- Vera Inácio
- Linking Landscape, Environment, Agriculture and Food (LEAF), Institute of Agronomy, University of Lisbon, Lisbon, Portugal
- *Correspondence: Vera Inácio,
| | - Madalena T. Martins
- Linking Landscape, Environment, Agriculture and Food (LEAF), Institute of Agronomy, University of Lisbon, Lisbon, Portugal
| | - José Graça
- Forest Research Center (CEF), Institute of Agronomy, University of Lisbon, Lisbon, Portugal
| | - Leonor Morais-Cecílio
- Linking Landscape, Environment, Agriculture and Food (LEAF), Institute of Agronomy, University of Lisbon, Lisbon, Portugal
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47
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Yatusevich R, Fedak H, Ciesielski A, Krzyczmonik K, Kulik A, Dobrowolska G, Swiezewski S. Antisense transcription represses Arabidopsis seed dormancy QTL DOG1 to regulate drought tolerance. EMBO Rep 2017; 18:2186-2196. [PMID: 29030481 PMCID: PMC5709759 DOI: 10.15252/embr.201744862] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 09/08/2017] [Accepted: 09/15/2017] [Indexed: 12/11/2022] Open
Abstract
Plants have developed multiple strategies to sense the external environment and to adapt growth accordingly. Delay of germination 1 (DOG1) is a major quantitative trait locus (QTL) for seed dormancy strength in Arabidopsis thaliana that is reported to be expressed exclusively in seeds. DOG1 is extensively regulated, with an antisense transcript (asDOG1) suppressing its expression in seeds. Here, we show that asDOG1 shows high levels in mature plants where it suppresses DOG1 expression under standard growth conditions. Suppression is released by shutting down antisense transcription, which is induced by the plant hormone abscisic acid (ABA) and drought. Loss of asDOG1 results in constitutive high-level DOG1 expression, conferring increased drought tolerance, while inactivation of DOG1 causes enhanced drought sensitivity. The unexpected role of DOG1 in environmental adaptation of mature plants is separate from its function in seed dormancy regulation. The requirement of asDOG1 to respond to ABA and drought demonstrates that antisense transcription is important for sensing and responding to environmental changes in plants.
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Affiliation(s)
- Ruslan Yatusevich
- Department of Protein Biosynthesis, Institute of Biochemistry and Biophysics, Warsaw, Poland
| | - Halina Fedak
- Department of Protein Biosynthesis, Institute of Biochemistry and Biophysics, Warsaw, Poland
| | | | - Katarzyna Krzyczmonik
- Department of Protein Biosynthesis, Institute of Biochemistry and Biophysics, Warsaw, Poland
| | - Anna Kulik
- Department of Plant Biochemistry, Institute of Biochemistry and Biophysics, Warsaw, Poland
| | - Grazyna Dobrowolska
- Department of Plant Biochemistry, Institute of Biochemistry and Biophysics, Warsaw, Poland
| | - Szymon Swiezewski
- Department of Protein Biosynthesis, Institute of Biochemistry and Biophysics, Warsaw, Poland
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48
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Kocheshkova AA, Kroupin PY, Bazhenov MS, Karlov GI, Pochtovyy AA, Upelniek VP, Belov VI, Divashuk MG. Pre-harvest sprouting resistance and haplotype variation of ThVp-1 gene in the collection of wheat-wheatgrass hybrids. PLoS One 2017; 12:e0188049. [PMID: 29131854 PMCID: PMC5683615 DOI: 10.1371/journal.pone.0188049] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 10/31/2017] [Indexed: 11/19/2022] Open
Abstract
The germplasm collection of 87 wheat-wheatgrass hybrids developed in Tsitisin Main Botanical Garden (Russia, Moscow) was evaluated for resistance to pre-harvest sprouting (PHS) by spike sprouting (SS) and germination index (GI) assays as well as for spike and grain features. The PHS resistance variation and haplotype polymorphism of the wheatgrass ThVp-1 and wheat TaVp-1B genes orthologues of Vp-1 was revealed in the studied collection. Four haplotypes of ThVp-1 were revealed: ThVp-1a (41% of the entries), ThVp-1b (13%), ThVp-1c (29%), and ThVp-1d (15%). The association between the allelic state of ThVp-1 and PHS resistance in the wheat-wheatgrass hybrids was shown: haplotype ThVp-1d of the wheatgrass Vp-1 gene is significantly associated with reduced PHS in the wheat-wheatgrass hybrids (mean SS 0.33, mean GI 0.64). The resistant entries may be perspective as a source of PHS resistance in the development of commercial cultivars of perennial wheat.
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Affiliation(s)
- A. A. Kocheshkova
- Center for Molecular Biotechnology, Russian State Agrarian University–Moscow Timiryazev Agricultural Academy, Moscow, Russia
| | - P. Yu. Kroupin
- Center for Molecular Biotechnology, Russian State Agrarian University–Moscow Timiryazev Agricultural Academy, Moscow, Russia
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - M. S. Bazhenov
- Center for Molecular Biotechnology, Russian State Agrarian University–Moscow Timiryazev Agricultural Academy, Moscow, Russia
| | - G. I. Karlov
- Center for Molecular Biotechnology, Russian State Agrarian University–Moscow Timiryazev Agricultural Academy, Moscow, Russia
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - A. A. Pochtovyy
- Center for Molecular Biotechnology, Russian State Agrarian University–Moscow Timiryazev Agricultural Academy, Moscow, Russia
| | - V. P. Upelniek
- Department of Distant Hybridization, N. V. Tsitsin Main Botanical Garden of Russian Academy of Sciences, Moscow, Russia
| | - V. I. Belov
- Department of Distant Hybridization, N. V. Tsitsin Main Botanical Garden of Russian Academy of Sciences, Moscow, Russia
| | - M. G. Divashuk
- Center for Molecular Biotechnology, Russian State Agrarian University–Moscow Timiryazev Agricultural Academy, Moscow, Russia
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
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49
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Narro-Diego L, López-González L, Jarillo JA, Piñeiro M. The PHD-containing protein EARLY BOLTING IN SHORT DAYS regulates seed dormancy in Arabidopsis. PLANT, CELL & ENVIRONMENT 2017; 40:2393-2405. [PMID: 28770581 DOI: 10.1111/pce.13046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 07/26/2017] [Accepted: 07/27/2017] [Indexed: 05/20/2023]
Abstract
The Arabidopsis protein EARLY BOLTING IN SHORT DAYS (EBS), a plant-specific transcriptional regulator, is involved in the control of flowering time by repressing the floral integrator FT. The EBS protein binds the H3K4me3 histone mark and interacts with histone deacetylases to modulate gene expression. Here, we show that EBS also participates in the regulation of seed dormancy. ebs mutations cause a reduction in seed dormancy, and the concurrent loss of function of the EBS homologue SHORT LIFE (SHL) enhances this dormancy alteration. Transcriptomic analyses in ebs mutant seeds uncovered the misregulation of several regulators of seed dormancy including the MADS box gene AGAMOUS-LIKE67 (AGL67). AGL67 interacts genetically with EBS in seed dormancy regulation, indicating that both loci act in the same pathway. Interestingly, EBS functions independently of the master regulator gene of dormancy DELAY OF GERMINATION 1 (DOG1) and other genes encoding chromatin remodelling factors involved in the control of seed dormancy. Altogether, these data show that EBS is a central repressor of germination during seed dormancy and that SHL acts redundantly with EBS in the control of this developmental process. Our observations suggest that a tightly regulated crosstalk among histone modifications is necessary for a proper control of seed dormancy.
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Affiliation(s)
- Laura Narro-Diego
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
| | - Leticia López-González
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
| | - Jose A Jarillo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
| | - Manuel Piñeiro
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
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50
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Xiao J, Jin R, Wagner D. Developmental transitions: integrating environmental cues with hormonal signaling in the chromatin landscape in plants. Genome Biol 2017; 18:88. [PMID: 28490341 PMCID: PMC5425979 DOI: 10.1186/s13059-017-1228-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Plant development is predominantly postembryonic and tuned in to respond to environmental cues. All living plant cells can be triggered to de-differentiate, assume different cell identities, or form a new organism. This developmental plasticity is thought to be an adaptation to the sessile lifestyle of plants. Recent discoveries have advanced our understanding of the orchestration of plant developmental switches by transcriptional master regulators, chromatin state changes, and hormone response pathways. Here, we review these recent advances with emphasis on the earliest stages of plant development and on the switch from pluripotency to differentiation in different plant organ systems.
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Affiliation(s)
- Jun Xiao
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Run Jin
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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