1
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Zhang Z, Zeng Y, Hou J, Li L. Advances in understanding the roles of plant HAT and HDAC in non-histone protein acetylation and deacetylation. PLANTA 2024; 260:93. [PMID: 39264431 DOI: 10.1007/s00425-024-04518-8] [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: 06/22/2024] [Accepted: 08/23/2024] [Indexed: 09/13/2024]
Abstract
MAIN CONCLUSION This review focuses on HATs and HDACs that modify non-histone proteins, summarizes functional mechanisms of non-histone acetylation as well as the roles of HATs and HDACs in rice and Arabidopsis. The growth and development of plants, as well as their responses to biotic and abiotic stresses, are governed by intricate gene and protein regulatory networks, in which epigenetic modifying enzymes play a crucial role. Histone lysine acetylation levels, modulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs), are well-studied in the realm of transcriptional regulation. However, the advent of advanced proteomics has unveiled that non-histone proteins also undergo acetylation, with its underlying mechanisms now being clarified. Indeed, non-histone acetylation influences protein functionality through diverse pathways, such as modulating protein stability, adjusting enzymatic activity, steering subcellular localization, influencing interactions with other post-translational modifications, and managing protein-protein and protein-DNA interactions. This review delves into the recent insights into the functional mechanisms of non-histone acetylation in plants. We also provide a summary of the roles of HATs and HDACs in rice and Arabidopsis, and explore their potential involvement in the regulation of non-histone proteins.
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Affiliation(s)
- Zihan Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yan Zeng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jiaqi Hou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| | - Lijia Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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2
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Arce RC, Mayta ML, Melzer M, Hajirezaei MR, Lodeyro AF, Carrillo N. Introduction of a terminal electron sink in chloroplasts decreases leaf cell expansion associated with higher proteasome activity and lower endoreduplication. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4625-4640. [PMID: 38364822 DOI: 10.1093/jxb/erae039] [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: 11/30/2023] [Accepted: 02/13/2024] [Indexed: 02/18/2024]
Abstract
Foliar development involves successive phases of cell proliferation and expansion that determine the final leaf size, and is characterized by an early burst of reactive oxygen species generated in the photosynthetic electron transport chain (PETC). Introduction of the alternative PETC acceptor flavodoxin in tobacco chloroplasts led to a reduction in leaf size associated to lower cell expansion, without affecting cell number per leaf. Proteomic analysis showed that the biogenesis of the PETC proceeded stepwise in wild-type leaves, with accumulation of light-harvesting proteins preceding that of electron transport components, which might explain the increased energy and electron transfer to oxygen and reactive oxygen species build-up at this stage. Flavodoxin expression did not affect biogenesis of the PETC but prevented hydroperoxide formation through its function as electron sink. Mature leaves from flavodoxin-expressing plants were shown to contain higher levels of transcripts encoding components of the proteasome, a key negative modulator of organ size. Proteome profiling revealed that this differential accumulation was initiated during expansion and led to increased proteasomal activity, whereas a proteasome inhibitor reverted the flavodoxin-dependent size phenotype. Cells expressing plastid-targeted flavodoxin displayed lower endoreduplication, also associated to decreased organ size. These results provide novel insights into the regulation of leaf growth by chloroplast-generated redox signals, and highlight the potential of alternative electron shuttles to investigate the link(s) between photosynthesis and plant development.
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Affiliation(s)
- Rocío C Arce
- Instituto de Biología Molecular y Celular de Rosario (IBR-UNR/CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), 2000 Rosario, Argentina
| | - Martín L Mayta
- Instituto de Biología Molecular y Celular de Rosario (IBR-UNR/CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), 2000 Rosario, Argentina
- Centro Interdisciplinario de Investigaciones en Ciencias de la Salud y del Comportamiento (CIICSAC), Facultad de Ciencias de la Salud, Universidad Adventista del Plata, 25 de Mayo 99, E3103XAF, Libertador San Martín, Entre Ríos, Argentina
| | - Michael Melzer
- Leibniz Institute of Plant Genetics and Crop Plant Research, OT Gatersleben, Corrensstrasse, D-06466 Stadt Seeland, Germany
| | - Mohammad-Reza Hajirezaei
- Leibniz Institute of Plant Genetics and Crop Plant Research, OT Gatersleben, Corrensstrasse, D-06466 Stadt Seeland, Germany
| | - Anabella F Lodeyro
- Instituto de Biología Molecular y Celular de Rosario (IBR-UNR/CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), 2000 Rosario, Argentina
| | - Néstor Carrillo
- Instituto de Biología Molecular y Celular de Rosario (IBR-UNR/CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), 2000 Rosario, Argentina
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3
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Wang W, Sung S. Chromatin sensing: integration of environmental signals to reprogram plant development through chromatin regulators. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4332-4345. [PMID: 38436409 PMCID: PMC11263488 DOI: 10.1093/jxb/erae086] [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: 12/19/2023] [Accepted: 02/29/2024] [Indexed: 03/05/2024]
Abstract
Chromatin regulation in eukaryotes plays pivotal roles in controlling the developmental regulatory gene network. This review explores the intricate interplay between chromatin regulators and environmental signals, elucidating their roles in shaping plant development. As sessile organisms, plants have evolved sophisticated mechanisms to perceive and respond to environmental cues, orchestrating developmental programs that ensure adaptability and survival. A central aspect of this dynamic response lies in the modulation of versatile gene regulatory networks, mediated in part by various chromatin regulators. Here, we summarized current understanding of the molecular mechanisms through which chromatin regulators integrate environmental signals, influencing key aspects of plant development.
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Affiliation(s)
- Wenli Wang
- Department of Molecular Biosciences, The University of Texas at Austin, TX 78712, USA
| | - Sibum Sung
- Department of Molecular Biosciences, The University of Texas at Austin, TX 78712, USA
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4
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Boycheva I, Bonchev G, Manova V, Stoilov L, Vassileva V. How Histone Acetyltransferases Shape Plant Photomorphogenesis and UV Response. Int J Mol Sci 2024; 25:7851. [PMID: 39063093 PMCID: PMC11276938 DOI: 10.3390/ijms25147851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
Higher plants have developed complex mechanisms to adapt to fluctuating environmental conditions with light playing a vital role in photosynthesis and influencing various developmental processes, including photomorphogenesis. Exposure to ultraviolet (UV) radiation can cause cellular damage, necessitating effective DNA repair mechanisms. Histone acetyltransferases (HATs) play a crucial role in regulating chromatin structure and gene expression, thereby contributing to the repair mechanisms. HATs facilitate chromatin relaxation, enabling transcriptional activation necessary for plant development and stress responses. The intricate relationship between HATs, light signaling pathways and chromatin dynamics has been increasingly understood, providing valuable insights into plant adaptability. This review explores the role of HATs in plant photomorphogenesis, chromatin remodeling and gene regulation, highlighting the importance of chromatin modifications in plant responses to light and various stressors. It emphasizes the need for further research on individual HAT family members and their interactions with other epigenetic factors. Advanced genomic approaches and genome-editing technologies offer promising avenues for enhancing crop resilience and productivity through targeted manipulation of HAT activities. Understanding these mechanisms is essential for developing strategies to improve plant growth and stress tolerance, contributing to sustainable agriculture in the face of a changing climate.
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Affiliation(s)
| | | | | | | | - Valya Vassileva
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (I.B.); (G.B.); (V.M.); (L.S.)
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5
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Chen Y, Guo P, Dong Z. The role of histone acetylation in transcriptional regulation and seed development. PLANT PHYSIOLOGY 2024; 194:1962-1979. [PMID: 37979164 DOI: 10.1093/plphys/kiad614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/09/2023] [Accepted: 10/29/2023] [Indexed: 11/20/2023]
Abstract
Histone acetylation is highly conserved across eukaryotes and has been linked to gene activation since its discovery nearly 60 years ago. Over the past decades, histone acetylation has been evidenced to play crucial roles in plant development and response to various environmental cues. Emerging data indicate that histone acetylation is one of the defining features of "open chromatin," while the role of histone acetylation in transcription remains controversial. In this review, we briefly describe the discovery of histone acetylation, the mechanism of histone acetylation regulating transcription in yeast and mammals, and summarize the research progress of plant histone acetylation. Furthermore, we also emphasize the effect of histone acetylation on seed development and its potential use in plant breeding. A comprehensive knowledge of histone acetylation might provide new and more flexible research perspectives to enhance crop yield and stress resistance.
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Affiliation(s)
- Yan Chen
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Peiguo Guo
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Zhicheng Dong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
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6
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Abdulraheem MI, Xiong Y, Moshood AY, Cadenas-Pliego G, Zhang H, Hu J. Mechanisms of Plant Epigenetic Regulation in Response to Plant Stress: Recent Discoveries and Implications. PLANTS (BASEL, SWITZERLAND) 2024; 13:163. [PMID: 38256717 PMCID: PMC10820249 DOI: 10.3390/plants13020163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/24/2024]
Abstract
Plant stress is a significant challenge that affects the development, growth, and productivity of plants and causes an adverse environmental condition that disrupts normal physiological processes and hampers plant survival. Epigenetic regulation is a crucial mechanism for plants to respond and adapt to stress. Several studies have investigated the role of DNA methylation (DM), non-coding RNAs, and histone modifications in plant stress responses. However, there are various limitations or challenges in translating the research findings into practical applications. Hence, this review delves into the recent recovery, implications, and applications of epigenetic regulation in response to plant stress. To better understand plant epigenetic regulation under stress, we reviewed recent studies published in the last 5-10 years that made significant contributions, and we analyzed the novel techniques and technologies that have advanced the field, such as next-generation sequencing and genome-wide profiling of epigenetic modifications. We emphasized the breakthrough findings that have uncovered specific genes or pathways and the potential implications of understanding plant epigenetic regulation in response to stress for agriculture, crop improvement, and environmental sustainability. Finally, we concluded that plant epigenetic regulation in response to stress holds immense significance in agriculture, and understanding its mechanisms in stress tolerance can revolutionize crop breeding and genetic engineering strategies, leading to the evolution of stress-tolerant crops and ensuring sustainable food production in the face of climate change and other environmental challenges. Future research in this field will continue to unveil the intricacies of epigenetic regulation and its potential applications in crop improvement.
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Affiliation(s)
- Mukhtar Iderawumi Abdulraheem
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Yani Xiong
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Abiodun Yusuff Moshood
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Gregorio Cadenas-Pliego
- Centro de Investigación en Química Aplicada, Blvd. Enrique Reyna 140, Saltillo 25294, Mexico;
| | - Hao Zhang
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
| | - Jiandong Hu
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
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7
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Bardani E, Kallemi P, Tselika M, Katsarou K, Kalantidis K. Spotlight on Plant Bromodomain Proteins. BIOLOGY 2023; 12:1076. [PMID: 37626962 PMCID: PMC10451976 DOI: 10.3390/biology12081076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 07/28/2023] [Accepted: 07/30/2023] [Indexed: 08/27/2023]
Abstract
Bromodomain-containing proteins (BRD-proteins) are the "readers" of histone lysine acetylation, translating chromatin state into gene expression. They act alone or as components of larger complexes and exhibit diverse functions to regulate gene expression; they participate in chromatin remodeling complexes, mediate histone modifications, serve as scaffolds to recruit transcriptional regulators or act themselves as transcriptional co-activators or repressors. Human BRD-proteins have been extensively studied and have gained interest as potential drug targets for various diseases, whereas in plants, this group of proteins is still not well investigated. In this review, we aimed to concentrate scientific knowledge on these chromatin "readers" with a focus on Arabidopsis. We organized plant BRD-proteins into groups based on their functions and domain architecture and summarized the published work regarding their interactions, activity and diverse functions. Overall, it seems that plant BRD-proteins are indispensable components and fine-tuners of the complex network plants have built to regulate development, flowering, hormone signaling and response to various biotic or abiotic stresses. This work will facilitate the understanding of their roles in plants and highlight BRD-proteins with yet undiscovered functions.
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Affiliation(s)
- Eirini Bardani
- Department of Biology, University of Crete, Voutes University Campus, 71500 Heraklion, Greece; (E.B.); (P.K.); (M.T.)
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013 Heraklion, Greece
| | - Paraskevi Kallemi
- Department of Biology, University of Crete, Voutes University Campus, 71500 Heraklion, Greece; (E.B.); (P.K.); (M.T.)
| | - Martha Tselika
- Department of Biology, University of Crete, Voutes University Campus, 71500 Heraklion, Greece; (E.B.); (P.K.); (M.T.)
| | - Konstantina Katsarou
- Department of Biology, University of Crete, Voutes University Campus, 71500 Heraklion, Greece; (E.B.); (P.K.); (M.T.)
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013 Heraklion, Greece
| | - Kriton Kalantidis
- Department of Biology, University of Crete, Voutes University Campus, 71500 Heraklion, Greece; (E.B.); (P.K.); (M.T.)
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013 Heraklion, Greece
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8
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Nunez-Vazquez R, Desvoyes B, Gutierrez C. Histone variants and modifications during abiotic stress response. FRONTIERS IN PLANT SCIENCE 2022; 13:984702. [PMID: 36589114 PMCID: PMC9797984 DOI: 10.3389/fpls.2022.984702] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 09/28/2022] [Indexed: 06/17/2023]
Abstract
Plants have developed multiple mechanisms as an adaptive response to abiotic stresses, such as salinity, drought, heat, cold, and oxidative stress. Understanding these regulatory networks is critical for coping with the negative impact of abiotic stress on crop productivity worldwide and, eventually, for the rational design of strategies to improve plant performance. Plant alterations upon stress are driven by changes in transcriptional regulation, which rely on locus-specific changes in chromatin accessibility. This process encompasses post-translational modifications of histone proteins that alter the DNA-histones binding, the exchange of canonical histones by variants that modify chromatin conformation, and DNA methylation, which has an implication in the silencing and activation of hypervariable genes. Here, we review the current understanding of the role of the major epigenetic modifications during the abiotic stress response and discuss the intricate relationship among them.
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Affiliation(s)
| | - Bénédicte Desvoyes
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Programa de Dinámica y Función del Genoma, Madrid, Spain
| | - Crisanto Gutierrez
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Programa de Dinámica y Función del Genoma, Madrid, Spain
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9
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Onosato H, Fujimoto G, Higami T, Sakamoto T, Yamada A, Suzuki T, Ozawa R, Matsunaga S, Seki M, Ueda M, Sako K, Galis I, Arimura GI. Sustained defense response via volatile signaling and its epigenetic transcriptional regulation. PLANT PHYSIOLOGY 2022; 189:922-933. [PMID: 35201346 PMCID: PMC9157098 DOI: 10.1093/plphys/kiac077] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/29/2022] [Indexed: 05/11/2023]
Abstract
Plants perceive volatiles emitted from herbivore-damaged neighboring plants to urgently adapt or prime their defense responses to prepare for forthcoming herbivores. Mechanistically, these volatiles can induce epigenetic regulation based on histone modifications that alter the transcriptional status of defense genes, but little is known about the underlying mechanisms. To understand the roles of such epigenetic regulation of plant volatile signaling, we explored the response of Arabidopsis (Arabidopsis thaliana) plants to the volatile β-ocimene. Defense traits of Arabidopsis plants toward larvae of Spodoptera litura were induced in response to β-ocimene, through enriched histone acetylation and elevated transcriptional levels of defense gene regulators, including ethylene response factor genes (ERF8 and ERF104) in leaves. The enhanced defense ability of the plants was maintained for 5 d but not over 10 d after exposure to β-ocimene, and this coincided with elevated expression of those ERFs in their leaves. An array of histone acetyltransferases, including HAC1, HAC5, and HAM1, were responsible for the induction and maintenance of the anti-herbivore property. HDA6, a histone deacetylase, played a role in the reverse histone remodeling. Collectively, our findings illuminate the role of epigenetic regulation in plant volatile signaling.
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Affiliation(s)
- Haruki Onosato
- Department of Biological Science and Technology, Faculty of Advanced Engineering, Tokyo University of Science, Tokyo 125-8585, Japan
| | - Genya Fujimoto
- Department of Biological Science and Technology, Faculty of Advanced Engineering, Tokyo University of Science, Tokyo 125-8585, Japan
| | - Tomota Higami
- Department of Biological Science and Technology, Faculty of Advanced Engineering, Tokyo University of Science, Tokyo 125-8585, Japan
| | - Takuya Sakamoto
- Department of Applied Biological Science, Graduate School of Science and Technology, Tokyo University of Science, Noda 278-8510, Japan
| | - Ayaka Yamada
- Department of Biological Science and Technology, Faculty of Advanced Engineering, Tokyo University of Science, Tokyo 125-8585, Japan
| | - Takamasa Suzuki
- College of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Japan
| | - Rika Ozawa
- Center for Ecological Research, Kyoto University, Otsu 520-2113, Japan
| | - Sachihiro Matsunaga
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8562, Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, Wako 351-0198, Japan
| | - Minoru Ueda
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
| | - Kaori Sako
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, Wako 351-0198, Japan
| | - Ivan Galis
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
| | - Gen-ichiro Arimura
- Department of Biological Science and Technology, Faculty of Advanced Engineering, Tokyo University of Science, Tokyo 125-8585, Japan
- Author for correspondence:
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10
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Guarino F, Cicatelli A, Castiglione S, Agius DR, Orhun GE, Fragkostefanakis S, Leclercq J, Dobránszki J, Kaiserli E, Lieberman-Lazarovich M, Sõmera M, Sarmiento C, Vettori C, Paffetti D, Poma AMG, Moschou PN, Gašparović M, Yousefi S, Vergata C, Berger MMJ, Gallusci P, Miladinović D, Martinelli F. An Epigenetic Alphabet of Crop Adaptation to Climate Change. Front Genet 2022; 13:818727. [PMID: 35251130 PMCID: PMC8888914 DOI: 10.3389/fgene.2022.818727] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/28/2022] [Indexed: 01/10/2023] Open
Abstract
Crop adaptation to climate change is in a part attributed to epigenetic mechanisms which are related to response to abiotic and biotic stresses. Although recent studies increased our knowledge on the nature of these mechanisms, epigenetics remains under-investigated and still poorly understood in many, especially non-model, plants, Epigenetic modifications are traditionally divided into two main groups, DNA methylation and histone modifications that lead to chromatin remodeling and the regulation of genome functioning. In this review, we outline the most recent and interesting findings on crop epigenetic responses to the environmental cues that are most relevant to climate change. In addition, we discuss a speculative point of view, in which we try to decipher the “epigenetic alphabet” that underlies crop adaptation mechanisms to climate change. The understanding of these mechanisms will pave the way to new strategies to design and implement the next generation of cultivars with a broad range of tolerance/resistance to stresses as well as balanced agronomic traits, with a limited loss of (epi)genetic variability.
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Affiliation(s)
- Francesco Guarino
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università Degli Studi di Salerno, Salerno, Italy
| | - Angela Cicatelli
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università Degli Studi di Salerno, Salerno, Italy
| | - Stefano Castiglione
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università Degli Studi di Salerno, Salerno, Italy
| | - Dolores R. Agius
- Centre of Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Gul Ebru Orhun
- Bayramic Vocational College, Canakkale Onsekiz Mart University, Canakkale, Turkey
| | | | - Julie Leclercq
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Institut Agro, Montpellier, France
| | - Judit Dobránszki
- Centre for Agricultural Genomics and Biotechnology, FAFSEM, University of Debrecen, Debrecen, Hungary
| | - Eirini Kaiserli
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Merike Sõmera
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Cecilia Sarmiento
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Cristina Vettori
- Institute of Biosciences and Bioresources (IBBR), National Research Council (CNR), Sesto Fiorentino, Italy
| | - Donatella Paffetti
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Florence, Italy
| | - Anna M. G. Poma
- Department of Clinical Medicine, Public Health, Life and Environmental Sciences, University of L’Aquila, Aquila, Italy
| | - Panagiotis N. Moschou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas, Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Greece
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Mateo Gašparović
- Chair of Photogrammetry and Remote Sensing, Faculty of Geodesy, University of Zagreb, Zagreb, Croatia
| | - Sanaz Yousefi
- Department of Horticultural Science, Bu-Ali Sina University, Hamedan, Iran
| | - Chiara Vergata
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Margot M. J. Berger
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, Bordeaux, France
| | - Philippe Gallusci
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, Bordeaux, France
| | - Dragana Miladinović
- Institute of Field and Vegetable Crops, National Institute of Republic of Serbia, Novi Sad, Serbia
- *Correspondence: Dragana Miladinović, ; Federico Martinelli,
| | - Federico Martinelli
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
- *Correspondence: Dragana Miladinović, ; Federico Martinelli,
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11
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Ojeda-Martinez D, Diaz I, Santamaria ME. Transcriptomic Landscape of Herbivore Oviposition in Arabidopsis: A Systematic Review. FRONTIERS IN PLANT SCIENCE 2022; 12:772492. [PMID: 35126411 PMCID: PMC8815302 DOI: 10.3389/fpls.2021.772492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
Herbivore oviposition produces all sorts of responses in plants, involving wide and complex genetic rearrangements. Many transcriptomic studies have been performed to understand this interaction, producing a bulk of transcriptomic data. However, the use of many transcriptomic techniques across the years, the lack of comparable transcriptomic context at the time of publication, and the use of outdated databases are limitations to understand this biological process. The current analysis intends to retrieve oviposition studies and process them with up-to-date techniques and updated databases. To reduce heterogeneities, the same processing techniques were applied, and Arabidopsis was selected to avoid divergencies on plant taxa stress response strategies. By doing so, we intended to understand the major mechanisms and regulatory processes linked to oviposition response. Differentially expressed gene (DEG) identification and co-expression network-based analyses were the main tools to achieve this goal. Two microarray studies and three RNA-seq analyses passed the screening criteria. The collected data pertained to the lepidopteran Pieris brassicae and the mite Tetranychus urticae, and covered a timeline from 3 to 144 h. Among the 18, 221 DEGs found, 15, 406 were exclusive of P. brassicae (72 h) and 801 were exclusive for the rest of the experiments. Excluding P. brassicae (72 h), shared genes on the rest of the experiments were twice the unique genes, indicating common response mechanisms were predominant. Enrichment analyses indicated that shared processes were circumscribed to earlier time points, and after 24 h, the divergences escalated. The response was characterized by patterns of time-dependent waves of unique processes. P. brassicae oviposition induced a rich response that shared functions across time points, while T. urticae eggs triggered less but more diverse time-dependent functions. The main processes altered were associated with hormonal cascades [e.g., salicilic acid (SA) and jasmonic acid (JA)], defense [reactive oxygen species (ROS) and glucosinolates], cell wall rearrangements, abiotic stress responses, and energy metabolism. Key gene drivers of the identified processes were also identified and presented. The current results enrich and clarify the information regarding the molecular behavior of the plant in response to oviposition by herbivores. This information is valuable for multiple stress response engineering tools, among other applications.
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Affiliation(s)
- Dairon Ojeda-Martinez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid – Instituto Nacional de Investigación y Tecnología Agraria y Alimentación, Madrid, Spain
| | - Isabel Diaz
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid – Instituto Nacional de Investigación y Tecnología Agraria y Alimentación, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - M. Estrella Santamaria
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid – Instituto Nacional de Investigación y Tecnología Agraria y Alimentación, Madrid, Spain
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12
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Wang Y, Huang C, Zeng W, Zhang T, Zhong C, Deng S, Tang T. Epigenetic and transcriptional responses underlying mangrove adaptation to UV-B. iScience 2021; 24:103148. [PMID: 34646986 PMCID: PMC8496181 DOI: 10.1016/j.isci.2021.103148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/31/2021] [Accepted: 09/15/2021] [Indexed: 12/02/2022] Open
Abstract
Tropical plants have adapted to strong solar ultraviolet (UV) radiation. Here we compare molecular responses of two tropical mangroves Avecennia marina and Rhizophora apiculata to high-dose UV-B. Whole-genome bisulfate sequencing indicates that high UV-B induced comparable hyper- or hypo-methylation in three sequence contexts (CG, CHG, and CHH, where H refers to A, T, or C) in A. marina but mainly CHG hypomethylation in R. apiculata. RNA and small RNA sequencing reveals UV-B induced relaxation of transposable element (TE) silencing together with up-regulation of TE-adjacent genes in R. apiculata but not in A. marina. Despite conserved upregulation of flavonoid biosynthesis and downregulation of photosynthesis genes caused by high UV-B, A. marina specifically upregulated ABC transporter and ubiquinone biosynthesis genes that are known to be protective against UV-B-induced damage. Our results point to divergent responses underlying plant UV-B adaptation at both the epigenetic and transcriptional level.
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Affiliation(s)
- Yushuai Wang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, People’s Republic of China
| | - Chenglong Huang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, People’s Republic of China
| | - Weishun Zeng
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, People’s Republic of China
| | - Tianyuan Zhang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, People’s Republic of China
| | - Cairong Zhong
- Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou 571100, Hainan, People’s Republic of China
| | - Shulin Deng
- CAS 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 510650, People’s Republic of China
- Xiaoliang Research Station for Tropical Coastal Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, People’s Republic of China
| | - Tian Tang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, People’s Republic of China
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13
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Jiang J, Ding AB, Liu F, Zhong X. Linking signaling pathways to histone acetylation dynamics in plants. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5179-5190. [PMID: 32333777 PMCID: PMC7475247 DOI: 10.1093/jxb/eraa202] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 04/22/2020] [Indexed: 05/04/2023]
Abstract
As sessile organisms, plants face versatile environmental challenges and require proper responses at multiple levels for survival. Epigenetic modification of DNA and histones is a conserved gene-regulatory mechanism and plays critical roles in diverse aspects of biological processes, ranging from genome defense and imprinting to development and physiology. In recent years, emerging studies have revealed the interplay between signaling transduction pathways, epigenetic modifications, and chromatin cascades. Specifically, histone acetylation and deacetylation dictate plant responses to environmental cues by modulating chromatin dynamics to regulate downstream gene expression as signaling outputs. In this review, we summarize current understandings of the link between plant signaling pathways and epigenetic modifications with a focus on histone acetylation and deacetylation.
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Affiliation(s)
- Jianjun Jiang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, Jiangsu, China
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - Adeline B Ding
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - Fengquan Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, Jiangsu, China
- Correspondence: or
| | - Xuehua Zhong
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
- Correspondence: or
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14
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Leng X, Thomas Q, Rasmussen SH, Marquardt S. A G(enomic)P(ositioning)S(ystem) for Plant RNAPII Transcription. TRENDS IN PLANT SCIENCE 2020; 25:744-764. [PMID: 32673579 DOI: 10.1016/j.tplants.2020.03.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/24/2020] [Accepted: 03/10/2020] [Indexed: 06/11/2023]
Abstract
Post-translational modifications (PTMs) of histone residues shape the landscape of gene expression by modulating the dynamic process of RNA polymerase II (RNAPII) transcription. The contribution of particular histone modifications to the definition of distinct RNAPII transcription stages remains poorly characterized in plants. Chromatin immunoprecipitation combined with next-generation sequencing (ChIP-seq) resolves the genomic distribution of histone modifications. Here, we review histone PTM ChIP-seq data in Arabidopsis thaliana and find support for a Genomic Positioning System (GPS) that guides RNAPII transcription. We review the roles of histone PTM 'readers', 'writers', and 'erasers', with a focus on the regulation of gene expression and biological functions in plants. The distinct functions of RNAPII transcription during the plant transcription cycle may rely, in part, on the characteristic histone PTM profiles that distinguish transcription stages.
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Affiliation(s)
- Xueyuan Leng
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Bülowsvej 34, 1870 Frederiksberg C, Denmark
| | - Quentin Thomas
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Bülowsvej 34, 1870 Frederiksberg C, Denmark
| | - Simon Horskjær Rasmussen
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Bülowsvej 34, 1870 Frederiksberg C, Denmark
| | - Sebastian Marquardt
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Bülowsvej 34, 1870 Frederiksberg C, Denmark.
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15
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Kim JH. Chromatin Remodeling and Epigenetic Regulation in Plant DNA Damage Repair. Int J Mol Sci 2019; 20:ijms20174093. [PMID: 31443358 PMCID: PMC6747262 DOI: 10.3390/ijms20174093] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 12/19/2022] Open
Abstract
DNA damage response (DDR) in eukaryotic cells is initiated in the chromatin context. DNA damage and repair depend on or have influence on the chromatin dynamics associated with genome stability. Epigenetic modifiers, such as chromatin remodelers, histone modifiers, DNA (de-)methylation enzymes, and noncoding RNAs regulate DDR signaling and DNA repair by affecting chromatin dynamics. In recent years, significant progress has been made in the understanding of plant DDR and DNA repair. SUPPRESSOR OF GAMMA RESPONSE1, RETINOBLASTOMA RELATED1 (RBR1)/E2FA, and NAC103 have been proven to be key players in the mediation of DDR signaling in plants, while plant-specific chromatin remodelers, such as DECREASED DNA METHYLATION1, contribute to chromatin dynamics for DNA repair. There is accumulating evidence that plant epigenetic modifiers are involved in DDR and DNA repair. In this review, I examine how DDR and DNA repair machineries are concertedly regulated in Arabidopsis thaliana by a variety of epigenetic modifiers directing chromatin remodeling and epigenetic modification. This review will aid in updating our knowledge on DDR and DNA repair in plants.
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Affiliation(s)
- Jin-Hong Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do 56212, Korea.
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16
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Zhang R, Huang G, Wang L, Zhou Q, Huang X. Effects of elevated ultraviolet-B radiation on root growth and chemical signaling molecules in plants. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 171:683-690. [PMID: 30658304 DOI: 10.1016/j.ecoenv.2019.01.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 12/26/2018] [Accepted: 01/09/2019] [Indexed: 05/13/2023]
Abstract
Ozone layer depletion leads to elevated ultraviolet-B (UV-B) radiation, which affects plant growth; however, little is known about the relationship between root growth and signaling molecules in roots. Therefore, in this work, simulated UV-B radiation was used to study the effects of elevated UV-B radiation on root growth of soybean seedlings and changes in the content of signaling molecules in roots. The results showed that compared with the control, the 2.63 kJ m-2 d-1 and 6.17 kJ m-2 d-1 elevated UV-B radiation treatments inhibited root growth, and root growth parameters (total root length, root surface area, root volume, average diameter, root tip number, and root dry weight) all decreased. For root signaling molecules, the content of nitric oxide, reactive oxygen species, abscisic acid, salicylic acid, and jasmonic acid increased, and the content of auxin, cytokinin, and gibberellin decreased. The above indices changed more significantly under the 6.17 kJ m-2 d-1 treatment. After withdrawal of the exposure, the above indices could be restored to a certain extent. These data indicated that UV-B radiation interfered with root growth by affecting the content of signaling molecules in roots, and the degree of the effects was related to the intensity of UV-B radiation. The results from this study provide a theoretical basis for studying the preliminary mechanism of elevated UV-B radiation on root growth and possible pathways that can mitigate UV-B radiation damage for root growth. ONE SENTENCE SUMMARY: The effects of elevated UV-B on root growth of soybean seedlings were regulated by signaling molecules, and the degree of the effects was related to the intensity of UV-B radiation.
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Affiliation(s)
- Rutao Zhang
- State Key Laboratory of Food Science and Technology, Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Guangrong Huang
- State Key Laboratory of Food Science and Technology, Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Lihong Wang
- State Key Laboratory of Food Science and Technology, Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Qing Zhou
- State Key Laboratory of Food Science and Technology, Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Cooperative Innovation Center of Water Treatment Technology and Materials, Suzhou University of Science and Technology, Suzhou 215009, China.
| | - Xiaohua Huang
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of Biomedical Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210046, China.
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17
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Gómez MS, Falcone Ferreyra ML, Sheridan ML, Casati P. Arabidopsis E2Fc is required for the DNA damage response under UV-B radiation epistatically over the microRNA396 and independently of E2Fe. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:749-764. [PMID: 30427087 DOI: 10.1111/tpj.14158] [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: 10/02/2018] [Revised: 10/25/2018] [Accepted: 11/02/2018] [Indexed: 05/17/2023]
Abstract
UV-B radiation inhibits plant growth, and this inhibition is, to a certain extent, regulated by miR396-mediated repression of Growth Regulating Transcription factors (GRFs). Moreover, E2Fe transcription factor also modulates Arabidopsis leaf growth. Here, we provide evidence that, at UV-B intensities that induce DNA damage, E2Fc participates in the inhibition of cell proliferation. We demonstrate that E2Fc-deficient plants show a lower inhibition of leaf size under UV-B conditions that damage DNA, decreased cell death after exposure and altered SOG1 and ATR expression. Interestingly, the previously reported participation of E2Fe in UV-B responses, which is a transcriptional target of E2Fc, is independent and different from that described for E2Fc. Conversely, we here demonstrate that E2Fc has an epistatic role over the miR396 pathway under UV-B conditions. Finally, we show that inhibition of cell proliferation by UV-B is independent of the regulation of class II TCP transcription factors. Together, our results demonstrate that E2Fc is required for miR396 activity on cell proliferation under UV-B, and that its role is independent of E2Fe, probably modulating DNA damage responses through the regulation of SOG1 and ATR transcript levels.
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Affiliation(s)
- María S Gómez
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - María L Falcone Ferreyra
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - María L Sheridan
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Paula Casati
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
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18
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Du S, Chen L, Ge L, Huang W. A Novel Loop: Mutual Regulation Between Epigenetic Modification and the Circadian Clock. FRONTIERS IN PLANT SCIENCE 2019; 10:22. [PMID: 30761168 PMCID: PMC6362098 DOI: 10.3389/fpls.2019.00022] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/08/2019] [Indexed: 05/26/2023]
Abstract
In response to periodic environmental fluctuations generated by the rotation of the earth, nearly all organisms have evolved an intrinsic timekeeper, the circadian clock, which can maintain approximate 24-h rhythmic oscillations in biological processes, ultimately conferring fitness benefits. In the model plant Arabidopsis, the core mechanics of the circadian clock can be described as a complex regulatory network of three feedback loops composed of core oscillator genes. Transcriptional regulation of each oscillator gene is necessary to maintain the structure of the circadian clock. As a gene transcription regulatory mechanism, the epigenetic modification of chromatin affects the spatiotemporal expression of multiple genes. Accumulating evidence indicates that epigenetic modification is associated with circadian clock function in animals and plants. In addition, the rhythms of epigenetic modification have a significant influence on the timing of molecular processes, including gene transcription. In this review, we summarize recent progress in research on the roles of histone acetylation, methylation, and phosphorylation in the regulation of clock gene expression in Arabidopsis.
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Affiliation(s)
- Shenxiu Du
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Liang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Liangfa Ge
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Wei Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
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19
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Bourbousse C, Barneche F, Laloi C. Plant Chromatin Catches the Sun. FRONTIERS IN PLANT SCIENCE 2019; 10:1728. [PMID: 32038692 PMCID: PMC6992579 DOI: 10.3389/fpls.2019.01728] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 12/09/2019] [Indexed: 05/08/2023]
Abstract
Plants use solar radiation as energy source for photosynthesis. They also take advantage of the information provided by the varying properties of sunlight, such as wavelength, orientation, and periodicity, to trigger physiological and developmental adaptations to a changing environment. After more than a century of research efforts in plant photobiology, multiple light signaling pathways converging onto chromatin-based mechanisms have now been identified, which in some instances play critical roles in plant phenotypic plasticity. In addition to locus-specific changes linked to transcription regulation, light signals impact higher-order chromatin organization. Here, we summarize current knowledge on how light can affect the global composition and the spatial distribution of chromatin domains. We introduce emerging questions on the functional links between light signaling and the epigenome, and further discuss how different chromatin regulatory layers may interconnect during plant adaptive responses to light.
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Affiliation(s)
- Clara Bourbousse
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- *Correspondence: Clara Bourbousse, ; Fredy Barneche,
| | - Fredy Barneche
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- *Correspondence: Clara Bourbousse, ; Fredy Barneche,
| | - Christophe Laloi
- Aix Marseille Univ, CEA, CNRS, BIAM, Luminy Génétique et Biophysique des Plantes, Marseille, France
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20
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Nisa MU, Huang Y, Benhamed M, Raynaud C. The Plant DNA Damage Response: Signaling Pathways Leading to Growth Inhibition and Putative Role in Response to Stress Conditions. FRONTIERS IN PLANT SCIENCE 2019; 10:653. [PMID: 31164899 PMCID: PMC6534066 DOI: 10.3389/fpls.2019.00653] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 04/30/2019] [Indexed: 05/02/2023]
Abstract
Maintenance of genome integrity is a key issue for all living organisms. Cells are constantly exposed to DNA damage due to replication or transcription, cellular metabolic activities leading to the production of Reactive Oxygen Species (ROS) or even exposure to DNA damaging agents such as UV light. However, genomes remain extremely stable, thanks to the permanent repair of DNA lesions. One key mechanism contributing to genome stability is the DNA Damage Response (DDR) that activates DNA repair pathways, and in the case of proliferating cells, stops cell division until DNA repair is complete. The signaling mechanisms of the DDR are quite well conserved between organisms including in plants where they have been investigated into detail over the past 20 years. In this review we summarize the acquired knowledge and recent advances regarding the DDR control of cell cycle progression. Studying the plant DDR is particularly interesting because of their mode of development and lifestyle. Indeed, plants develop largely post-embryonically, and form new organs through the activity of meristems in which cells retain the ability to proliferate. In addition, they are sessile organisms that are permanently exposed to adverse conditions that could potentially induce DNA damage in all cell types including meristems. In the second part of the review we discuss the recent findings connecting the plant DDR to responses to biotic and abiotic stresses.
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21
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Pfab A, Bruckmann A, Nazet J, Merkl R, Grasser KD. The Adaptor Protein ENY2 Is a Component of the Deubiquitination Module of the Arabidopsis SAGA Transcriptional Co-activator Complex but not of the TREX-2 Complex. J Mol Biol 2018; 430:1479-1494. [PMID: 29588169 DOI: 10.1016/j.jmb.2018.03.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 03/20/2018] [Accepted: 03/20/2018] [Indexed: 12/26/2022]
Abstract
The conserved nuclear protein ENY2 (Sus1 in yeast) is involved in coupling transcription and mRNA export in yeast and metazoa, as it is a component both of the transcriptional co-activator complex SAGA and of the mRNA export complex TREX-2. Arabidopsis thaliana ENY2 is widely expressed in the plant and it localizes to the nucleoplasm, but unlike its yeast/metazoan orthologs, it is not enriched in the nuclear envelope. Affinity purification of ENY2 in combination with mass spectrometry revealed that it co-purified with SAGA components, but not with the nuclear pore-associated TREX-2. In addition, further targeted proteomics analyses by reciprocal tagging established the composition of the Arabidopsis SAGA complex consisting of the four modules HATm, SPTm, TAFm and DUBm, and that several SAGA subunits occur in alternative variants. While the HATm, SPTm and TAFm robustly co-purified with each other, the deubiquitination module (DUBm) appears to associate with the other SAGA modules more weakly/dynamically. Consistent with a homology model of the Arabidopsis DUBm, the SGF11 protein interacts directly with ENY2 and UBP22. Plants depleted in the DUBm components, SGF11 or ENY2, are phenotypically only mildly affected, but they contain increased levels of ubiquitinated histone H2B, indicating that the SAGA-DUBm has histone deubiquitination activity in plants. In addition to transcription-related proteins (i.e., transcript elongation factors, Mediator), many splicing factors were found to associate with SAGA, linking the SAGA complex and ongoing transcription with mRNA processing.
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Affiliation(s)
- Alexander Pfab
- Department of Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Astrid Bruckmann
- Department for Biochemistry I, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Julian Nazet
- Department for Biochemistry II, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Rainer Merkl
- Department for Biochemistry II, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Klaus D Grasser
- Department of Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany.
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