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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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2
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Wang F, Li CH, Liu Y, He LF, Li P, Guo JX, Zhang N, Zhao B, Guo YD. Plant responses to abiotic stress regulated by histone acetylation. FRONTIERS IN PLANT SCIENCE 2024; 15:1404977. [PMID: 39081527 PMCID: PMC11286584 DOI: 10.3389/fpls.2024.1404977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 07/01/2024] [Indexed: 08/02/2024]
Abstract
In eukaryotes, histone acetylation and deacetylation play an important role in the regulation of gene expression. Histone acetylation levels are reversibly regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs). Increasing evidence highlights histone acetylation plays essential roles in the regulation of gene expression in plant response to environmental stress. In this review, we discussed the recent advance of histone acetylation in the regulation of abiotic stress responses including temperature, light, salt and drought stress. This information will contribute to our understanding of how plants adapt to environmental changes. As the mechanisms of epigenetic regulation are conserved in many plants, research in this field has potential applications in improvement of agricultural productivity.
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Affiliation(s)
- Fei Wang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Chong-Hua Li
- College of Horticulture, China Agricultural University, Beijing, China
| | - Ying Liu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Ling-Feng He
- College of Horticulture, China Agricultural University, Beijing, China
| | - Ping Li
- College of Horticulture, China Agricultural University, Beijing, China
| | - Jun-Xin Guo
- College of Horticulture, China Agricultural University, Beijing, China
| | - Na Zhang
- College of Horticulture, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Sanya, China
| | - Bing Zhao
- College of Horticulture, China Agricultural University, Beijing, China
| | - Yang-Dong Guo
- College of Horticulture, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Sanya, China
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3
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Huq E, Lin C, Quail PH. Light signaling in plants-a selective history. PLANT PHYSIOLOGY 2024; 195:213-231. [PMID: 38431282 PMCID: PMC11060691 DOI: 10.1093/plphys/kiae110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/15/2023] [Accepted: 02/16/2024] [Indexed: 03/05/2024]
Abstract
In addition to providing the radiant energy that drives photosynthesis, sunlight carries signals that enable plants to grow, develop and adapt optimally to the prevailing environment. Here we trace the path of research that has led to our current understanding of the cellular and molecular mechanisms underlying the plant's capacity to perceive and transduce these signals into appropriate growth and developmental responses. Because a fully comprehensive review was not possible, we have restricted our coverage to the phytochrome and cryptochrome classes of photosensory receptors, while recognizing that the phototropin and UV classes also contribute importantly to the full scope of light-signal monitoring by the plant.
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Affiliation(s)
- Enamul Huq
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Chentao Lin
- Basic Forestry and Plant Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Peter H Quail
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Plant Gene Expression Center, Agricultural Research Service, US Department of Agriculture, Albany, CA 94710, USA
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4
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Wang W, Kim J, Martinez TS, Huq E, Sung S. COP1 controls light-dependent chromatin remodeling. Proc Natl Acad Sci U S A 2024; 121:e2312853121. [PMID: 38349881 PMCID: PMC10895365 DOI: 10.1073/pnas.2312853121] [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: 07/26/2023] [Accepted: 01/03/2024] [Indexed: 02/15/2024] Open
Abstract
Light is a crucial environmental factor that impacts various aspects of plant development. Phytochromes, as light sensors, regulate myriads of downstream genes to mediate developmental reprogramming in response to changes in environmental conditions. CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) is an E3 ligase for a number of substrates in light signaling, acting as a central repressor of photomorphogenesis. The interplay between phytochrome B (phyB) and COP1 forms an antagonistic regulatory module that triggers extensive gene expression reprogramming when exposed to light. Here, we uncover a role of COP1 in light-dependent chromatin remodeling through the regulation of VIL1 (VIN3-LIKE 1)/VERNALIZATION 5, a Polycomb protein. VIL1 directly interacts with phyB and regulates photomorphogenesis through the formation of repressive chromatin loops at downstream growth-promoting genes in response to light. Furthermore, we reveal that COP1 governs light-dependent formation of chromatin loop and limiting a repressive histone modification to fine-tune expressions of growth-promoting genes during photomorphogenesis through VIL1.
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Affiliation(s)
- Wenli Wang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Junghyun Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Teresa S Martinez
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Enamul Huq
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Sibum Sung
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
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Xue Q, Yang Y, Li H, Li X, Zou L, Li T, Ma H, Qi H, Wang J, Yu T. Functions and mechanisms of protein lysine butyrylation (Kbu): Therapeutic implications in human diseases. Genes Dis 2023; 10:2479-2490. [PMID: 37554202 PMCID: PMC10404885 DOI: 10.1016/j.gendis.2022.10.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 09/27/2022] [Accepted: 10/20/2022] [Indexed: 11/30/2022] Open
Abstract
Post-translational modifications (PTM) are covalent modifications of proteins or peptides caused by proteolytic cleavage or the attachment of moieties to one or more amino acids. PTMs play essential roles in biological function and regulation and have been linked with several diseases. Modifications of protein acylation (Kac), a type of PTM, are known to induce epigenetic regulatory processes that promote various diseases. Thus, an increasing number of studies focusing on acylation modifications are being undertaken. Butyrylation (Kbu) is a new acylation process found in animals and plants. Kbu has been recently linked to the onset and progression of several diseases, such as cancer, cardiovascular diseases, diabetes, and vascular dementia. Moreover, the mode of action of certain drugs used in the treatment of lymphoma and colon cancer is based on the regulation of butyrylation levels, suggesting that butyrylation may play a therapeutic role in these diseases. In addition, butyrylation is also commonly involved in rice gene expression and thus plays an important role in the growth, development, and metabolism of rice. The tools and analytical methods that could be utilized for the prediction and detection of lysine butyrylation have also been investigated. This study reviews the potential role of histone Kbu, as well as the mechanisms underlying this process. It also summarizes various enzymes and analytical methods associated with Kbu, with the goal of providing new insights into the role of Kbu in gene regulation and diseases.
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Affiliation(s)
- Qianqian Xue
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, China
| | - Yanyan Yang
- Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, Shandong 266021, China
| | - Hong Li
- Clinical Laboratory, Central Laboratory. The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, Shandong 266000, China
| | - Xiaoxin Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, China
| | - Lu Zou
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, China
| | - Tianxiang Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, China
| | - Huibo Ma
- Department of Vascular Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, China
| | - Hongzhao Qi
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, China
| | - Jianxun Wang
- Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, Shandong 266021, China
| | - Tao Yu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, China
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, China
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Lee SW, Choi D, Moon H, Kim S, Kang H, Paik I, Huq E, Kim DH. PHYTOCHROME-INTERACTING FACTORS are involved in starch degradation adjustment via inhibition of the carbon metabolic regulator QUA-QUINE STARCH in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:110-123. [PMID: 36710626 DOI: 10.1111/tpj.16124] [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: 04/27/2021] [Revised: 01/19/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
As sessile organisms, plants encounter dynamic and challenging environments daily, including abiotic/biotic stresses. The regulation of carbon and nitrogen allocations for the synthesis of plant proteins, carbohydrates, and lipids is fundamental for plant growth and adaption to its surroundings. Light, one of the essential environmental signals, exerts a substantial impact on plant metabolism and resource partitioning (i.e., starch). However, it is not fully understood how light signaling affects carbohydrate production and allocation in plant growth and development. An orphan gene unique to Arabidopsis thaliana, named QUA-QUINE STARCH (QQS) is involved in the metabolic processes for partitioning of carbon and nitrogen among proteins and carbohydrates, thus influencing leaf, seed composition, and plant defense in Arabidopsis. In this study, we show that PHYTOCHROME-INTERACTING bHLH TRANSCRIPTION FACTORS (PIFs), including PIF4, are required to suppress QQS during the period at dawn, thus preventing overconsumption of starch reserves. QQS expression is significantly de-repressed in pif4 and pifQ, while repressed by overexpression of PIF4, suggesting that PIF4 and its close homologs (PIF1, PIF3, and PIF5) act as negative regulators of QQS expression. In addition, we show that the evening complex, including ELF3 is required for active expression of QQS, thus playing a positive role in starch catabolism during night-time. Furthermore, QQS is epigenetically suppressed by DNA methylation machinery, whereas histone H3 K4 methyltransferases (e.g., ATX1, ATX2, and ATXR7) and H3 acetyltransferases (e.g., HAC1 and HAC5) are involved in the expression of QQS. This study demonstrates that PIF light signaling factors help plants utilize optimal amounts of starch during the night and prevent overconsumption of starch before its biosynthesis during the upcoming day.
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Affiliation(s)
- Sang Woo Lee
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Dasom Choi
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Heewon Moon
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Sujeong Kim
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Hajeong Kang
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Inyup Paik
- Department of Molecular Biosciences, the University of Texas at Austin, Texas, 78712, USA
| | - Enamul Huq
- Department of Molecular Biosciences, the University of Texas at Austin, Texas, 78712, USA
| | - Dong-Hwan Kim
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
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Zhang L, Wu J, Liang J, Lin R, Sun C, Dai Q, Zhang L, Guo H, Zhao R, Wang X. Conserved noncoding sequences correlate with distant gene contacts in Arabidopsis and Brassica. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023. [PMID: 36762577 DOI: 10.1111/jipb.13465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
Physical contact between genes distant on chromosomes is a potentially important way for genes to coordinate their expressions. To investigate the potential importance of distant contacts, we performed high-throughput chromatin conformation capture (Hi-C) experiments on leaf nuclei isolated from Brassica rapa and Brassica oleracea. We then combined our results with published Hi-C data from Arabidopsis thaliana. We found that distant genes come into physical contact and do so preferentially between the proximal promoter of one gene and the downstream region of another gene. Genes with higher numbers of conserved noncoding sequences (CNSs) nearby were more likely to have contact with distant genes. With more CNSs came higher numbers of transcription factor binding sites and more histone modifications associated with the activity. In addition, for the genes we studied, distant contacting genes with CNSs were more likely to be transcriptionally coordinated. These observations suggest that CNSs may enrich active histone modifications and recruit transcription factors, correlating with distant contacts to ensure coordinated expression. This study advances our knowledge of gene contacts and provides insights into the relationship between CNSs and distant gene contacts in plants.
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Affiliation(s)
- Lei Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jian Wu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jianli Liang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Runmao Lin
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chao Sun
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Qirui Dai
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lupeng Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huiling Guo
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ranze Zhao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaowu Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Burkart RC, Eljebbawi A, Stahl Y. Come together now: Dynamic body-formation of key regulators integrates environmental cues in plant development. FRONTIERS IN PLANT SCIENCE 2022; 13:1052107. [PMID: 36452084 PMCID: PMC9702078 DOI: 10.3389/fpls.2022.1052107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 10/25/2022] [Indexed: 06/17/2023]
Abstract
Plants as sessile organisms are constantly exposed to changing environmental conditions, challenging their growth and development. Indeed, not only above-ground organs but also the underground root system must adapt accordingly. Consequently, plants respond to these constraints at a gene-regulatory level to ensure their survival and well-being through key transcriptional regulators involved in different developmental processes. Recently, intrinsically disordered domains within these regulators are emerging as central nodes necessary not only for interactions with other factors but also for their partitioning into biomolecular condensates, so-called bodies, possibly driven by phase separation. Here, we summarize the current knowledge about body-forming transcriptional regulators important for plant development and highlight their functions in a possible environmental context. In this perspective article, we discuss potential mechanisms for the formation of membrane-less bodies as an efficient and dynamic program needed for the adaptation to external cues with a particular focus on the Arabidopsis root. Hereby, we aim to provide a perspective for future research on transcriptional regulators to investigate body formation as an expeditious mechanism of plant-environment interactions.
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Affiliation(s)
- Rebecca C. Burkart
- Institute for Developmental Genetics, Heinrich-Heine University, Düsseldorf, Germany
| | - Ali Eljebbawi
- Institute for Developmental Genetics, Heinrich-Heine University, Düsseldorf, Germany
| | - Yvonne Stahl
- Institute for Developmental Genetics, Heinrich-Heine University, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine University, Düsseldorf, Germany
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Calderon RH, Dalton J, Zhang Y, Quail PH. Shade triggers posttranscriptional PHYTOCHROME-INTERACTING FACTOR-dependent increases in H3K4 trimethylation. PLANT PHYSIOLOGY 2022; 190:1915-1926. [PMID: 35674379 PMCID: PMC9614472 DOI: 10.1093/plphys/kiac282] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
The phytochrome (phy)-PHYTOCHROME-INTERACTING FACTOR (PIF) sensory module perceives and transduces light signals to direct target genes (DTGs), which then drive the adaptational responses in plant growth and development appropriate to the prevailing environment. These signals include the first exposure of etiolated seedlings to sunlight upon emergence from subterranean darkness and the change in color of the light that is filtered through, or reflected from, neighboring vegetation ("shade"). Previously, we identified three broad categories of rapidly signal-responsive genes: those repressed by light and conversely induced by shade; those repressed by light, but subsequently unresponsive to shade; and those responsive to shade only. Here, we investigate the potential role of epigenetic chromatin modifications in regulating these contrasting patterns of phy-PIF module-induced expression of DTGs in Arabidopsis (Arabidopsis thaliana). Using RNA-seq and ChIP-seq to determine time-resolved profiling of transcript and histone 3 lysine 4 trimethylation (H3K4me3) levels, respectively, we show that, whereas the initial dark-to-light transition triggers a rapid, apparently temporally coincident decline of both parameters, the light-to-shade transition induces similarly rapid increases in transcript levels that precede increases in H3K4me3 levels. Together with other recent findings, these data raise the possibility that, rather than being causal in the shade-induced expression changes, H3K4me3 may function to buffer the rapidly fluctuating shade/light switching that is intrinsic to vegetational canopies under natural sunlight conditions.
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Affiliation(s)
- Robert H Calderon
- Department of Plant and Microbial Biology, University of California, Berkeley, California, 94720, USA
- Plant Gene Expression Center, Agriculture Research Service, US Department of Agriculture, Albany, California, 94710, USA
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, 901 87, Sweden
| | - Jutta Dalton
- Department of Plant and Microbial Biology, University of California, Berkeley, California, 94720, USA
- Plant Gene Expression Center, Agriculture Research Service, US Department of Agriculture, Albany, California, 94710, USA
| | - Yu Zhang
- Department of Plant and Microbial Biology, University of California, Berkeley, California, 94720, USA
- Plant Gene Expression Center, Agriculture Research Service, US Department of Agriculture, Albany, California, 94710, USA
- US Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Peter H Quail
- Department of Plant and Microbial Biology, University of California, Berkeley, California, 94720, USA
- Plant Gene Expression Center, Agriculture Research Service, US Department of Agriculture, Albany, California, 94710, USA
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