101
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Locato V, Cimini S, De Gara L. ROS and redox balance as multifaceted players of cross-tolerance: epigenetic and retrograde control of gene expression. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3373-3391. [PMID: 29722828 DOI: 10.1093/jxb/ery168] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 04/27/2018] [Indexed: 05/07/2023]
Abstract
Retrograde pathways occurring between chloroplasts, mitochondria, and the nucleus involve oxidative and antioxidative signals that, working in a synergistic or antagonistic mode, control the expression of specific patterns of genes following stress perception. Increasing evidence also underlines the relevance of mitochondrion-chloroplast-nucleus crosstalk in modulating the whole cellular redox metabolism by a controlled and integrated flux of information. Plants can maintain the acquired tolerance by a stress memory, also operating at the transgenerational level, via epigenetic and miRNA-based mechanisms controlling gene expression. Data discussed in this review strengthen the idea that ROS, redox signals, and shifts in cellular redox balance permeate the signalling network leading to cross-tolerance. The identification of specific ROS/antioxidative signatures leading a plant to different fates under stress is pivotal for identifying strategies to monitor and increase plant fitness in a changing environment. This review provides an update of the plant redox signalling network implicated in stress responses, in particular in cross-tolerance acquisition. The interplay between reactive oxygen species (ROS), ROS-derived signals, and antioxidative pathways is also discussed in terms of plant acclimation to stress in the short and long term.
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Affiliation(s)
- Vittoria Locato
- Unit of Food Science and Human Nutrition, Campus Bio-Medico University, Rome, Italy
| | - Sara Cimini
- Unit of Food Science and Human Nutrition, Campus Bio-Medico University, Rome, Italy
| | - Laura De Gara
- Unit of Food Science and Human Nutrition, Campus Bio-Medico University, Rome, Italy
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102
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Yuan Y, Chen S. Widespread antisense transcription of Populus genome under drought. Mol Genet Genomics 2018; 293:1017-1033. [PMID: 29876646 DOI: 10.1007/s00438-018-1456-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 05/31/2018] [Indexed: 12/18/2022]
Abstract
Antisense transcription is widespread in many genomes and plays important regulatory roles in gene expression. The objective of our study was to investigate the extent and functional relevance of antisense transcription in forest trees. We employed Populus, a model tree species, to probe the antisense transcriptional response of tree genome under drought, through stranded RNA-seq analysis. We detected nearly 48% of annotated Populus gene loci with antisense transcripts and 44% of them with co-transcription from both DNA strands. Global distribution of reads pattern across annotated gene regions uncovered that antisense transcription was enriched in untranslated regions while sense reads were predominantly mapped in coding exons. We further detected 1185 drought-responsive sense and antisense gene loci and identified a strong positive correlation between the expression of antisense and sense transcripts. Additionally, we assessed the antisense expression in introns and found a strong correlation between intronic expression and exonic expression, confirming antisense transcription of introns contributes to transcriptional activity of Populus genome under drought. Finally, we functionally characterized drought-responsive sense-antisense transcript pairs through gene ontology analysis and discovered that functional groups including transcription factors and histones were concordantly regulated at both sense and antisense transcriptional level. Overall, our study demonstrated the extensive occurrence of antisense transcripts of Populus genes under drought and provided insights into genome structure, regulation pattern and functional significance of drought-responsive antisense genes in forest trees. Datasets generated in this study serve as a foundation for future genetic analysis to improve our understanding of gene regulation by antisense transcription.
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Affiliation(s)
- Yinan Yuan
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA.
| | - Su Chen
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
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103
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Colinas M, Goossens A. Combinatorial Transcriptional Control of Plant Specialized Metabolism. TRENDS IN PLANT SCIENCE 2018; 23:324-336. [PMID: 29395832 DOI: 10.1016/j.tplants.2017.12.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/14/2017] [Accepted: 12/21/2017] [Indexed: 05/23/2023]
Abstract
Plants produce countless specialized compounds of diverse chemical nature and biological activities. Their biosynthesis often exclusively occurs either in response to environmental stresses or is limited to dedicated anatomical structures. In both scenarios, regulation of biosynthesis appears to be mainly controlled at the transcriptional level, which is generally dependent on a combined interplay of DNA-related mechanisms and the activity of transcription factors that may act in a combinatorial manner. How environmental and developmental cues are integrated into a coordinated cell type-specific stress response has only partially been unraveled so far. Building on the available examples from (metabolic) gene expression, here we propose theoretical models of how this integration of signals may occur at the level of transcriptional control.
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Affiliation(s)
- Maite Colinas
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 927, B-9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 927, B-9052 Ghent, Belgium
| | - Alain Goossens
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 927, B-9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 927, B-9052 Ghent, Belgium.
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104
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Markus C, Pecinka A, Karan R, Barney JN, Merotto A. Epigenetic regulation - contribution to herbicide resistance in weeds? PEST MANAGEMENT SCIENCE 2018; 74:275-281. [PMID: 28888062 DOI: 10.1002/ps.4727] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 09/04/2017] [Accepted: 09/05/2017] [Indexed: 05/10/2023]
Abstract
Continuous use of herbicides has resulted in the evolution of resistance to all major herbicide modes of action worldwide. Besides the well-documented cases of newly acquired resistance through genetic changes, epigenetic regulation may also contribute to herbicide resistance in weeds. Epigenetics involves processes that modify the expression of specific genetic elements without changes in the DNA sequence, and play an important role in re-programming gene expression. Epigenetic modifications can be induced spontaneously, genetically or environmentally. Stress-induced epigenetic changes are normally reverted soon after stress exposure, although in specific cases they can also be carried over multiple generations, thereby having a selective benefit. Here, we provide an overview of the basis of epigenetic regulation in plants and discuss the possible effect of epigenetic changes on herbicide resistance. The understanding of these epigenetic changes would add a new perspective to our knowledge of environmental and management stresses and their effects on the evolution of herbicide resistance in weeds. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Catarine Markus
- Department of Crop Science, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Ales Pecinka
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ratna Karan
- Agronomy Department, University of Florida, Gainesville, FL, USA
| | - Jacob N Barney
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, USA
| | - Aldo Merotto
- Department of Crop Science, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
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105
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Ueda M, Matsui A, Nakamura T, Abe T, Sunaoshi Y, Shimada H, Seki M. Versatility of HDA19-deficiency in increasing the tolerance of Arabidopsis to different environmental stresses. PLANT SIGNALING & BEHAVIOR 2018; 13:e1475808. [PMID: 30047814 PMCID: PMC6149488 DOI: 10.1080/15592324.2018.1475808] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 05/09/2018] [Indexed: 05/21/2023]
Abstract
UNLABELLED Histone acetylation is controlled by HATs and HDACs, which are essential epigenetic elements that regulate plant response to environmental stresses. A previous study revealed that a deficiency in an HDAC isoform (HDA19) increases tolerance to high salinity stress in the Arabidopsis wild-type Col-0 background. Here, the increased tolerance of hda19 to drought and heat stresses is demonstrated. Results indicate that hda19 plants have greater tolerance than wild-type plants to stress conditions. The data indicate that the stress response pathway coordinated by HDA19 plays a pivotal role in increasing tolerance to a variety of different abiotic stresses in Arabidopsis, including salinity, drought, and heat. The greater level of tolerance of hda19 plants to several different environmental stresses suggests that HDA19 represents a promising target for pharmacological manipulation in order to enhance abiotic stress tolerance in plants. ABBREVIATIONS HAT, histone acetyltransferase; HDAC, histone deacetylase; HSF, heat shock transcription factor; RPD3, reduced potassium dependency 3; SIRT, Silent Information Regulator 2.
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Affiliation(s)
- M. Ueda
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa Japan
- Core Research for Evolutional Science and Technology, (CREST) Japan Science and Technology Agency (JST), Kawaguchi, Saitama Japan
| | - A. Matsui
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, Saitama Japan
| | - T. Nakamura
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa Japan
- Department of Biological Science and Technology, Tokyo University of Science, Tokyo, Japan
| | - T. Abe
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa Japan
| | - Y. Sunaoshi
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa Japan
| | - H. Shimada
- Department of Biological Science and Technology, Tokyo University of Science, Tokyo, Japan
| | - M. Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa Japan
- Core Research for Evolutional Science and Technology, (CREST) Japan Science and Technology Agency (JST), Kawaguchi, Saitama Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, Saitama Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa Japan
- CONTACT Motoaki Seki
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106
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Wang X, Shi X, Chen S, Ma C, Xu S. Evolutionary Origin, Gradual Accumulation and Functional Divergence of Heat Shock Factor Gene Family with Plant Evolution. FRONTIERS IN PLANT SCIENCE 2018; 9:71. [PMID: 29456547 PMCID: PMC5801592 DOI: 10.3389/fpls.2018.00071] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 01/15/2018] [Indexed: 05/09/2023]
Abstract
Plants, as sessile organisms, evolved a complex and functionally diverse heat shock factor (HSF) gene family to cope with various environmental stresses. However, the limited evolution studies of the HSF gene family have hindered our understanding of environmental adaptations in plants. In this study, a comprehensive evolution analysis on the HSF gene family was performed in 51 representative plant species. Our results demonstrated that the HSFB group which lacks a typical AHA activation domain, was the most ancient, and is under stronger purifying selection pressure in the subsequent evolutionary processes. While, dramatic gene expansion and functional divergence occurred at evolution timescales corresponding to plant land inhabit, which contribute to the emergence and diversification of the HSFA and HSFC groups in land plants. During the plant evolution, the ancestral functions of HSFs were maintained by strong purifying pressure that acted on the DNA binding domain, while the variable oligomerization domain and motif organization of HSFs underwent functional divergence and generated novel subfamilies. At the same time, variations were further accumulated with plant evolution, and this resulted in remarkable functional diversification among higher plant lineages, including distinct HSF numbers and selection pressures of several HSF subfamilies between monocots and eudicots, highlighting the fundamental differences in different plant lineages in response to environmental stresses. Taken together, our study provides novel insights into the evolutionary origin, pattern and selection pressure of plant HSFs and delineates critical clues that aid our understanding of the adaptation processes of plants to terrestrial environments.
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Affiliation(s)
- Xiaoming Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Xue Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Siyuan Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, China
- Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Chuang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, China
- Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Shengbao Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
- *Correspondence: Shengbao Xu
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107
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Neves DM, Almeida LADH, Santana-Vieira DDS, Freschi L, Ferreira CF, Soares Filho WDS, Costa MGC, Micheli F, Coelho Filho MA, Gesteira ADS. Recurrent water deficit causes epigenetic and hormonal changes in citrus plants. Sci Rep 2017; 7:13684. [PMID: 29057930 PMCID: PMC5651809 DOI: 10.1038/s41598-017-14161-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 10/06/2017] [Indexed: 11/09/2022] Open
Abstract
The present study evaluated the physiological, molecular and hormonal parameters from scion/rootstock interaction of citrus plants during recurrent water deficit. Responses of the Valencia (VO) scion variety grafted on two rootstocks with different soil water extraction capacities, Rangpur Lime (RL) and Sunki Maravilha (SM), during three successive periods of water deficit: plants exposed to a single episode of water deficit (WD1) and plants exposed to two (WD2) and three (WD3) recurrent periods of WD were compared. The combinations VO/RL and VO/SM presented polymorphic alterations of epigenetic marks and hormonal (i.e. abscisic acid, auxins and salicylicacid) profiles, which were particularly prominent when VO/SM plantswere exposed toWD3 treatment. Upon successive drought events, the VO/SM combination presented acclimatization characteristics that enable higher tolerance to water deficit by increasing transpiration (E), stomatal conductance (g s ) and photosynthetic rate (A), which in turn may have facilitated the whole plant survival. Besides providing comprehensive data on the scion/rootstock interactions upon successive stress events, this study brings the first dataset suggesting that epigenetic alterations in citrus plants triggered by recurrent water deficit lead to improved drought tolerance in this crop species.
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Affiliation(s)
- Diana Matos Neves
- Departamento de Biologia, Centro de Genética e Biologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus-Bahia, 45662-900, Brazil
| | | | - Dayse Drielly Souza Santana-Vieira
- Departamento de Ciências Exatas e Tecnológicas, Universidade Estadual do Sudoeste da Bahia, Vitória da Conquista-Bahia, 45083-900, Brazil.,Departamento de Ciências Agrárias, Universidade Federal do Recôncavo da Bahia, Cruz das Almas-Bahia, 44380-000, Brazil
| | - Luciano Freschi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, 05508-090, Brazil
| | | | | | - Marcio Gilberto Cardoso Costa
- Departamento de Biologia, Centro de Genética e Biologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus-Bahia, 45662-900, Brazil
| | - Fabienne Micheli
- Departamento de Biologia, Centro de Genética e Biologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus-Bahia, 45662-900, Brazil.,CIRAD -UMR AGAP, F-34398, Montpellier, France
| | | | - Abelmon da Silva Gesteira
- Departamento de Biologia, Centro de Genética e Biologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus-Bahia, 45662-900, Brazil. .,Embrapa-Mandioca e Fruticultura, Cruz das Almas-Bahia, 44380-000, Brazil.
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108
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Secco D, Whelan J, Rouached H, Lister R. Nutrient stress-induced chromatin changes in plants. CURRENT OPINION IN PLANT BIOLOGY 2017; 39:1-7. [PMID: 28441589 DOI: 10.1016/j.pbi.2017.04.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/18/2017] [Accepted: 04/01/2017] [Indexed: 05/17/2023]
Abstract
The ability of plants to appropriately respond to the soil nutrient availability is of primary importance for their development and to complete their life cycle. Deciphering these multifaceted adaptive mechanisms remains a major challenge for scientists to date. Recent technological breakthroughs now enable to assess the dynamism and complexity of these processes at unprecedented resolution. In this review, we present some of the most recent findings on the involvement of histone modifications, histone variants and DNA methylation in response to nutrient stresses as well as discussing the potential roles these chromatin changes could serve as priming or as trans-generational stress memory mechanisms.
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Affiliation(s)
- David Secco
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia; Biochimie et Physiologie Moléculaire des Plantes, CNRS, INRA, Montpellier SupAgro, UM, Montpellier, France.
| | - James Whelan
- Department of Animal, Plant and Soil Science, School of Life Science, ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Australia
| | - Hatem Rouached
- Biochimie et Physiologie Moléculaire des Plantes, CNRS, INRA, Montpellier SupAgro, UM, Montpellier, France
| | - Ryan Lister
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia
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109
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Haak DC, Fukao T, Grene R, Hua Z, Ivanov R, Perrella G, Li S. Multilevel Regulation of Abiotic Stress Responses in Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:1564. [PMID: 29033955 PMCID: PMC5627039 DOI: 10.3389/fpls.2017.01564] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 08/28/2017] [Indexed: 05/18/2023]
Abstract
The sessile lifestyle of plants requires them to cope with stresses in situ. Plants overcome abiotic stresses by altering structure/morphology, and in some extreme conditions, by compressing the life cycle to survive the stresses in the form of seeds. Genetic and molecular studies have uncovered complex regulatory processes that coordinate stress adaptation and tolerance in plants, which are integrated at various levels. Investigating natural variation in stress responses has provided important insights into the evolutionary processes that shape the integrated regulation of adaptation and tolerance. This review primarily focuses on the current understanding of how transcriptional, post-transcriptional, post-translational, and epigenetic processes along with genetic variation orchestrate stress responses in plants. We also discuss the current and future development of computational tools to identify biologically meaningful factors from high dimensional, genome-scale data and construct the signaling networks consisting of these components.
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Affiliation(s)
- David C. Haak
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, BlacksburgVA, United States
| | - Takeshi Fukao
- Department of Crop and Soil Environmental Sciences, Virginia Tech, BlacksburgVA, United States
| | - Ruth Grene
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, BlacksburgVA, United States
| | - Zhihua Hua
- Department of Environmental and Plant Biology, Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, AthensOH, United States
| | - Rumen Ivanov
- Institut für Botanik, Heinrich-Heine-Universität DüsseldorfDüsseldorf, Germany
| | - Giorgio Perrella
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of GlasgowGlasgow, United Kingdom
| | - Song Li
- Department of Crop and Soil Environmental Sciences, Virginia Tech, BlacksburgVA, United States
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110
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Differential expression by chromatin modifications of alcohol dehydrogenase 1 of Chorispora bungeana in cold stress. Gene 2017; 636:1-16. [PMID: 28912063 DOI: 10.1016/j.gene.2017.09.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 09/03/2017] [Accepted: 09/08/2017] [Indexed: 12/18/2022]
Abstract
Epigenetic modifications regulate plant genes to cope with a variety of environmental stresses. Chorispora bungeana is an alpine subnival plant with strong tolerance to multiple abiotic stresses, especially cold stress. In this study, we characterized the alcohol dehydrogenase 1 gene from Chorispora bungeana, CbADH1, that is up-regulated in cold conditions. Overexpression of CbADH1 in Arabidopsis thaliana improved cold tolerance, as indicated by a decreased lethal temperature (LT50). Chromatin immunoprecipitation assays showed that histone H3 is removed from the promoter region and the middle-coding region of the gene. H3K9 acetylation and H3K4 trimethylation increased throughout the gene and in the proximal promoter region, respectively. Moreover, increased Ser5P and Ser2P polymerase II accumulation further indicated changes in the transcription initiation and elongation of CbADH1 were due to the cold stress. Taken together, our results suggested that CbADH1 is highly expressed during cold stress, and is regulated by epigenetic modifications. This study expands our understanding of the regulation of gene expression by epigenetic modifications in response to environmental cues.
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111
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Kumar J, Singh S, Singh M, Srivastava PK, Mishra RK, Singh VP, Prasad SM. Transcriptional regulation of salinity stress in plants: A short review. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.plgene.2017.04.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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112
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Chen WW, Xu JM, Jin JF, Lou HQ, Fan W, Yang JL. Genome-Wide Transcriptome Analysis Reveals Conserved and Distinct Molecular Mechanisms of Al Resistance in Buckwheat (Fagopyrum esculentum Moench) Leaves. Int J Mol Sci 2017; 18:ijms18091859. [PMID: 28846612 PMCID: PMC5618508 DOI: 10.3390/ijms18091859] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 08/16/2017] [Accepted: 08/17/2017] [Indexed: 11/16/2022] Open
Abstract
Being an Al-accumulating crop, buckwheat detoxifies and tolerates Al not only in roots but also in leaves. While much progress has recently been made toward Al toxicity and resistance mechanisms in roots, little is known about the molecular basis responsible for detoxification and tolerance processes in leaves. Here, we carried out transcriptome analysis of buckwheat leaves in response to Al stress (20 µM, 24 h). We obtained 33,931 unigenes with 26,300 unigenes annotated in the NCBI database, and identified 1063 upregulated and 944 downregulated genes under Al stress. Functional category analysis revealed that genes related to protein translation, processing, degradation and metabolism comprised the biological processes most affected by Al, suggesting that buckwheat leaves maintain flexibility under Al stress by rapidly reprogramming their physiology and metabolism. Analysis of genes related to transcription regulation revealed that a large proportion of chromatin-regulation genes are specifically downregulated by Al stress, whereas transcription factor genes are overwhelmingly upregulated. Furthermore, we identified 78 upregulated and 22 downregulated genes that encode transporters. Intriguingly, only a few genes were overlapped with root Al-regulated transporter genes, which include homologs of AtMATE, ALS1, STAR1, ALS3 and a divalent ion symporter. In addition, we identified a subset of genes involved in development, in which genes associated with flowering regulation were important. Based on these data, it is proposed that buckwheat leaves develop conserved and distinct mechanisms to cope with Al toxicity.
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Affiliation(s)
- Wei Wei Chen
- Research Centre for Plant RNA Signaling , College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China.
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8, Canada.
| | - Jia Meng Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Jian Feng Jin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
| | - He Qiang Lou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Wei Fan
- College of Resource and Environment, Yunnan Agricultural University, Kunming 650201, China.
| | - Jian Li Yang
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8, Canada.
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
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113
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Santa-Cruz D, Pacienza N, Zilli C, Pagano E, Balestrasse K, Yannarelli G. Heme oxygenase up-regulation under ultraviolet-B radiation is not epigenetically restricted and involves specific stress-related transcriptions factors. Redox Biol 2017; 12:549-557. [PMID: 28384610 PMCID: PMC5382145 DOI: 10.1016/j.redox.2017.03.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 03/10/2017] [Indexed: 01/05/2023] Open
Abstract
Heme oxygenase-1 (HO-1) plays a protective role against oxidative stress in plants. The mechanisms regulating its expression, however, remain unclear. Here we studied the methylation state of a GC rich HO-1 promoter region and the expression of several stress-related transcription factors (TFs) in soybean plants subjected to ultraviolet-B (UV-B) radiation. Genomic DNA and total RNA were isolated from leaves of plants irradiated with 7.5 and 15kJm-2 UV-B. A 304bp HO-1 promoter region was amplified by PCR from sodium bisulfite-treated DNA, cloned into pGEMT plasmid vector and evaluated by DNA sequencing. Bisulfite sequencing analysis showed similar HO-1 promoter methylation levels in control and UV-B-treated plants (C: 3.4±1.3%; 7.5: 2.6±0.5%; 15: 3.1±1.1%). Interestingly, HO-1 promoter was strongly unmethylated in control plants. Quantitative RT-PCR analysis of TFs showed that GmMYB177, GmMYBJ6, GmWRKY21, GmNAC11, GmNAC20 and GmGT2A but not GmWRK13 and GmDREB were induced by UV-B radiation. The expression of several TFs was also enhanced by hemin, a potent and specific HO inducer, inferring that they may mediate HO-1 up-regulation. These results suggest that soybean HO-1 gene expression is not epigenetically regulated. Moreover, the low level of HO-1 promoter methylation suggests that this antioxidant enzyme can rapidly respond to environmental stress. Finally, this study has identified some stress-related TFs involved in HO-1 up-regulation under UV-B radiation.
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Affiliation(s)
- Diego Santa-Cruz
- Laboratorio de Regulación Génica y Células Madre, Instituto de Medicina Traslacional, Trasplante y Bioingeniería (IMeTTyB), Universidad Favaloro-CONICET, Buenos Aires, Argentina; Universidad de Buenos Aires (UBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones en Biociencias Agrícolas y Ambientales (INBA), Facultad de Agronomía, Buenos Aires, Argentina
| | - Natalia Pacienza
- Laboratorio de Regulación Génica y Células Madre, Instituto de Medicina Traslacional, Trasplante y Bioingeniería (IMeTTyB), Universidad Favaloro-CONICET, Buenos Aires, Argentina
| | - Carla Zilli
- Universidad de Buenos Aires (UBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones en Biociencias Agrícolas y Ambientales (INBA), Facultad de Agronomía, Buenos Aires, Argentina
| | - Eduardo Pagano
- Universidad de Buenos Aires (UBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones en Biociencias Agrícolas y Ambientales (INBA), Facultad de Agronomía, Buenos Aires, Argentina
| | - Karina Balestrasse
- Universidad de Buenos Aires (UBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones en Biociencias Agrícolas y Ambientales (INBA), Facultad de Agronomía, Buenos Aires, Argentina.
| | - Gustavo Yannarelli
- Laboratorio de Regulación Génica y Células Madre, Instituto de Medicina Traslacional, Trasplante y Bioingeniería (IMeTTyB), Universidad Favaloro-CONICET, Buenos Aires, Argentina.
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114
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Lämke J, Bäurle I. Epigenetic and chromatin-based mechanisms in environmental stress adaptation and stress memory in plants. Genome Biol 2017; 18:124. [PMID: 28655328 PMCID: PMC5488299 DOI: 10.1186/s13059-017-1263-6] [Citation(s) in RCA: 356] [Impact Index Per Article: 50.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Plants frequently have to weather both biotic and abiotic stressors, and have evolved sophisticated adaptation and defense mechanisms. In recent years, chromatin modifications, nucleosome positioning, and DNA methylation have been recognized as important components in these adaptations. Given their potential epigenetic nature, such modifications may provide a mechanistic basis for a stress memory, enabling plants to respond more efficiently to recurring stress or even to prepare their offspring for potential future assaults. In this review, we discuss both the involvement of chromatin in stress responses and the current evidence on somatic, intergenerational, and transgenerational stress memory.
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Affiliation(s)
- Jörn Lämke
- University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht-Strasse 24-25, 14476, Potsdam, Germany
| | - Isabel Bäurle
- University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht-Strasse 24-25, 14476, Potsdam, Germany.
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115
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Patanun O, Ueda M, Itouga M, Kato Y, Utsumi Y, Matsui A, Tanaka M, Utsumi C, Sakakibara H, Yoshida M, Narangajavana J, Seki M. The Histone Deacetylase Inhibitor Suberoylanilide Hydroxamic Acid Alleviates Salinity Stress in Cassava. FRONTIERS IN PLANT SCIENCE 2016; 7:2039. [PMID: 28119717 PMCID: PMC5220070 DOI: 10.3389/fpls.2016.02039] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 12/20/2016] [Indexed: 05/20/2023]
Abstract
Cassava (Manihot esculenta Crantz) demand has been rising because of its various applications. High salinity stress is a major environmental factor that interferes with normal plant growth and limits crop productivity. As well as genetic engineering to enhance stress tolerance, the use of small molecules is considered as an alternative methodology to modify plants with desired traits. The effectiveness of histone deacetylase (HDAC) inhibitors for increasing tolerance to salinity stress has recently been reported. Here we use the HDAC inhibitor, suberoylanilide hydroxamic acid (SAHA), to enhance tolerance to high salinity in cassava. Immunoblotting analysis reveals that SAHA treatment induces strong hyper-acetylation of histones H3 and H4 in roots, suggesting that SAHA functions as the HDAC inhibitor in cassava. Consistent with increased tolerance to salt stress under SAHA treatment, reduced Na+ content and increased K+/Na+ ratio were detected in SAHA-treated plants. Transcriptome analysis to discover mechanisms underlying salinity stress tolerance mediated through SAHA treatment reveals that SAHA enhances the expression of 421 genes in roots under normal condition, and 745 genes at 2 h and 268 genes at 24 h under both SAHA and NaCl treatment. The mRNA expression of genes, involved in phytohormone [abscisic acid (ABA), jasmonic acid (JA), ethylene, and gibberellin] biosynthesis pathways, is up-regulated after high salinity treatment in SAHA-pretreated roots. Among them, an allene oxide cyclase (MeAOC4) involved in a crucial step of JA biosynthesis is strongly up-regulated by SAHA treatment under salinity stress conditions, implying that JA pathway might contribute to increasing salinity tolerance by SAHA treatment. Our results suggest that epigenetic manipulation might enhance tolerance to high salinity stress in cassava.
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Affiliation(s)
- Onsaya Patanun
- Plant Biochemistry and Molecular Genetics Laboratory, Department of Biotechnology, Faculty of Science, Mahidol UniversityBangkok, Thailand
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - Minoru Ueda
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
- CREST, Japan Science and Technology AgencySaitama, Japan
| | - Misao Itouga
- Plant Productivity Systems Research Group, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - Yukari Kato
- Plant Productivity Systems Research Group, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - Yoshinori Utsumi
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - Akihiro Matsui
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - Maho Tanaka
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - Chikako Utsumi
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
- CREST, Japan Science and Technology AgencySaitama, Japan
| | - Hitoshi Sakakibara
- Plant Productivity Systems Research Group, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource ScienceSaitama, Japan
| | - Jarunya Narangajavana
- Plant Biochemistry and Molecular Genetics Laboratory, Department of Biotechnology, Faculty of Science, Mahidol UniversityBangkok, Thailand
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
- CREST, Japan Science and Technology AgencySaitama, Japan
- Plant Genomic Network Science Division, Kihara Institute for Biological Research, Yokohama City UniversityYokohama, Japan
- *Correspondence: Motoaki Seki
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