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Tu A, Wu M, Jiang Y, Guo L, Guo Y, Wang J, Xu G, Shi J, Chen J, Yang J, Zhong K. Regulation of Disease-Resistance Genes against CWMV Infection by NbHAG1-Mediated H3K36ac. Int J Mol Sci 2024; 25:2800. [PMID: 38474046 DOI: 10.3390/ijms25052800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/22/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Post-translational modification of proteins plays a critical role in plant-pathogen interactions. Here, we demonstrate in Nicotiana benthamiana that knockout of NbHAG1 promotes Chinese wheat mosaic virus (CWMV) infection, whereas NbHAG1 overexpression inhibits infection. Transcriptome sequencing indicated that a series of disease resistance-related genes were up-regulated after overexpression of NbHAG1. In addition, cleavage under targets and tagmentation (Cut&Tag)-qPCR results demonstrated that NbHAG1 may activate the transcription of its downstream disease-resistance genes by facilitating the acetylation level of H3K36ac. Therefore, we suggest that NbHAG1 is an important positive regulator of resistance to CWMV infestation.
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Affiliation(s)
- Aizhu Tu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Mila Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Yaoyao Jiang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Lidan Guo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Yunfei Guo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jinnan Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Gecheng Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jingjing Shi
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jian Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Kaili Zhong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
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2
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Doll NM, Van Hautegem T, Schilling N, De Rycke R, De Winter F, Fendrych M, Nowack MK. Endosperm cell death promoted by NAC transcription factors facilitates embryo invasion in Arabidopsis. Curr Biol 2023; 33:3785-3795.e6. [PMID: 37633282 PMCID: PMC7615161 DOI: 10.1016/j.cub.2023.08.003] [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: 05/16/2023] [Revised: 07/27/2023] [Accepted: 08/01/2023] [Indexed: 08/28/2023]
Abstract
In flowering plants, two fertilization products develop within the limited space of the seed: the embryo and the surrounding nutritive endosperm. The final size of the endosperm is modulated by the degree of embryo growth. In Arabidopsis thaliana, the endosperm expands rapidly after fertilization, but later gets invaded by the embryo that occupies most of the seed volume at maturity, surrounded by a single remaining aleurone-like endosperm layer.1,2,3,4 Embryo invasion is facilitated by the endosperm-expressed bHLH-type transcription factor ZHOUPI, which promotes weakening of endosperm cell walls.5,6 Endosperm elimination in zou mutants is delayed, and embryo growth is severely affected; the endosperm finally collapses around the dwarf embryo, causing the shriveled appearance of mature zou seeds.5,6,7 However, whether ZHOUPI facilitates mechanical endosperm destruction by the invading embryo or whether an active programmed cell death (PCD) process causes endosperm elimination has been subject to debate.2,8 Here we show that developmental PCD controlled by multiple NAC transcription factors in the embryo-adjacent endosperm promotes gradual endosperm elimination. Misexpressing the NAC transcription factor KIRA1 in the entire endosperm caused total endosperm elimination, generating aleurone-less mature seeds. Conversely, dominant and recessive higher-order NAC mutants led to delayed endosperm elimination and impaired cell corpse clearance. Promoting PCD in the zhoupi mutant partially rescued its embryo growth defects, while the endosperm in a zhoupi nac higher-order mutant persisted until seed desiccation. These data suggest that a combination of cell wall weakening and PCD jointly facilitates embryo invasion by an active auto-elimination of endosperm cells.
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Affiliation(s)
- Nicolas M Doll
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; VIB-UGENT Center of Plant Systems Biology, 9052 Ghent, Belgium.
| | - Tom Van Hautegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; VIB-UGENT Center of Plant Systems Biology, 9052 Ghent, Belgium
| | - Neeltje Schilling
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; VIB-UGENT Center of Plant Systems Biology, 9052 Ghent, Belgium; Institute of Biochemistry and Biology, Potsdam University, Potsdam, 14476 OT Golm, Germany
| | - Riet De Rycke
- Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium; VIB Center for Inflammation Research, Ghent University, 9052 Ghent, Belgium; VIB Bioimaging Core, Ghent University, 9052 Ghent, Belgium
| | - Freya De Winter
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; VIB-UGENT Center of Plant Systems Biology, 9052 Ghent, Belgium
| | - Matyáš Fendrych
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; VIB-UGENT Center of Plant Systems Biology, 9052 Ghent, Belgium
| | - Moritz K Nowack
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; VIB-UGENT Center of Plant Systems Biology, 9052 Ghent, Belgium.
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3
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Xie SS, Duan CG. Epigenetic regulation of plant immunity: from chromatin codes to plant disease resistance. ABIOTECH 2023; 4:124-139. [PMID: 37581024 PMCID: PMC10423193 DOI: 10.1007/s42994-023-00101-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/01/2023] [Indexed: 08/16/2023]
Abstract
Facing a deteriorating natural environment and an increasing serious food crisis, bioengineering-based breeding is increasing in importance. To defend against pathogen infection, plants have evolved multiple defense mechanisms, including pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI). A complex regulatory network acts downstream of these PTI and ETI pathways, including hormone signal transduction and transcriptional reprogramming. In recent years, increasing lines of evidence show that epigenetic factors act, as key regulators involved in the transcriptional reprogramming, to modulate plant immune responses. Here, we summarize current progress on the regulatory mechanism of DNA methylation and histone modifications in plant defense responses. In addition, we also discuss the application of epigenetic mechanism-based resistance strategies in plant disease breeding.
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Affiliation(s)
- Si-Si Xie
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
- University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Cheng-Guo Duan
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
- University of the Chinese Academy of Sciences, Beijing, 100049 China
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4
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Zhang Z, Qian H, Wang Z, Pang Y, Guan X, Poetsch A, Wang D. Characterization of histone acetyltransferases and deacetylases and their roles in response to dehydration stress in Pyropia yezoensis (Rhodophyta). FRONTIERS IN PLANT SCIENCE 2023; 14:1133021. [PMID: 37260940 PMCID: PMC10227436 DOI: 10.3389/fpls.2023.1133021] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 04/12/2023] [Indexed: 06/02/2023]
Abstract
Histone acetylation is one of the most pivotal epigenetic mechanisms in eukaryotes and has been tightly linked to the regulation of various genes controlling growth, development and response to environmental stresses in both animals and plants. Till date, the association of histone acetylation to dehydration stress in red algae and genes encoding the enzymes responsible for histone acetylation: histone acetyltransferases (HATs) or histone deacetylases (HDACs), remains largely unknown. In this study, in silico analysis of the red seaweed Pyropia yezoensis identified 6 HAT genes and 10 HDAC genes. These genes displayed good synteny in genome loci with their Pyropia haitanensis orthologs except for a putative gene duplication event in HDAC and a loss of one HAT gene in P. yezoensis. According to the conserved domains and phylogenetic analysis, they encoded three GCNA5-, one TAFII250- and one MYST-HAT, as well as five HDA1-and five SIRT-HDACs. The sirtuin-domain of Py06502 harbored a ~100 aa insert and interestingly, this insertion was specifically observed in Bangiales species. Two nuclear-localized HATs were transcriptionally up-regulated at the early stage of dehydration and so were two nuclear HDA1s when moderate dehydration started, suggesting their potential roles in modulating downstream gene expression to facilitate dehydration adaptation by changing histone acetylation patterns on relevant regulatory elements. This was experimentally confirmed by the increased decline in photosynthesis efficiency during dehydration when HAT and HDAC activities were inhibited by SAHA and MB-3, respectively. Transcriptional patterns of multiple dehydration-responsive genes after water loss were strongly affected by MB-3 or SAHA treatment. This study provides the first insight into the regulation and function of HAT/HDAC during stress adaptation in red algae.
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Affiliation(s)
- Zehao Zhang
- Key Laboratory of Marine Genetics and Breeding (OUC), Ministry of Education, Qingdao, China
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Huijuan Qian
- Key Laboratory of Marine Genetics and Breeding (OUC), Ministry of Education, Qingdao, China
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhongshi Wang
- Key Laboratory of Marine Genetics and Breeding (OUC), Ministry of Education, Qingdao, China
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Ying Pang
- Key Laboratory of Marine Genetics and Breeding (OUC), Ministry of Education, Qingdao, China
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaowei Guan
- Key Laboratory of Marine Genetics and Breeding (OUC), Ministry of Education, Qingdao, China
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Ansgar Poetsch
- Key Laboratory of Marine Genetics and Breeding (OUC), Ministry of Education, Qingdao, China
- Department of Plant Biochemistry, Ruhr University Bochum, Bochum, North Rhine-Westphalia, Germany
| | - Dongmei Wang
- Key Laboratory of Marine Genetics and Breeding (OUC), Ministry of Education, Qingdao, China
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
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5
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Yan H, Chen H, Liao Q, Xia M, Yao T, Peng L, Zou L, Zhao G, Zhao J, Wu DT. Genome-Wide Identification of Histone Deacetylases and Their Roles Related with Light Response in Tartary Buckwheat ( Fagopyrum tataricum). Int J Mol Sci 2023; 24:ijms24098090. [PMID: 37175799 PMCID: PMC10179446 DOI: 10.3390/ijms24098090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
Histone deacetylases (HDACs), known as histone acetylation erasers, function crucially in plant growth and development. Although there are abundant reports focusing on HDACs of Arabidopsis and illustrating their important roles, the knowledge of HDAC genes in Tartary buckwheat (Polygonales Polygonaceae Fagopyrum tataricum (L.) Gaertn) is still scarce. In the study, a total of 14 HDAC genes were identified and divided into three main groups: Reduced Potassium Dependency-3/His-52 tone Deacetylase 1 (RPD3/HDA1), Silent Information Regulator 2 (SIR2), and the plant-53 specific HD2. Domain and motif composition analysis showed there were conserved domains and motifs in members from the same subfamilies. The 14 FtHDACs were distributed asymmetrically on 7 chromosomes, with three segmental events and one tandem duplication event identified. The prediction of the cis-element in promoters suggested that FtHDACs probably acted in numerous biological processes including plant growth, development, and response to environmental signals. Furthermore, expression analysis based on RNA-seq data displayed that all FtHDAC genes were universally and distinctly expressed in diverse tissues and fruit development stages. In addition, we found divergent alterations in FtHDACs transcript abundance in response to different light conditions according to RNA-seq and RT-qPCR data, indicating that five FtHDACs might be involved in light response. Our findings could provide fundamental information for the HDAC gene family and supply several targets for future function analysis of FtHDACs related with light response of Tartary buckwheat.
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Affiliation(s)
- Huiling Yan
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Province Engineering Technology Research Center of Coarse Cereal Industralization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Hongxu Chen
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Province Engineering Technology Research Center of Coarse Cereal Industralization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Qingxia Liao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Province Engineering Technology Research Center of Coarse Cereal Industralization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Mengying Xia
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Province Engineering Technology Research Center of Coarse Cereal Industralization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Tian Yao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Province Engineering Technology Research Center of Coarse Cereal Industralization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Lianxin Peng
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Province Engineering Technology Research Center of Coarse Cereal Industralization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Liang Zou
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Province Engineering Technology Research Center of Coarse Cereal Industralization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Gang Zhao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Province Engineering Technology Research Center of Coarse Cereal Industralization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Jianglin Zhao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Province Engineering Technology Research Center of Coarse Cereal Industralization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Ding-Tao Wu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Province Engineering Technology Research Center of Coarse Cereal Industralization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
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6
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Bisht A, Eekhout T, Canher B, Lu R, Vercauteren I, De Jaeger G, Heyman J, De Veylder L. PAT1-type GRAS-domain proteins control regeneration by activating DOF3.4 to drive cell proliferation in Arabidopsis roots. THE PLANT CELL 2023; 35:1513-1531. [PMID: 36747478 PMCID: PMC10118276 DOI: 10.1093/plcell/koad028] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/05/2023] [Accepted: 01/16/2023] [Indexed: 05/22/2023]
Abstract
Plant roots possess remarkable regenerative potential owing to their ability to replenish damaged or lost stem cells. ETHYLENE RESPONSE FACTOR 115 (ERF115), one of the key molecular elements linked to this potential, plays a predominant role in the activation of regenerative cell divisions. However, the downstream operating molecular machinery driving wound-activated cell division is largely unknown. Here, we biochemically and genetically identified the GRAS-domain transcription factor SCARECROW-LIKE 5 (SCL5) as an interaction partner of ERF115 in Arabidopsis thaliana. Although nonessential under control growth conditions, SCL5 acts redundantly with the related PHYTOCHROME A SIGNAL TRANSDUCTION 1 (PAT1) and SCL21 transcription factors to activate the expression of the DNA-BINDING ONE FINGER 3.4 (DOF3.4) transcription factor gene. DOF3.4 expression is wound-inducible in an ERF115-dependent manner and, in turn, activates D3-type cyclin expression. Accordingly, ectopic DOF3.4 expression drives periclinal cell division, while its downstream D3-type cyclins are essential for the regeneration of a damaged root. Our data highlight the importance and redundant roles of the SCL5, SCL21, and PAT1 transcription factors in wound-activated regeneration processes and pinpoint DOF3.4 as a key downstream element driving regenerative cell division.
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Affiliation(s)
- Anchal Bisht
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Thomas Eekhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Balkan Canher
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Ran Lu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Ilse Vercauteren
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Jefri Heyman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
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Rai N, Neugart S, Schröter D, Lindfors AV, Aphalo PJ. Responses of flavonoids to solar UV radiation and gradual soil drying in two Medicago truncatula accessions. Photochem Photobiol Sci 2023:10.1007/s43630-023-00404-6. [PMID: 36995651 DOI: 10.1007/s43630-023-00404-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 02/28/2023] [Indexed: 03/31/2023]
Abstract
Ground level UV-B (290-315 nm) and UV-A (315-400 nm) radiation regulates multiple aspects of plant growth and development. In a natural environment, UV radiation interacts in a complex manner with other environmental factors (e.g., drought) to regulate plants' morphology, physiology, and growth. To assess the interactive effects of UV radiation and soil drying on plants' secondary metabolites and transcript abundance, we performed a field experiment using two different accessions of Medicago truncatula (F83005-5 French origin and Jemalong A17 Australian origin). Plants were grown for 37 days under long-pass filters to assess the effects of UV short wavelength (290-350 nm, UVsw) and UV-A long wavelength (350-400 nm, UV-Alw). Soil-water deficit was induced by not watering half of the plants during the last seven days of the experiment. The two accessions differed in the concentration of flavonoids in the leaf epidermis and in the whole leaf: F83005-5 had higher concentration than Jemalong A17. They also differed in the composition of the flavonoids: a greater number of apigenin derivatives than tricin derivatives in Jemalong A17 and the opposite in F83005-5. Furthermore, UVsw and soil drying interacted positively to regulate the biosynthesis of flavonoids in Jemalong A17 through an increase in transcript abundance of CHALCONE SYNTHASE (CHS). However, in F83005-5, this enhanced CHS transcript abundance was not detected. Taken together the observed metabolite and gene transcript responses suggest differences in mechanisms for acclimation and stress tolerance between the accessions.
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Affiliation(s)
- Neha Rai
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Center, University of Helsinki, Helsinki, Finland.
- Department of Plant Sciences, University of Geneva, Geneva, Switzerland.
| | - Susanne Neugart
- Division of Quality and Sensory of Plant Products, Department of Crop Sciences, Georg-August-Universität Göttingen, Göttingen, Germany
| | - David Schröter
- Research Area of Plant Quality and Food Security, Leibniz Institute of Vegetable and Ornamental Crops e. V., Grossbeeren, Germany
| | | | - Pedro J Aphalo
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Center, University of Helsinki, Helsinki, Finland
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8
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van Ekelenburg YS, Hornslien KS, Van Hautegem T, Fendrych M, Van Isterdael G, Bjerkan KN, Miller JR, Nowack MK, Grini PE. Spatial and temporal regulation of parent-of-origin allelic expression in the endosperm. PLANT PHYSIOLOGY 2023; 191:986-1001. [PMID: 36437711 PMCID: PMC9922421 DOI: 10.1093/plphys/kiac520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Genomic imprinting promotes differential expression of parental alleles in the endosperm of flowering plants and is regulated by epigenetic modification such as DNA methylation and histone tail modifications in chromatin. After fertilization, the endosperm develops through a syncytial stage before it cellularizes and becomes a nutrient source for the growing embryo. Regional compartmentalization has been shown both in early and late endosperm development, and different transcriptional domains suggest divergent spatial and temporal regional functions. The analysis of the role of parent-of-origin allelic expression in the endosperm as a whole and the investigation of domain-specific functions have been hampered by the inaccessibility of the tissue for high-throughput transcriptome analyses and contamination from surrounding tissue. Here, we used fluorescence-activated nuclear sorting (FANS) of nuclear targeted GFP fluorescent genetic markers to capture parental-specific allelic expression from different developmental stages and specific endosperm domains. This approach allowed us to successfully identify differential genomic imprinting with temporal and spatial resolution. We used a systematic approach to report temporal regulation of imprinted genes in the endosperm, as well as region-specific imprinting in endosperm domains. Analysis of our data identified loci that are spatially differentially imprinted in one domain of the endosperm, while biparentally expressed in other domains. These findings suggest that the regulation of genomic imprinting is dynamic and challenge the canonical mechanisms for genomic imprinting.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Paul E Grini
- Authors for correspondence: E-mail: (P.E.G.), (K.S.H.)
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9
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Induction of Somatic Embryogenesis in Plants: Different Players and Focus on WUSCHEL and WUS-RELATED HOMEOBOX (WOX) Transcription Factors. Int J Mol Sci 2022; 23:ijms232415950. [PMID: 36555594 PMCID: PMC9781121 DOI: 10.3390/ijms232415950] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
In plants, other cells can express totipotency in addition to the zygote, thus resulting in embryo differentiation; this appears evident in apomictic and epiphyllous plants. According to Haberlandt's theory, all plant cells can regenerate a complete plant if the nucleus and the membrane system are intact. In fact, under in vitro conditions, ectopic embryos and adventitious shoots can develop from many organs of the mature plant body. We are beginning to understand how determination processes are regulated and how cell specialization occurs. However, we still need to unravel the mechanisms whereby a cell interprets its position, decides its fate, and communicates it to others. The induction of somatic embryogenesis might be based on a plant growth regulator signal (auxin) to determine an appropriate cellular environment and other factors, including stress and ectopic expression of embryo or meristem identity transcription factors (TFs). Still, we are far from having a complete view of the regulatory genes, their target genes, and their action hierarchy. As in animals, epigenetic reprogramming also plays an essential role in re-establishing the competence of differentiated cells to undergo somatic embryogenesis. Herein, we describe the functions of WUSCHEL-RELATED HOMEOBOX (WOX) transcription factors in regulating the differentiation-dedifferentiation cell process and in the developmental phase of in vitro regenerated adventitious structures.
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Su J, Yao Z, Wu Y, Lee J, Jeong J. Minireview: Chromatin-based regulation of iron homeostasis in plants. FRONTIERS IN PLANT SCIENCE 2022; 13:959840. [PMID: 36186078 PMCID: PMC9523571 DOI: 10.3389/fpls.2022.959840] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/31/2022] [Indexed: 05/26/2023]
Abstract
Plants utilize delicate mechanisms to effectively respond to changes in the availability of nutrients such as iron. The responses to iron status involve controlling gene expression at multiple levels. The regulation of iron deficiency response by a network of transcriptional regulators has been extensively studied and recent research has shed light on post-translational control of iron homeostasis. Although not as considerably investigated, an increasing number of studies suggest that histone modification and DNA methylation play critical roles during iron deficiency and contribute to fine-tuning iron homeostasis in plants. This review will focus on the current understanding of chromatin-based regulation on iron homeostasis in plants highlighting recent studies in Arabidopsis and rice. Understanding iron homeostasis in plants is vital, as it is not only relevant to fundamental biological questions, but also to agriculture, biofortification, and human health. A comprehensive overview of the effect and mechanism of chromatin-based regulation in response to iron status will ultimately provide critical insights in elucidating the complexities of iron homeostasis and contribute to improving iron nutrition in plants.
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Affiliation(s)
- Justin Su
- Department of Biology, Amherst College, Amherst, MA, United States
| | - Zhujun Yao
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, China
| | - Yixuan Wu
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, China
| | - Joohyun Lee
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, China
| | - Jeeyon Jeong
- Department of Biology, Amherst College, Amherst, MA, United States
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11
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Zhao Z, Qi Y, Yang Z, Cheng L, Sharif R, Raza A, Chen P, Hou D, Li Y. Exploring the Agrobacterium-mediated transformation with CRISPR/Cas9 in cucumber (Cucumis sativus L.). Mol Biol Rep 2022; 49:11481-11490. [PMID: 36057005 DOI: 10.1007/s11033-022-07558-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 05/03/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUNDS The narrow genetic basis of cucumber makes breeding of this species difficult. CRISPR/Cas9 system is characteristic of simple design, low cost and high efficiency, which has opened a new path for cucumber functional genetics and the development of cucumber mocular breeding. However, the immature genetic transformation system is the main limiting factor for applying this technology in cucumber. METHODS AND RESULTS In this study, a Histochemical β-glucuronidase (GUS) assay was used to analyze the effect of various parameters, including slight scratch of explants, pre-culture time, acetosyringone (AS) concentration, infection time in Agrobacterium solution, and co-culture period on the transformation efficiency. The results showed that the explants slightly scratched after cutting, pre-cultured for 1 day, Agrobacterium bacterial solution containing AS, and 20 min length of infection could significantly increase the GUS staining rate of explants. On this basis, two sequences with high specificity (sgRNA-1 and sgRNA-2) targeted different loci of gene CsGCN5 were designed. The corresponding vectors Cas9-sgRNA-1 and Cas9-sgRNA-2 were constructed and transformed using the above-optimized cucumber genetic transformation system, and three and two PCR positive lines were obtained from 210 and 207 explants, respectively. No sequence mutation at target loci of CsGCN5 was detected in the Cas9-sgRNA-1 transformed three PCR positive lines. However, one mutant line with targeted homozygous change was recognized from the Cas9-sgRNA-2 transformed two PCR positive lines. CONCLUSION In this study, 2.4‰ of total explants had directed mutation in the CsGCN5 gene. The results in the present study would be beneficial to further optimize and improve the efficiency of the genetic transformation of cucumber.
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Affiliation(s)
- Ziyao Zhao
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
- College of Horticulture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Yaguang Qi
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhimin Yang
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Liyu Cheng
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Rahat Sharif
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Ali Raza
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Peng Chen
- College of Life Science, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Dong Hou
- Vegetable Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, Gansu, China
| | - Yuhong Li
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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12
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ADA2b and GCN5 Affect Cytokinin Signaling by Modulating Histone Acetylation and Gene Expression during Root Growth of Arabidopsis thaliana. PLANTS 2022; 11:plants11101335. [PMID: 35631760 PMCID: PMC9148027 DOI: 10.3390/plants11101335] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 05/14/2022] [Accepted: 05/16/2022] [Indexed: 11/16/2022]
Abstract
In Arabidopsis thaliana, the histone acetyltransferase GCN5 and the associated coactivator ADA2b regulate root growth and affect gene expression. The cytokinin signaling reporter TCS::GFP was introduced into gcn5-1, ada2b-1, and ada2a-2, as well as the ada2a-2ada2b-1 mutants. The early root growth (4 to 7 days post-germination) was analyzed using cellular and molecular approaches. TCS signal accumulated from the fourth to seventh days of root growth in the wild-type columella cells. In contrast, ada2b-1 and gcn5-1 and ada2a-2ada2b-1 double mutants displayed reduced TCS expression relative to wild type. Gene expression analysis showed that genes associated with cytokinin homeostasis were downregulated in the roots of gcn5-1 and ada2b-1 mutants compared to wild-type plants. H3K14 acetylation was affected in the promoters of cytokinin synthesis and catabolism genes during root growth of Arabidopsis. Therefore, GCN5 and ADA2b are positive regulators of cytokinin signaling during root growth by modulating histone acetylation and the expression of genes involved in cytokinin synthesis and catabolism. Auxin application in the roots of wild-type seedlings increased TCS::GFP expression. In contrast, ada2b and ada2ada2b mutant plants do not show the auxin-induced TCS signal, suggesting that GCN5 and ADA2b are required for the auxin-induced cytokinin signaling in early root growth.
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13
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Insights into the Histone Acetylation-Mediated Regulation of the Transcription Factor Genes That Control the Embryogenic Transition in the Somatic Cells of Arabidopsis. Cells 2022; 11:cells11050863. [PMID: 35269485 PMCID: PMC8909028 DOI: 10.3390/cells11050863] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/10/2022] [Accepted: 02/28/2022] [Indexed: 02/01/2023] Open
Abstract
Somatic embryogenesis (SE), which is a process that involves the in vitro-induced embryogenic reprogramming of plant somatic cells, requires dynamic changes in the cell transcriptome. These changes are fine-tuned by many genetic and epigenetic factors, including posttranslational histone modifications such as histone acetylation. Antagonistically acting enzymes, histone acetyltransferases (HATs) and deacetylases (HDACs), which control histone acetylation in many developmental processes, are believed to control SE. However, the function of specific HAT/HDACs and the genes that are subjected to histone acetylation-mediated regulation during SE have yet to be revealed. Here, we present the global and gene-specific changes in histone acetylation in Arabidopsis explants that are undergoing SE. In the TSA (trichostatin A)-induced SE, we demonstrate that H3 and H4 acetylation might control the expression of the critical transcription factor (TF) genes of a vital role in SE, including LEC1, LEC2 (LEAFY COTYLEDON 1; 2), FUS3 (FUSCA 3) and MYB118 (MYB DOMAIN PROTEIN 118). Within the HATs and HDACs, which mainly positively regulate SE, we identified HDA19 as negatively affecting SE by regulating LEC1, LEC2 and BBM. Finally, we provide some evidence on the role of HDA19 in the histone acetylation-mediated regulation of LEC2 during SE. Our results reveal an essential function of histone acetylation in the epigenetic mechanisms that control the TF genes that play critical roles in the embryogenic reprogramming of plant somatic cells. The results implicate the complexity of Hac-related gene regulation in embryogenic induction and point to differences in the regulatory mechanisms that are involved in auxin- and TSA-induced SE.
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14
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Ramirez-Prado JS, Benhamed M. Three bona fide plant-specific SAGA subunits and their regulatory function. MOLECULAR PLANT 2021; 14:1033-1035. [PMID: 34058400 DOI: 10.1016/j.molp.2021.05.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 05/21/2021] [Accepted: 05/26/2021] [Indexed: 06/12/2023]
Affiliation(s)
- J S Ramirez-Prado
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium; Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, Orsay 91405, France; Institute of Plant Sciences Paris-Saclay, Université de Paris, CNRS, INRAE, Orsay (IPS2) 91405, France
| | - M Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, Orsay 91405, France; Institute of Plant Sciences Paris-Saclay, Université de Paris, CNRS, INRAE, Orsay (IPS2) 91405, France; Institut Universitaire de France (IUF), Paris, France.
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15
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Updated Mechanisms of GCN5-The Monkey King of the Plant Kingdom in Plant Development and Resistance to Abiotic Stresses. Cells 2021; 10:cells10050979. [PMID: 33922251 PMCID: PMC8146787 DOI: 10.3390/cells10050979] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 04/12/2021] [Accepted: 04/19/2021] [Indexed: 12/12/2022] Open
Abstract
Histone modifications are the main epigenetic mechanisms that regulate gene expression, chromatin structure, and plant development, among which histone acetylation is one of the most important and studied epigenetic modifications. Histone acetylation is believed to enhance DNA access and promote transcription. GENERAL CONTROL NON-REPRESSIBLE 5 (GCN5), a well-known enzymatic protein responsible for the lysine acetylation of histone H3 and H4, is a universal and crucial histone acetyltransferase involved in gene transcription and plant development. Many studies have found that GCN5 plays important roles in the different development stages of Arabidopsis. In terms of exogenous stress conditions, GCN5 is also involved in the responses to heat stress, cold stress, and nutrient element deficiency by regulating the related gene expression to maintain the homeostasis of some key metabolites (e.g., cellulose) or ions (e.g., phosphate, iron); in addition, GCN5 is involved in the phytohormone pathways such as ethylene, auxin, and salicylic acid to play various roles during the plant lifecycle. Some of the pathways involved by GCN5 also interwind to regulate specific physiological processes or developmental stages. Here, interactions between various developmental events and stress-resistant pathways mediated by GCN5 are comprehensively addressed and the underlying mechanisms are discussed in the plant. Studies with some interacting factors such as ADA2b provided valuable information for the complicated histone acetylation mechanisms. We also suggest the future focuses for GCN5 functions and mechanisms such as functions in seed development/germination stages, exploration of novel interaction factors, identification of more protein substrates, and application of advanced biotechnology-CRISPR in crop genetic improvement, which would be helpful for the complete illumination of roles and mechanisms of GCN5.
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16
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Jing Y, Guo Q, Lin R. The SNL-HDA19 histone deacetylase complex antagonizes HY5 activity to repress photomorphogenesis in Arabidopsis. THE NEW PHYTOLOGIST 2021; 229:3221-3236. [PMID: 33245784 DOI: 10.1111/nph.17114] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/19/2020] [Indexed: 05/25/2023]
Abstract
Reprogramming of the transcriptome during photomorphogenesis requires dynamic changes in chromatin and distribution of histone modifications. However, the chromatin-based regulation of this process remains to be elucidated. Here, we identify the conserved SWI-INDEPENDENT3 LIKE (SNL)-HISTONE DEACETYLASE19 (HDA19) deacetylase complex, including HDA19 and SNL1-SNL6, as a negative regulator of the light signaling pathway. Light-repression of HDA19 and SNLs expression is mediated by photoreceptors. HDA19 and SNLs are required for histone deacetylation and chromatin inactivation of PHYA gene. We further examined the interaction between SNL-HDA19 complex and ELONGATED HYPOCOTYL5 (HY5), and their antagonistic regulation on the expressions of target genes. The HDA19 deacetylase complex is recruited by HY5 to the chromatin regions of two positive light signaling genes, HY5 and B-BOX CONTAINING PROTEIN 22 (BBX22), thereby reduces the accessibility and histone acetylation and represses their expression. HDA19, SNL1, and HY5 associate with the same regulatory regions of HY5 and BBX22, and HY5 binding to these loci is enhanced upon SNL-HDA19 dysfunction. Our study reveals a crucial role for the HDA19 deacetylase complex in light signaling and demonstrates that the functional interplay between chromatin regulators and transcription factors regulates photomorphogenetic responses to the changing light environments.
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Affiliation(s)
- Yanjun Jing
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Qiang Guo
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rongcheng Lin
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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17
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Kundariya H, Yang X, Morton K, Sanchez R, Axtell MJ, Hutton SF, Fromm M, Mackenzie SA. MSH1-induced heritable enhanced growth vigor through grafting is associated with the RdDM pathway in plants. Nat Commun 2020; 11:5343. [PMID: 33093443 PMCID: PMC7582163 DOI: 10.1038/s41467-020-19140-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/24/2020] [Indexed: 12/20/2022] Open
Abstract
Plants transmit signals long distances, as evidenced in grafting experiments that create distinct rootstock-scion junctions. Noncoding small RNA is a signaling molecule that is graft transmissible, participating in RNA-directed DNA methylation; but the meiotic transmissibility of graft-mediated epigenetic changes remains unclear. Here, we exploit the MSH1 system in Arabidopsis and tomato to introduce rootstock epigenetic variation to grafting experiments. Introducing mutations dcl2, dcl3 and dcl4 to the msh1 rootstock disrupts siRNA production and reveals RdDM targets of methylation repatterning. Progeny from grafting experiments show enhanced growth vigor relative to controls. This heritable enhancement-through-grafting phenotype is RdDM-dependent, involving 1380 differentially methylated genes, many within auxin-related gene pathways. Growth vigor is associated with robust root growth of msh1 graft progeny, a phenotype associated with auxin transport based on inhibitor assays. Large-scale field experiments show msh1 grafting effects on tomato plant performance, heritable over five generations, demonstrating the agricultural potential of epigenetic variation. The meiotic transmissibility and progeny phenotypic influence of graft-mediated epigenetic changes remain unclear. Here, the authors use the msh1 mutant in the rootstock to trigger heritable enhanced growth vigor in Arabidopsis and tomato, and show it is associated with the RNA-directed DNA methylation pathway.
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Affiliation(s)
- Hardik Kundariya
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, USA.,Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Xiaodong Yang
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Kyla Morton
- EpiCrop Technologies, Inc., Lincoln, NE, USA
| | - Robersy Sanchez
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Michael J Axtell
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Samuel F Hutton
- Gulf Coast Research and Education Center, IFAS, University of Florida, Wimauma, FL, USA
| | | | - Sally A Mackenzie
- Departments of Biology and Plant Science, The Pennsylvania State University, University Park, PA, USA.
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18
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Kim S, Piquerez SJM, Ramirez-Prado JS, Mastorakis E, Veluchamy A, Latrasse D, Manza-Mianza D, Brik-Chaouche R, Huang Y, Rodriguez-Granados NY, Concia L, Blein T, Citerne S, Bendahmane A, Bergounioux C, Crespi M, Mahfouz MM, Raynaud C, Hirt H, Ntoukakis V, Benhamed M. GCN5 modulates salicylic acid homeostasis by regulating H3K14ac levels at the 5' and 3' ends of its target genes. Nucleic Acids Res 2020; 48:5953-5966. [PMID: 32396165 PMCID: PMC7293002 DOI: 10.1093/nar/gkaa369] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 04/27/2020] [Accepted: 05/02/2020] [Indexed: 01/01/2023] Open
Abstract
The modification of histones by acetyl groups has a key role in the regulation of chromatin structure and transcription. The Arabidopsis thaliana histone acetyltransferase GCN5 regulates histone modifications as part of the Spt-Ada-Gcn5 Acetyltransferase (SAGA) transcriptional coactivator complex. GCN5 was previously shown to acetylate lysine 14 of histone 3 (H3K14ac) in the promoter regions of its target genes even though GCN5 binding did not systematically correlate with gene activation. Here, we explored the mechanism through which GCN5 controls transcription. First, we fine-mapped its GCN5 binding sites genome-wide and then used several global methodologies (ATAC-seq, ChIP-seq and RNA-seq) to assess the effect of GCN5 loss-of-function on the expression and epigenetic regulation of its target genes. These analyses provided evidence that GCN5 has a dual role in the regulation of H3K14ac levels in their 5′ and 3′ ends of its target genes. While the gcn5 mutation led to a genome-wide decrease of H3K14ac in the 5′ end of the GCN5 down-regulated targets, it also led to an increase of H3K14ac in the 3′ ends of GCN5 up-regulated targets. Furthermore, genome-wide changes in H3K14ac levels in the gcn5 mutant correlated with changes in H3K9ac at both 5′ and 3′ ends, providing evidence for a molecular link between the depositions of these two histone modifications. To understand the biological relevance of these regulations, we showed that GCN5 participates in the responses to biotic stress by repressing salicylic acid (SA) accumulation and SA-mediated immunity, highlighting the role of this protein in the regulation of the crosstalk between diverse developmental and stress-responsive physiological programs. Hence, our results demonstrate that GCN5, through the modulation of H3K14ac levels on its targets, controls the balance between biotic and abiotic stress responses and is a master regulator of plant-environmental interactions.
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Affiliation(s)
- Soonkap Kim
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France.,Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Sophie J M Piquerez
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France.,School of Life Sciences and Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
| | - Juan S Ramirez-Prado
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Emmanouil Mastorakis
- School of Life Sciences and Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
| | - Alaguraj Veluchamy
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - David Latrasse
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Deborah Manza-Mianza
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Rim Brik-Chaouche
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Ying Huang
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Natalia Y Rodriguez-Granados
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Lorenzo Concia
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Thomas Blein
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Sylvie Citerne
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles 78000, France
| | - Abdelhafid Bendahmane
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Catherine Bergounioux
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Martin Crespi
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Magdy M Mahfouz
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Cécile Raynaud
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Heribert Hirt
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France.,Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Vardis Ntoukakis
- School of Life Sciences and Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France.,Institut Universitaire de France (IUF)
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19
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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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20
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Jing Y, Lin R. Transcriptional regulatory network of the light signaling pathways. THE NEW PHYTOLOGIST 2020; 227:683-697. [PMID: 32289880 DOI: 10.1111/nph.16602] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 03/19/2020] [Indexed: 05/18/2023]
Abstract
The developmental program by which plants respond is tightly controlled by a complex cascade in which photoreceptors perceive and transduce the light signals that drive signaling processes and direct the transcriptional reprogramming, yielding specific cellular responses. The molecular mechanisms involved in the transcriptional regulation include light-regulated nuclear localization (the phytochromes and UVR8) and nuclear accumulation (the cryptochrome, cry2) of photoreceptors. This regulatory cascade also includes master regulatory transcription factors (TFs) that bridge photoreceptor activation with chromatin remodeling and regulate the expression of numerous light-responsive genes. Light signaling-related TFs often function as signal convergence points in concert with TFs in other signaling pathways to integrate complex endogenous and environmental cues that help the plant adapt to the surrounding environment. Increasing evidence suggests that chromatin modifications play a critical role in regulating light-responsive gene expression and provide an additional layer of light signaling regulation. Here, we provide an overview of our current knowledge of the transcriptional regulatory network involved in the light response, particularly the roles of TFs and chromatin in regulating light-responsive gene expression.
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Affiliation(s)
- Yanjun Jing
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Rongcheng Lin
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Beijing, 100093, China
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21
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Grasser KD, Rubio V, Barneche F. Multifaceted activities of the plant SAGA complex. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194613. [PMID: 32745625 DOI: 10.1016/j.bbagrm.2020.194613] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 07/27/2020] [Accepted: 07/27/2020] [Indexed: 12/22/2022]
Abstract
From yeast to human, the Spt-Ada-GCN5-acetyltransferase (SAGA) gigantic complex modifies chromatin during RNA polymerase II initiation and elongation steps to facilitate transcription. Its enzymatic activity involves a histone acetyltransferase module (HATm) that acetylates multiple lysine residues on the N-terminal tails of histones H2B and H3 and a deubiquitination module (DUBm) that triggers co-transcriptional deubiquitination of histone H2B. With a few notable exceptions described in this review, most SAGA subunits identified in yeast and metazoa are present in plants. Studies from the last 20 years have unveiled that different SAGA subunits are involved in gene expression regulation during the plant life cycle and in response to various types of stress or environmental cues. Their functional analysis in the Arabidopsis thaliana model species is increasingly shedding light on their intrinsic properties and how they can themselves be regulated during plant adaptive responses. Recent biochemical studies have also uncovered multiple associations between plant SAGA and chromatin machineries linked to RNA Pol II transcription. Still, considerably less is known about the molecular links between SAGA or SAGA-like complexes and chromatin dynamics during transcription in Arabidopsis and other plant species. We summarize the emerging knowledge on plant SAGA complex composition and activity, with a particular focus on the best-characterized subunits from its HAT (such as GCN5) and DUB (such as UBP22) modules, and implication of these ensembles in plant development and adaptive responses.
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Affiliation(s)
- Klaus D Grasser
- Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany.
| | - Vicente Rubio
- Plant Molecular Genetics Dept., Centro Nacional de Biotecnología (CNB-CSIC), Darwin, 3, 28049 Madrid, Spain.
| | - Fredy Barneche
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.
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Wang T, Xing J, Liu Z, Zheng M, Yao Y, Hu Z, Peng H, Xin M, Zhou D, Ni Z. Histone acetyltransferase GCN5-mediated regulation of long non-coding RNA At4 contributes to phosphate starvation response in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:6337-6348. [PMID: 31401648 PMCID: PMC6859718 DOI: 10.1093/jxb/erz359] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 07/19/2019] [Indexed: 05/04/2023]
Abstract
Phosphate availability is becoming a limiting environmental factor that inhibits plant growth and development. Here, we demonstrated that mutation of the histone acetyltransferase GCN5 impaired phosphate starvation responses (PSRs) in Arabidopsis. Transcriptome analysis revealed that 888 GCN5-regulated candidate genes were potentially involved in responding to phosphate starvation. ChIP assay indicated that four genes, including a long non-coding RNA (lncRNA) At4, are direct targets of GCN5 in PSR regulation. In addition, GCN5-mediated H3K9/14 acetylation of At4 determined dynamic At4 expression. Consistent with the function of At4 in phosphate distribution, mutation of GCN5 impaired phosphate accumulation between shoots and roots under phosphate deficiency condition, whereas constitutive expression of At4 in gcn5 mutants partially restored phosphate relocation. Further evidence proved that GCN5 regulation of At4 influenced the miRNA miR399 and its target PHO2 mRNA level. Taken together, we propose that GCN5-mediated histone acetylation plays a crucial role in PSR regulation via the At4-miR399-PHO2 pathway and provides a new epigenetic mechanism for the regulation of lncRNA in plants.
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Affiliation(s)
- Tianya Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement (Beijing Municipality), China Agricultural University, Beijing, China
- College of Agronomy and Biotechnology, China Agricultural University, Haidian District, Beijing, China
| | - Jiewen Xing
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement (Beijing Municipality), China Agricultural University, Beijing, China
- College of Agronomy and Biotechnology, China Agricultural University, Haidian District, Beijing, China
| | - Zhenshan Liu
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement (Beijing Municipality), China Agricultural University, Beijing, China
- College of Agronomy and Biotechnology, China Agricultural University, Haidian District, Beijing, China
| | - Mei Zheng
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement (Beijing Municipality), China Agricultural University, Beijing, China
- College of Agronomy and Biotechnology, China Agricultural University, Haidian District, Beijing, China
| | - Yingyin Yao
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement (Beijing Municipality), China Agricultural University, Beijing, China
- College of Agronomy and Biotechnology, China Agricultural University, Haidian District, Beijing, China
| | - Zhaorong Hu
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement (Beijing Municipality), China Agricultural University, Beijing, China
- College of Agronomy and Biotechnology, China Agricultural University, Haidian District, Beijing, China
| | - Huiru Peng
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement (Beijing Municipality), China Agricultural University, Beijing, China
- College of Agronomy and Biotechnology, China Agricultural University, Haidian District, Beijing, China
| | - Mingming Xin
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement (Beijing Municipality), China Agricultural University, Beijing, China
- College of Agronomy and Biotechnology, China Agricultural University, Haidian District, Beijing, China
| | - Daoxiu Zhou
- Institut of Plant Science Paris-Saclay, Université Paris sud, Orsay, France
| | - Zhongfu Ni
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement (Beijing Municipality), China Agricultural University, Beijing, China
- College of Agronomy and Biotechnology, China Agricultural University, Haidian District, Beijing, China
- Correspondence:
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Wang T, Jia Q, Wang W, Hussain S, Ahmed S, Zhou DX, Ni Z, Wang S. GCN5 modulates trichome initiation in Arabidopsis by manipulating histone acetylation of core trichome initiation regulator genes. PLANT CELL REPORTS 2019; 38:755-765. [PMID: 30927071 DOI: 10.1007/s00299-019-02404-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 03/19/2019] [Indexed: 05/25/2023]
Abstract
Histone acetyltransferase GCN5 affects trichome initiation via mediating the expression of some core trichome initiation regulator genes in Arabidopsis. GENERAL CONTROL NON-REPRESSED PROTEIN5 (GCN5), a histone acetyltransferase involved in the regulation of cell differentiation, organ development, secondary metabolism, and plant responses to abiotic stresses, has recently been shown to modulate trichome branching in Arabidopsis. Here, we provide evidence that GCN5 is also involved in the regulation of trichome initiation. We found that mutation of GCN5 led to increased leaf trichome density in Arabidopsis. Quantitative RT-PCR results showed that the expression of CPC, GL1, GL2, and GL3, four well-known core trichome initiation regulator genes, was decreased in the gcn5 mutants. ChIP assays indicated that these four trichome initiation regulator genes are direct targets of GCN5. Consistent with these results, GCN5-mediated H3K14/K9 acetylation levels on the TSS regions of these genes were decreased. On the other hand, leaf trichome density was reduced in plants overexpressing GCN5, and both the transcript levels and GCN5-binding enrichments of CPC, GL1, GL2, and GL3 genes were elevated. Taken together, these data suggests that GCN5 affects trichome initiation by modulating the transcription activities of trichome initiation regulator genes via H3K9/14 acetylation.
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Affiliation(s)
- Tianya Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Qiming Jia
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Wei Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Saddam Hussain
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Sajjad Ahmed
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Dao-Xiu Zhou
- Institute of Plant Science Paris-Saclay, Université Paris Sud, 91405, Orsay, France
| | - Zhongfu Ni
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Shucai Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
- College of Life Science, Linyi University, Linyi, 276000, China.
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Bourbousse C, Barneche F. A Dynamic Signaling Path to Chromatin-Level Control of Plant Drought Response. MOLECULAR PLANT 2019; 12:292-294. [PMID: 30738193 DOI: 10.1016/j.molp.2019.01.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 01/18/2019] [Accepted: 01/28/2019] [Indexed: 06/09/2023]
Affiliation(s)
- Clara Bourbousse
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005 Paris, France.
| | - Fredy Barneche
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005 Paris, France.
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Park EY, Tsuyuki KM, Hu F, Lee J, Jeong J. PRC2-Mediated H3K27me3 Contributes to Transcriptional Regulation of FIT-Dependent Iron Deficiency Response. FRONTIERS IN PLANT SCIENCE 2019; 10:627. [PMID: 31156682 PMCID: PMC6532572 DOI: 10.3389/fpls.2019.00627] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 04/26/2019] [Indexed: 05/21/2023]
Abstract
Iron is an essential micronutrient for nearly all organisms, but excessive iron can lead to the formation of cytotoxic reactive oxygen species. Therefore, iron acquisition and homeostasis must be tightly regulated. Plants have evolved complex mechanisms to optimize their use of iron, which is one of the most limiting nutrients in the soil. In particular, transcriptional regulation is vital for regulating iron in plants, and much work has revealed the role of transcription factors on this front. Our study adds novel insights to the transcriptional regulation of iron homeostasis in plants by showing that chromatin remodeling via histone 3 lysine 27 trimethylation (H3K27me3) modulates the expression of FIT-dependent genes under iron deficiency. We provide evidence that FIT-dependent iron acquisition genes, IRT1 and FRO2, as well as FIT itself are direct targets of PRC2-mediated H3K27me3. In the clf mutant, which lacks the predominant H3K27 tri-methyltransferase, induction of FIT, FRO2, IRT1, and other FIT-regulated genes in roots is significantly higher under iron deficient conditions than in wild type. Furthermore, we observe that clf mutants are more tolerant to iron deficiency than wild type, indicating that gene expression levels appear to be limiting the plants ability to access iron. We propose that H3K27me3 attenuates the induction of FIT-target genes under iron deficiency and hypothesize that this may serve as a mechanism to restrict the maximum level of induction of iron acquisition genes to prevent iron overload.
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Affiliation(s)
- Emily Y. Park
- Program in Biochemistry and Biophysics, Amherst College, Amherst, MA, United States
| | - Kaitlyn M. Tsuyuki
- Program in Biochemistry and Biophysics, Amherst College, Amherst, MA, United States
- Department of Biology, Amherst College, Amherst, MA, United States
| | - Fengling Hu
- Department of Biology, Amherst College, Amherst, MA, United States
| | - Joohyun Lee
- Program in Biochemistry and Biophysics, Amherst College, Amherst, MA, United States
- Department of Biology, Amherst College, Amherst, MA, United States
| | - Jeeyon Jeong
- Program in Biochemistry and Biophysics, Amherst College, Amherst, MA, United States
- Department of Biology, Amherst College, Amherst, MA, United States
- *Correspondence: Jeeyon Jeong,
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Chu J, Chen Z. Molecular identification of histone acetyltransferases and deacetylases in lower plant Marchantia polymorpha. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 132:612-622. [PMID: 30336381 DOI: 10.1016/j.plaphy.2018.10.012] [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: 06/18/2018] [Revised: 09/18/2018] [Accepted: 10/10/2018] [Indexed: 06/08/2023]
Abstract
Histone is the core component of nucleosome and modification of amino acid residues on histone tails is one of the most pivotal epigenetic regulatory mechanisms. Histone acetylation or deacetylation is carried out by two groups of proteins: histone acetyltransferases (HATs) or histone deacetylases (HDACs), and has been proven to be tightly linked to regulation of gene expression in animals and vascular plants. The biological functions of HATs and HDACs in non-flowering plants remain largely unknown. We found that there are seven MpHAT genes and twelve MpHDAC genes present in the Marchantia genome, and the comprehensive protein sequence analysis of the HAT and HDAC families was introduced to investigate their potential functions. On the basis of the functional domain analysis, eight MpHATs and twelve MpHDACs contain the conserved functional domains as the defining feature of each family. Phylogenetic trees of all families of MpHATs and MpHDACs along with their homologs from different plant and green algae species were constructed to illustrate evolutionary relationship of HAT and HDAC proteins. We found both SIR2 family and RPD3/HDA1 superfamily possess lower plant-specific proteins indicating the potential unknown functions of HATs and HDACs in Marchantia and other lower plant or algae species. Subcellular localization prediction suggests that MpHATs and MpHDACs are likely functioning in various organelles. Expression analysis shows that all MpHAT and MpHDAC genes are expressed in all tissues with differences at the transcriptional level. In addition, their expression patterns were altered in response to various treatments with plant hormones and environmental stress. We concluded that all MpHATs and MpHDACs are functional proteins in Marchantia and involved in various signaling pathways. Marchantia could have developed a complex histone acetylation epigenetic mechanism to regulate growth and development, as well as responses to environment.
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Affiliation(s)
- Jiashu Chu
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, 1 Nanyang Walk, Singapore, 637616, Singapore
| | - Zhong Chen
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, 1 Nanyang Walk, Singapore, 637616, Singapore.
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27
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Poulios S, Vlachonasios KE. Synergistic action of GCN5 and CLAVATA1 in the regulation of gynoecium development in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2018; 220:593-608. [PMID: 30027613 DOI: 10.1111/nph.15303] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/24/2018] [Indexed: 05/29/2023]
Abstract
In Arabidopsis thaliana the CLAVATA1 (CLV1) receptor and GENERAL CONTROL NON DEREPRESSIBLE 5 (GCN5) histone acetyltransferase both regulate inflorescence meristem size and affect the expression of the meristem-promoting transcription factor WUSCHEL (WUS). Single and multiple mutants of GCN5 and CLAVATA members, were analysed for their gynoecium development, using morphological, physiological, genetic and molecular approaches. The clv1-1gcn5-1 double mutants exhibited novel phenotypes including elongated gynoecia with reduced valves and enlarged stigma and style, indicating a synergistic action of CLAVATA signaling and GCN5 action in the development of the gynoecium. Reporter line and gene expression analysis showed that clv1-1gcn5-1 plants have altered auxin and cytokinin response, distribution and ectopic overexpression of WUS. WUS expression was found in the style of wild-type gynoecia stage 10-13, suggesting a possible novel role for WUS in the development of the style. CLV1 and GCN5 are regulators of apical-basal and mediolateral polarity of the Arabidopsis gynoecium. They affect gynoecium morphogenesis through the negative regulation of auxin biosynthesis and promotion of polar auxin transport. They also promote cytokinin signaling in the carpel margin meristem and negatively regulate it at the stigma. Finally, they synergistically suppress WUS at the centre of the gynoecium.
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Affiliation(s)
- Stylianos Poulios
- Department of Botany, School of Biology, Faculty of Science, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
| | - Konstantinos E Vlachonasios
- Department of Botany, School of Biology, Faculty of Science, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
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28
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Kotak J, Saisana M, Gegas V, Pechlivani N, Kaldis A, Papoutsoglou P, Makris A, Burns J, Kendig AL, Sheikh M, Kuschner CE, Whitney G, Caiola H, Doonan JH, Vlachonasios KE, McCain ER, Hark AT. The histone acetyltransferase GCN5 and the transcriptional coactivator ADA2b affect leaf development and trichome morphogenesis in Arabidopsis. PLANTA 2018; 248:613-628. [PMID: 29846775 DOI: 10.1007/s00425-018-2923-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/23/2018] [Indexed: 06/08/2023]
Abstract
The histone acetyltransferase GCN5 and associated transcriptional coactivator ADA2b are required to couple endoreduplication and trichome branching. Mutation of ADA2b also disrupts the relationship between ploidy and leaf cell size. Dynamic chromatin structure has been established as a general mechanism by which gene function is temporally and spatially regulated, but specific chromatin modifier function is less well understood. To address this question, we have investigated the role of the histone acetyltransferase GCN5 and the associated coactivator ADA2b in developmental events in Arabidopsis thaliana. Arabidopsis plants with T-DNA insertions in GCN5 (also known as HAG1) or ADA2b (also known as PROPORZ1) display pleiotropic phenotypes including dwarfism and floral defects affecting fertility. We undertook a detailed characterization of gcn5 and ada2b phenotypic effects in rosette leaves and trichomes to establish a role for epigenetic control in these developmental processes. ADA2b and GCN5 play specific roles in leaf tissue, affecting cell growth and division in rosette leaves often in complex and even opposite directions. Leaves of gcn5 plants display overall reduced ploidy levels, while ada2b-1 leaves show increased ploidy. Endoreduplication leading to increased ploidy is also known to contribute to normal trichome morphogenesis. We demonstrate that gcn5 and ada2b mutants display alterations in the number and patterning of trichome branches, with ada2b-1 and gcn5-1 trichomes being significantly less branched, while gcn5-6 trichomes show increased branching. Elongation of the trichome stalk and branches also vary in different mutant backgrounds, with stalk length having an inverse relationship with branch number. Taken together, our data indicate that, in Arabidopsis, leaves and trichomes ADA2b and GCN5 are required to couple nuclear content with cell growth and morphogenesis.
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Affiliation(s)
- Jenna Kotak
- Biology Department, Muhlenberg College, Allentown, PA, USA
- Molecular Biology, Cell Biology, and Biochemistry Department, Brown University, Providence, RI, USA
| | - Marina Saisana
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Vasilis Gegas
- National Plant Phenomics Centre, Aberystwyth University, Aberystwyth, UK
- Limagrain UK Ltd, Joseph Nickerson Research Centre, Rothwell, Market Rasen, Lincolnshire, UK
| | - Nikoletta Pechlivani
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Athanasios Kaldis
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Panagiotis Papoutsoglou
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Athanasios Makris
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Julia Burns
- Biology Department, Muhlenberg College, Allentown, PA, USA
| | | | - Minnah Sheikh
- Biology Department, Muhlenberg College, Allentown, PA, USA
| | | | | | - Hanna Caiola
- Biology Department, Muhlenberg College, Allentown, PA, USA
| | - John H Doonan
- National Plant Phenomics Centre, Aberystwyth University, Aberystwyth, UK
| | | | | | - Amy T Hark
- Biology Department, Muhlenberg College, Allentown, PA, USA.
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Wang T, Xing J, Liu X, Yao Y, Hu Z, Peng H, Xin M, Zhou DX, Zhang Y, Ni Z. GCN5 contributes to stem cuticular wax biosynthesis by histone acetylation of CER3 in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:2911-2922. [PMID: 29506042 PMCID: PMC5972625 DOI: 10.1093/jxb/ery077] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 02/20/2018] [Indexed: 05/06/2023]
Abstract
Cuticular wax is a major component of the surface cuticle of plants, which performs crucial functions in optimizing plant growth. Histone acetylation regulates gene expression in diverse biological processes, but its role in cuticular wax synthesis is not well understood. In this study, we observed that mutations of the Arabidopsis thaliana histone acetyltransferase GENERAL CONTROL NON-REPRESSED PROTEIN5 (GCN5) impaired the accumulation of stem cuticular wax. Three target genes of GCN5, ECERIFERUM3 (CER3), CER26, and CER1-LIKE1 (CER1-L1), were identified by RNA-seq and ChIP assays. H3K9/14 acetylation levels at the promoter regions of CER3, CER26, and CER1-L1 were consistently and significantly decreased in the gcn5-2 mutant as compared to the wild-type. Notably, overexpression of CER3 in the gcn5-2 mutant rescued the defect in stem cuticular wax biosynthesis. Collectively, these data demonstrate that GCN5 is involved in stem cuticular wax accumulation by modulating CER3 expression via H3K9/14 acetylation, which underlines the important role of histone acetylation in cuticular wax biosynthesis.
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Affiliation(s)
- Tianya Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement (Beijing Municipality), China Agricultural University, Beijing, China
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Jiewen Xing
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement (Beijing Municipality), China Agricultural University, Beijing, China
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Xinye Liu
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement (Beijing Municipality), China Agricultural University, Beijing, China
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yingyin Yao
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement (Beijing Municipality), China Agricultural University, Beijing, China
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Zhaorong Hu
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement (Beijing Municipality), China Agricultural University, Beijing, China
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Huiru Peng
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement (Beijing Municipality), China Agricultural University, Beijing, China
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Mingming Xin
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement (Beijing Municipality), China Agricultural University, Beijing, China
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Dao-Xiu Zhou
- Institute of Plant Science Paris-Saclay, Université Paris Sud, 91405 Orsay, France
| | - Yirong Zhang
- National Maize Improvement Center, China Agricultural University, Beijing, China
| | - Zhongfu Ni
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement (Beijing Municipality), China Agricultural University, Beijing, China
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- Correspondence:
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30
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Identification and functional characterisation of an allene oxide synthase from grapevine (Vitis vinifera L. Sauvignon blanc). Mol Biol Rep 2018; 45:263-277. [DOI: 10.1007/s11033-018-4159-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 01/31/2018] [Indexed: 01/01/2023]
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Martel A, Brar H, Mayer BF, Charron JB. Diversification of the Histone Acetyltransferase GCN5 through Alternative Splicing in Brachypodium distachyon. FRONTIERS IN PLANT SCIENCE 2017; 8:2176. [PMID: 29312415 PMCID: PMC5743026 DOI: 10.3389/fpls.2017.02176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/12/2017] [Indexed: 06/07/2023]
Abstract
The epigenetic modulatory SAGA complex is involved in various developmental and stress responsive pathways in plants. Alternative transcripts of the SAGA complex's enzymatic subunit GCN5 have been identified in Brachypodium distachyon. These splice variants differ based on the presence and integrity of their conserved domain sequences: the histone acetyltransferase domain, responsible for catalytic activity, and the bromodomain, involved in acetyl-lysine binding and genomic loci targeting. GCN5 is the wild-type transcript, while alternative splice sites result in the following transcriptional variants: L-GCN5, which is missing the bromodomain and S-GCN5, which lacks the bromodomain as well as certain motifs of the histone acetyltransferase domain. Absolute mRNA quantification revealed that, across eight B. distachyon accessions, GCN5 was the dominant transcript isoform, accounting for up to 90% of the entire transcript pool, followed by L-GCN5 and S-GCN5. A cycloheximide treatment further revealed that the S-GCN5 splice variant was degraded through the nonsense-mediated decay pathway. All alternative BdGCN5 transcripts displayed similar transcript profiles, being induced during early exposure to heat and displaying higher levels of accumulation in the crown, compared to aerial tissues. All predicted protein isoforms localize to the nucleus, which lends weight to their purported epigenetic functions. S-GCN5 was incapable of forming an in vivo protein interaction with ADA2, the transcriptional adaptor that links the histone acetyltransferase subunit to the SAGA complex, while both GCN5 and L-GCN5 interacted with ADA2, which suggests that a complete histone acetyltransferase domain is required for BdGCN5-BdADA2 interaction in vivo. Thus, there has been a diversification in BdGCN5 through alternative splicing that has resulted in differences in conserved domain composition, transcript fate and in vivo protein interaction partners. Furthermore, our results suggest that B. distachyon may harbor compositionally distinct SAGA-like complexes that differ based on their histone acetyltransferase subunit.
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Chen F, Fu B, Pan Y, Zhang C, Wen H, Weng Y, Chen P, Li Y. Fine mapping identifies CsGCN5 encoding a histone acetyltransferase as putative candidate gene for tendril-less1 mutation (td-1) in cucumber. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1549-1558. [PMID: 28466109 DOI: 10.1007/s00122-017-2909-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/13/2017] [Indexed: 05/10/2023]
Abstract
Next-generation sequencing-aided map-based cloning delimited the cucumber tendril - less1 ( td - 1 ) locus into a 190.7-kb region in chromosome 6 harboring a putative, novel-function candidate gene encoding a histone acetyltransferase ( CsGCN5 ). The tendril initiated from the lateral meristem is an important and characteristic organ for the species in the Cucurbitaceae family including cucumber (Cucumis sativus L.). While the tendril has its evolutionary significance, it also poses a nuisance in cucumber cultivation under protected environments in which tendril-less cucumber has its advantages. From an EMS mutagenesis population, we identified a tendril-less mutant B007, which was controlled by a recessive gene td-1. Through next-generation sequencing-aided map-based cloning, we show CsGCN5 (Cucumis sativus GENERAL CONTROL NONDEREPRESSIBLE 5), a cucumber gene for a histone acetyltransferase as the most possible candidate for td-1. A non-synonymous SNP in the first exon of CsGCN5 resulted in an amino-acid substitution from Asp (D) in the wild type to Asn (N) in the tendril-less mutant. The candidacy of CsGCN5 was further confirmed by multiple lines of evidence in both biparental and natural cucumber populations. Non-significant expression of CsGCN5 in multiple organs was found between the wild type and the mutant. CsGCN5 exhibited strong expression in the tendril of wild-type plants suggesting its important roles in growth and development of plant tendrils. The identification and characterization of the td-1 mutant from the present study provided a useful tool in understanding the molecular mechanisms of tendril organogenesis and investigation of novel functions of the histone acetyltransferase in cucumber.
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Affiliation(s)
- Feifan Chen
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Bingbing Fu
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yupeng Pan
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
| | - Chaowen Zhang
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Haifan Wen
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yiqun Weng
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
- USDA-ARS, Vegetable Crops Research Unit, 1575 Linden Drive, Madison, WI, 53706, USA
| | - Peng Chen
- College of Life Science, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Yuhong Li
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Wang L, Zhang F, Rode S, Chin KK, Ko EE, Kim J, Iyer VR, Qiao H. Ethylene induces combinatorial effects of histone H3 acetylation in gene expression in Arabidopsis. BMC Genomics 2017; 18:538. [PMID: 28716006 PMCID: PMC5512946 DOI: 10.1186/s12864-017-3929-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 07/06/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Histone acetylation and deacetylation are essential for gene regulation and have been implicated in the regulation of plant hormone responses. Many studies have indicated the role of histone acetylation in ethylene signaling; however, few studies have investigated how ethylene signaling regulates the genomic landscape of chromatin states. Recently, we found that ethylene can specifically elevate histone H3K14 acetylation and the non-canonical histone H3K23 acetylation in etiolated seedlings and the gene activation is positively associated with the elevation of H3K14Ac and H3K23Ac in response to ethylene. To assess the role of H3K9, H3K14, and H3K23 histone modifications in the ethylene response, we examined how ethylene regulates histone acetylation and the transcriptome at global level and in ethylene regulated genes both in wild type (Col-0) and ein2-5 seedlings. RESULTS Our results revealed that H3K9Ac, H3K14Ac, and H3K23Ac are preferentially enriched around the transcription start sites and are positively correlated with gene expression levels in Col-0 and ein2-5 seedlings both with and without ethylene treatment. In the absence of ethylene, no combinatorial effect of H3K9Ac, H3K14Ac, and H3K23Ac on gene expression was detected. In the presence of ethylene, however, combined enrichment of the three histone acetylation marks was associated with high gene expression levels, and this ethylene-induced change was EIN2 dependent. In addition, we found that ethylene-regulated genes are expressed at medium or high levels, and a group of ethylene regulated genes are marked by either one of H3K9Ac, H3K14Ac or H3K23Ac. In this group of genes, the levels of H3K9Ac were altered by ethylene, but in the absence of ethylene the levels of H3K9Ac and peak breadths are distinguished in up- and down- regulated genes. In the presence of ethylene, the changes in the peak breadths and levels of H3K14Ac and H3K23Ac are required for the alteration of gene expressions. CONCLUSIONS Our study reveals that the plant hormone ethylene induces combinatorial effects of H3K9Ac, K14Ac and K23Ac histone acetylation in gene expression genome widely. Further, for a group of ethylene regulated genes, in the absence of ethylene the levels and the covered breadths of H3K9Ac are the preexist markers for distinguishing up- and down- regulated genes, the change in the peak breadths and levels of H3K14Ac and H3K23Ac are required for the alteration of gene expression in the presence of ethylene.
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Affiliation(s)
- Likai Wang
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, 78712, Texas, USA.,The Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, 78712, Texas, USA.,Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Fan Zhang
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, 78712, Texas, USA.,The Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, 78712, Texas, USA.,Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Siddharth Rode
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Kevin K Chin
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Eun Esther Ko
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Jonghwan Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Vishwanath R Iyer
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, 78712, Texas, USA.,The Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, 78712, Texas, USA.,Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Hong Qiao
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, 78712, Texas, USA. .,The Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, 78712, Texas, USA. .,Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, 78712, USA.
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Aboulela M, Tanaka Y, Nishimura K, Mano S, Nishimura M, Ishiguro S, Kimura T, Nakagawa T. Development of an R4 dual-site (R4DS) gateway cloning system enabling the efficient simultaneous cloning of two desired sets of promoters and open reading frames in a binary vector for plant research. PLoS One 2017; 12:e0177889. [PMID: 28520787 PMCID: PMC5433782 DOI: 10.1371/journal.pone.0177889] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 05/04/2017] [Indexed: 02/06/2023] Open
Abstract
Vast numbers of proteins work cooperatively to exert their functions in various cells. In order to understand the functions and molecular mechanisms of these proteins in plants, analyses of transgenic plants that concomitantly express two protein-coding genes are often required. We developed a novel Gateway cloning technology-compatible binary vector system, the R4 dual-site (R4DS) Gateway cloning system, which enables the easy and efficient cloning of two desired sets of promoters and open reading frames (ORFs) into a binary vector using promoter and ORF entry clones. In this system, C-terminal fusions with 17 kinds of tags including visible reporters and epitope tags are available for each ORF, and selection by four kinds of resistance markers is possible. We verified that the R4DS Gateway cloning system functioned well in Arabidopsis thaliana by observing the expression and localization patterns of fluorescent proteins fused with organelle-targeting signals and driven by stomatal-lineage specific promoters. We also confirmed that the two cloning sites in the R4DS Gateway cloning system were equivalent and independently regulated. The results obtained indicate that the R4DS Gateway cloning system facilitates detailed comparisons of the expression patterns of two promoters as well as co-localization and interaction analyses of two proteins in specific cells in plants.
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Affiliation(s)
- Mostafa Aboulela
- Department of Molecular and Functional Genomics, Interdisciplinary Center for Science Research, Organization for Research, Shimane University, Matsue, Japan
- Bioresources Science, The United Graduate School of Agricultural Sciences, Tottori University, Tottori, Japan
- Department of Botany and Microbiology, Faculty of Science, Assiut University, Assiut, Egypt
| | - Yuji Tanaka
- Department of Molecular and Functional Genomics, Interdisciplinary Center for Science Research, Organization for Research, Shimane University, Matsue, Japan
| | - Kohji Nishimura
- Department of Molecular and Functional Genomics, Interdisciplinary Center for Science Research, Organization for Research, Shimane University, Matsue, Japan
- Bioresources Science, The United Graduate School of Agricultural Sciences, Tottori University, Tottori, Japan
| | - Shoji Mano
- Department of Evolutionary Biology and Biodiversity, National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
| | - Mikio Nishimura
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, Japan
| | - Sumie Ishiguro
- Department of Biological Mechanisms and Functions, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Tetsuya Kimura
- Department of Life Sciences, Graduate School of Bioresources, Mie University, Tsu, Japan
| | - Tsuyoshi Nakagawa
- Department of Molecular and Functional Genomics, Interdisciplinary Center for Science Research, Organization for Research, Shimane University, Matsue, Japan
- Bioresources Science, The United Graduate School of Agricultural Sciences, Tottori University, Tottori, Japan
- * E-mail:
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Tang Y, Liu X, Liu X, Li Y, Wu K, Hou X. Arabidopsis NF-YCs Mediate the Light-Controlled Hypocotyl Elongation via Modulating Histone Acetylation. MOLECULAR PLANT 2017; 10:260-273. [PMID: 27876642 DOI: 10.1016/j.molp.2016.11.007] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 11/14/2016] [Accepted: 11/14/2016] [Indexed: 05/20/2023]
Abstract
Light is a crucial environmental signal that promotes photomorphogenesis, the developmental process with a series of light-dependent alterations for plants to adapt various external challenges. Chromatin modification has been proposed to be involved in such light-mediated growth, but the underlying mechanism is still elusive. In this study, we identified four Arabidopsis thaliana Nuclear Factor-YC homologs, NF-YC1, NF-YC3, NF-YC4, and NF-YC9 (NF-YCs), which function redundantly as repressors of light-controlled hypocotyl elongation via histone deacetylation. Obvious etiolation phenotypes are observed in NF-YCs loss-of-function mutant seedlings grown under light conditions, including significant elongated hypocotyls and fewer opened cotyledons. We found that NF-YCs interact with histone deacetylase HDA15 in the light, co-target the promoters of a set of hypocotyl elongation-related genes, and modulate the levels of histone H4 acetylation on the associated chromatins, thus repressing gene expression. In contrast, NF-YC-HDA15 complex is dismissed from the target genes in the dark, resulting in increased level of H4 acetylation and consequent etiolated growth. Further analyses revealed that transcriptional repression activity of NF-YCs on the light-controlled hypocotyl elongation partially depends on the deacetylation activity of HDA15, and loss of HDA15 function could rescue the short-hypocotyl phenotype of NF-YCs overexpression plants. Taken together, our results indicate that NF-YC1, NF-YC3, NF-YC4, and NF-YC9 function as transcriptional co-repressors by interacting with HDA15 to inhibit hypocotyl elongation in photomorphogenesis during the early seedling stage. Our findings highlight that NF-YCs can modulate plant development in response to environmental cues via epigenetic regulation.
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Affiliation(s)
- Yang Tang
- 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, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xuncheng Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Xu Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yuge Li
- 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, China
| | - Keqiang Wu
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei
| | - Xingliang Hou
- 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, China.
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Zang X, Geng X, Wang F, Liu Z, Zhang L, Zhao Y, Tian X, Ni Z, Yao Y, Xin M, Hu Z, Sun Q, Peng H. Overexpression of wheat ferritin gene TaFER-5B enhances tolerance to heat stress and other abiotic stresses associated with the ROS scavenging. BMC PLANT BIOLOGY 2017; 17:14. [PMID: 28088182 PMCID: PMC5237568 DOI: 10.1186/s12870-016-0958-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 12/20/2016] [Indexed: 05/03/2023]
Abstract
BACKGROUND The yield of wheat (Triticum aestivum L.), an important crop, is adversely affected by heat stress in many regions of the world. However, the molecular mechanisms underlying thermotolerance are largely unknown. RESULTS A novel ferritin gene, TaFER, was identified from our previous heat stress-responsive transcriptome analysis of a heat-tolerant wheat cultivar (TAM107). TaFER was mapped to chromosome 5B and named TaFER-5B. Expression pattern analysis revealed that TaFER-5B was induced by heat, polyethylene glycol (PEG), H2O2 and Fe-ethylenediaminedi(o-hydroxyphenylacetic) acid (Fe-EDDHA). To confirm the function of TaFER-5B in wheat, TaFER-5B was transformed into the wheat cultivar Jimai5265 (JM5265), and the transgenic plants exhibited enhanced thermotolerance. To examine whether the function of ferritin from mono- and dico-species is conserved, TaFER-5B was transformed into Arabidopsis, and overexpression of TaFER-5B functionally complemented the heat stress-sensitive phenotype of a ferritin-lacking mutant of Arabidopsis. Moreover, TaFER-5B is essential for protecting cells against heat stress associated with protecting cells against ROS. In addition, TaFER-5B overexpression also enhanced drought, oxidative and excess iron stress tolerance associated with the ROS scavenging. Finally, TaFER-5B transgenic Arabidopsis and wheat plants exhibited improved leaf iron content. CONCLUSIONS Our results suggest that TaFER-5B plays an important role in enhancing tolerance to heat stress and other abiotic stresses associated with the ROS scavenging.
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Affiliation(s)
- Xinshan Zang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, NO.2 Yuanmingyuan Xi Road, Haidian District, Beijing, 100193 China
| | - Xiaoli Geng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, NO.2 Yuanmingyuan Xi Road, Haidian District, Beijing, 100193 China
| | - Fei Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, NO.2 Yuanmingyuan Xi Road, Haidian District, Beijing, 100193 China
| | - Zhenshan Liu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, NO.2 Yuanmingyuan Xi Road, Haidian District, Beijing, 100193 China
| | - Liyuan Zhang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, NO.2 Yuanmingyuan Xi Road, Haidian District, Beijing, 100193 China
| | - Yue Zhao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, NO.2 Yuanmingyuan Xi Road, Haidian District, Beijing, 100193 China
| | - Xuejun Tian
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, NO.2 Yuanmingyuan Xi Road, Haidian District, Beijing, 100193 China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, NO.2 Yuanmingyuan Xi Road, Haidian District, Beijing, 100193 China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, NO.2 Yuanmingyuan Xi Road, Haidian District, Beijing, 100193 China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, NO.2 Yuanmingyuan Xi Road, Haidian District, Beijing, 100193 China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, NO.2 Yuanmingyuan Xi Road, Haidian District, Beijing, 100193 China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, NO.2 Yuanmingyuan Xi Road, Haidian District, Beijing, 100193 China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, NO.2 Yuanmingyuan Xi Road, Haidian District, Beijing, 100193 China
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Wang T, Xing J, Liu X, Liu Z, Yao Y, Hu Z, Peng H, Xin M, Zhou DX, Zhang Y, Ni Z. Histone acetyltransferase general control non-repressed protein 5 (GCN5) affects the fatty acid composition of Arabidopsis thaliana seeds by acetylating fatty acid desaturase3 (FAD3). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:794-808. [PMID: 27500884 DOI: 10.1111/tpj.13300] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 08/02/2016] [Accepted: 08/05/2016] [Indexed: 06/06/2023]
Abstract
Seed oils are important natural resources used in the processing and preparation of food. Histone modifications represent key epigenetic mechanisms that regulate gene expression, plant growth and development. However, histone modification events during fatty acid (FA) biosynthesis are not well understood. Here, we demonstrate that a mutation of the histone acetyltransferase GCN5 can decrease the ratio of α-linolenic acid (ALA) to linoleic acid (LA) in seed oil. Using RNA-Seq and ChIP assays, we identified FAD3, LACS2, LPP3 and PLAIIIβ as the targets of GCN5. Notably, the GCN5-dependent H3K9/14 acetylation of FAD3 determined the expression levels of FAD3 in Arabidopsis thaliana seeds, and the ratio of ALA/LA in the gcn5 mutant was rescued to the wild-type levels through the overexpression of FAD3. The results of this study indicated that GCN5 modulated FA biosynthesis by affecting the acetylation levels of FAD3. We provide evidence that histone acetylation is involved in FA biosynthesis in Arabidopsis seeds and might contribute to the optimization of the nutritional structure of edible oils through epigenetic engineering.
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Affiliation(s)
- Tianya Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre (Beijing), Beijing, 100193, China
- Department of Plant Genetics & Breeding, China Agricultural University, Yuanmingyuan Xi Road No. 2, Haidian District, Beijing, 100193, China
| | - Jiewen Xing
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre (Beijing), Beijing, 100193, China
- Department of Plant Genetics & Breeding, China Agricultural University, Yuanmingyuan Xi Road No. 2, Haidian District, Beijing, 100193, China
| | - Xinye Liu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre (Beijing), Beijing, 100193, China
- Department of Plant Genetics & Breeding, China Agricultural University, Yuanmingyuan Xi Road No. 2, Haidian District, Beijing, 100193, China
| | - Zhenshan Liu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre (Beijing), Beijing, 100193, China
- Department of Plant Genetics & Breeding, China Agricultural University, Yuanmingyuan Xi Road No. 2, Haidian District, Beijing, 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre (Beijing), Beijing, 100193, China
- Department of Plant Genetics & Breeding, China Agricultural University, Yuanmingyuan Xi Road No. 2, Haidian District, Beijing, 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre (Beijing), Beijing, 100193, China
- Department of Plant Genetics & Breeding, China Agricultural University, Yuanmingyuan Xi Road No. 2, Haidian District, Beijing, 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre (Beijing), Beijing, 100193, China
- Department of Plant Genetics & Breeding, China Agricultural University, Yuanmingyuan Xi Road No. 2, Haidian District, Beijing, 100193, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre (Beijing), Beijing, 100193, China
- Department of Plant Genetics & Breeding, China Agricultural University, Yuanmingyuan Xi Road No. 2, Haidian District, Beijing, 100193, China
| | - Dao-Xiu Zhou
- Institute of Plant Science Paris-Saclay, Université Paris Sud, 91405, Orsay, France
| | - Yirong Zhang
- National Maize Improvement Centre of China, China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre (Beijing), Beijing, 100193, China
- Department of Plant Genetics & Breeding, China Agricultural University, Yuanmingyuan Xi Road No. 2, Haidian District, Beijing, 100193, China
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Velanis CN, Herzyk P, Jenkins GI. Regulation of transcription by the Arabidopsis UVR8 photoreceptor involves a specific histone modification. PLANT MOLECULAR BIOLOGY 2016; 92:425-443. [PMID: 27534420 PMCID: PMC5080334 DOI: 10.1007/s11103-016-0522-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 08/02/2016] [Indexed: 05/21/2023]
Abstract
The photoreceptor UV RESISTANCE LOCUS 8 (UVR8) specifically mediates photomorphogenic responses to UV-B wavelengths. UVR8 acts by regulating transcription of a set of genes, but the underlying mechanisms are unknown. Previous research indicated that UVR8 can associate with chromatin, but the specificity and functional significance of this interaction are not clear. Here we show, by chromatin immunoprecipitation, that UV-B exposure of Arabidopsis increases acetylation of lysines K9 and/or K14 of histone H3 at UVR8-regulated gene loci in a UVR8-dependent manner. The transcription factors HY5 and/or HYH, which mediate UVR8-regulated transcription, are also required for this chromatin modification, at least for the ELIP1 gene. Furthermore, sequencing of the immunoprecipitated DNA revealed that all UV-B-induced enrichments in H3K9,14diacetylation across the genome are UVR8-dependent, and approximately 40 % of the enriched loci contain known UVR8-regulated genes. In addition, inhibition of histone acetylation by anacardic acid reduces the UV-B induced, UVR8 mediated expression of ELIP1 and CHS. No evidence was obtained in yeast 2-hybrid assays for a direct interaction between either UVR8 or HY5 and several proteins involved in light-regulated histone modification, nor for the involvement of these proteins in UVR8-mediated responses in plants, although functional redundancy between proteins could influence the results. In summary, this study shows that UVR8 regulates a specific chromatin modification associated with transcriptional regulation of a set of UVR8-target genes.
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Affiliation(s)
- Christos N Velanis
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bower Building, Glasgow, G12 8QQ, UK
| | - Pawel Herzyk
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bower Building, Glasgow, G12 8QQ, UK
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, G61 1QH, UK
| | - Gareth I Jenkins
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bower Building, Glasgow, G12 8QQ, UK.
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Baerenfaller K, Shu H, Hirsch-Hoffmann M, Fütterer J, Opitz L, Rehrauer H, Hennig L, Gruissem W. Diurnal changes in the histone H3 signature H3K9ac|H3K27ac|H3S28p are associated with diurnal gene expression in Arabidopsis. PLANT, CELL & ENVIRONMENT 2016; 39:2557-2569. [PMID: 27487196 DOI: 10.1111/pce.12811] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 07/26/2016] [Accepted: 07/27/2016] [Indexed: 05/18/2023]
Abstract
Post-translational chromatin modifications are an important regulatory mechanism in light signalling and circadian clock function. The regulation of diurnal transcript level changes requires fine-tuning of the expression of generally active genes depending on the prevailing environmental conditions. We investigated the association of histone modifications H3K4me3, H3K9ac, H3K9me2, H3S10p, H3K27ac, H3K27me3 and H3S28p with diurnal changes in transcript expression using chromatin immunoprecipitations followed by sequencing (ChIP-Seq) in fully expanded leaves 6 of Arabidopsis thaliana grown in short-day optimal and water-deficit conditions. We identified a differential H3K9ac, H3K27ac and H3S28p signature between end-of-day and end-of-night that is correlated with changes in diurnal transcript levels. Genes with this signature have particular over-represented promoter elements and encode proteins that are significantly enriched for transcription factors, circadian clock and starch catabolic process. Additional activating modifications were prevalent in optimally watered (H3S10p) and in water-deficit (H3K4me3) plants. The data suggest a mechanism for diurnal transcript level regulation in which reduced binding of repressive transcription factors facilitates activating H3K9ac, H3K27ac and H3S28p chromatin modifications. The presence of activating chromatin modification patterns on genes only at times of the day when their expression is required can explain why some genes are differentially inducible during the diurnal cycle.
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Affiliation(s)
| | - Huan Shu
- Department of Biology, ETH Zurich, Zurich, 8092, Switzerland
- Program of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | | | | | - Lennart Opitz
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, 8057, Switzerland
| | - Hubert Rehrauer
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, 8057, Switzerland
| | - Lars Hennig
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, SE-75007, Sweden
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Abstract
Reversible histone acetylation and deacetylation at the N-terminus of histone tails play a crucial role in regulation of gene activity. Hyperacetylation of histones relaxes chromatin structure and is associated with transcriptional activation, whereas hypoacetylation of histones induces chromatin compaction and gene repression. Histone acetylation and deacetylation are catalyzed by histone acetyltransferases (HATs) and histone deacetylases (HDACs), respectively. Emerging evidences revealed that plant HATs and HDACs play essential roles in regulation of gene expression in plant development and plant responses to environmental stresses. Furthermore, HATs and HDACs were shown to interact with various chromatin-remodeling factors and transcription factors involved in transcriptional regulation of multiple developmental processes.
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Affiliation(s)
- X Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - S Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - C-W Yu
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - C-Y Chen
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - K Wu
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan.
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Zhang CJ, Hou XM, Tan LM, Shao CR, Huang HW, Li YQ, Li L, Cai T, Chen S, He XJ. The Arabidopsis acetylated histone-binding protein BRAT1 forms a complex with BRP1 and prevents transcriptional silencing. Nat Commun 2016; 7:11715. [PMID: 27273316 PMCID: PMC4899616 DOI: 10.1038/ncomms11715] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 04/21/2016] [Indexed: 12/20/2022] Open
Abstract
Transposable elements and other repetitive DNA sequences are usually subject to DNA methylation and transcriptional silencing. However, anti-silencing mechanisms that promote transcription in these regions are not well understood. Here, we describe an anti-silencing factor, Bromodomain and ATPase domain-containing protein 1 (BRAT1), which we identified by a genetic screen in Arabidopsis thaliana. BRAT1 interacts with an ATPase domain-containing protein, BRP1 (BRAT1 Partner 1), and both prevent transcriptional silencing at methylated genomic regions. Although BRAT1 mediates DNA demethylation at a small set of loci targeted by the 5-methylcytosine DNA glycosylase ROS1, the involvement of BRAT1 in anti-silencing is largely independent of DNA demethylation. We also demonstrate that the bromodomain of BRAT1 binds to acetylated histone, which may facilitate the prevention of transcriptional silencing. Thus, BRAT1 represents a potential link between histone acetylation and transcriptional anti-silencing at methylated genomic regions, which may be conserved in eukaryotes. Transposons and repetitive sequences are typically subject to transcription silencing. Here, Zhang et al. find that the bromodomain-containing protein BRAT1 forms a complex with BRP1, recognizes histone acetylation and acts to prevent transcriptional silencing in Arabidopsis.
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Affiliation(s)
- Cui-Jun Zhang
- National Institute of Biological Sciences, No. 7, Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Xiao-Mei Hou
- National Institute of Biological Sciences, No. 7, Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Lian-Mei Tan
- National Institute of Biological Sciences, No. 7, Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Chang-Rong Shao
- National Institute of Biological Sciences, No. 7, Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Huan-Wei Huang
- National Institute of Biological Sciences, No. 7, Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Yong-Qiang Li
- National Institute of Biological Sciences, No. 7, Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Lin Li
- National Institute of Biological Sciences, No. 7, Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Tao Cai
- National Institute of Biological Sciences, No. 7, Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - She Chen
- National Institute of Biological Sciences, No. 7, Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Xin-Jian He
- National Institute of Biological Sciences, No. 7, Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
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42
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Chitikova Z, Steiner FA. Cell type-specific epigenome profiling using affinity-purified nuclei. Genesis 2016; 54:160-9. [PMID: 26789661 DOI: 10.1002/dvg.22919] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 01/08/2016] [Accepted: 01/14/2016] [Indexed: 11/08/2022]
Abstract
The development of a multicellular organism from a single zygote depends on the differentiation of progenitor cells to specialized cell types. The differentiation of these cell types is associated with changes in gene expression and the underlying chromatin landscape. To understand how these processes are regulated, it is desirable to understand how the chromatin features that constitute the epigenome differ between cell types at any given time during development. INTACT, a method for the cell type-specific purification of nuclei that can be used for the isolation of both RNA and chromatin, has emerged as a powerful tool to simultaneously study gene expression and chromatin profiles specifically in cell types of interest. In this review, we focus on the application of INTACT to different model organisms and discuss its potential for profiling cell types in their developmental context.
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Affiliation(s)
- Zhanna Chitikova
- Department of Molecular Biology, Sciences III, University of Geneva, Geneva, Switzerland
| | - Florian A Steiner
- Department of Molecular Biology, Sciences III, University of Geneva, Geneva, Switzerland
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Poulios S, Vlachonasios KE. Synergistic action of histone acetyltransferase GCN5 and receptor CLAVATA1 negatively affects ethylene responses in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:905-18. [PMID: 26596766 DOI: 10.1093/jxb/erv503] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
GENERAL CONTROL NON-REPRESSIBLE 5 (GCN5) is a histone acetyltransferase (HAT) and the catalytic subunit of several multicomponent HAT complexes that acetylate lysine residues of histone H3. Mutants in AtGCN5 display pleiotropic developmental defects including aberrant meristem function. Shoot apical meristem (SAM) maintenance is regulated by CLAVATA1 (CLV1), a receptor kinase that controls the size of the shoot and floral meristems. Upon activation through CLV3 binding, CLV1 signals to the transcription factor WUSCHEL (WUS), restricting WUS expression and thus the meristem size. We hypothesized that GCN5 and CLV1 act together to affect SAM function. Using genetic and molecular approaches, we generated and characterized clv gcn5 mutants. Surprisingly, the clv1-1 gcn5-1 double mutant exhibited constitutive ethylene responses, suggesting that GCN5 and CLV signaling act synergistically to inhibit ethylene responses in Arabidopsis. This genetic and molecular interaction was mediated by ETHYLENE INSENSITIVE 3/ EIN3-LIKE1 (EIN3/EIL1) transcription factors. Our data suggest that signals from the CLV transduction pathway reach the GCN5-containing complexes in the nucleus and alter the histone acetylation status of ethylene-responsive genes, thus translating the CLV information to transcriptional activity and uncovering a link between histone acetylation and SAM maintenance in the complex mode of ethylene signaling.
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Affiliation(s)
- Stylianos Poulios
- Department of Botany, School of Biology, Faculty of Science, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Konstantinos E Vlachonasios
- Department of Botany, School of Biology, Faculty of Science, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
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Yamamuro C, Zhu JK, Yang Z. Epigenetic Modifications and Plant Hormone Action. MOLECULAR PLANT 2016; 9:57-70. [PMID: 26520015 PMCID: PMC5575749 DOI: 10.1016/j.molp.2015.10.008] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 09/27/2015] [Accepted: 10/22/2015] [Indexed: 05/18/2023]
Abstract
The action of phytohormones in plants requires the spatiotemporal regulation of their accumulation and responses at various levels. Recent studies reveal an emerging relationship between the function of phytohormones and epigenetic modifications. In particular, evidence suggests that auxin biosynthesis, transport, and signal transduction is modulated by microRNAs and epigenetic factors such as histone modification, chromatin remodeling, and DNA methylation. Furthermore, some phytohormones have been shown to affect epigenetic modifications. These findings are shedding light on the mode of action of phytohormones and are opening up a new avenue of research on phytohormones as well as on the mechanisms regulating epigenetic modifications.
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Affiliation(s)
- Chizuko Yamamuro
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; Horticultural Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, PRC.
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
| | - Zhenbiao Yang
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
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Zhang Y, Nan J, Yu B. OMICS Technologies and Applications in Sugar Beet. FRONTIERS IN PLANT SCIENCE 2016; 7:900. [PMID: 27446130 PMCID: PMC4916227 DOI: 10.3389/fpls.2016.00900] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/07/2016] [Indexed: 05/08/2023]
Abstract
Sugar beet is a species of the Chenopodiaceae family. It is an important sugar crop that supplies approximately 35% of the sugar in the world. Sugar beet M14 line is a unique germplasm that contains genetic materials from Beta vulgaris L. and Beta corolliflora Zoss. And exhibits tolerance to salt stress. In this review, we have summarized OMICS technologies and applications in sugar beet including M14 for identification of novel genes, proteins related to biotic and abiotic stresses, apomixes and metabolites related to energy and food. An OMICS overview for the discovery of novel genes, proteins and metabolites in sugar beet has helped us understand the complex mechanisms underlying many processes such as apomixes, tolerance to biotic and abiotic stresses. The knowledge gained is valuable for improving the tolerance of sugar beet and other crops to biotic and abiotic stresses as well as for enhancing the yield of sugar beet for energy and food production.
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Affiliation(s)
- Yongxue Zhang
- Key Laboratory of Molecular Biology of Heilongjiang Province, College of Life Sciences, Heilongjiang UniversityHarbin, China
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang UniversityHarbin, China
| | - Jingdong Nan
- Key Laboratory of Molecular Biology of Heilongjiang Province, College of Life Sciences, Heilongjiang UniversityHarbin, China
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang UniversityHarbin, China
| | - Bing Yu
- Key Laboratory of Molecular Biology of Heilongjiang Province, College of Life Sciences, Heilongjiang UniversityHarbin, China
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang UniversityHarbin, China
- *Correspondence: Bing Yu
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Salvini M, Fambrini M, Giorgetti L, Pugliesi C. Molecular aspects of zygotic embryogenesis in sunflower (Helianthus annuus L.): correlation of positive histone marks with HaWUS expression and putative link HaWUS/HaL1L. PLANTA 2016; 243:199-215. [PMID: 26377219 DOI: 10.1007/s00425-015-2405-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 09/06/2015] [Indexed: 06/05/2023]
Abstract
The link HaWUS/ HaL1L , the opposite transcriptional behavior, and the decrease/increase in positive histone marks bond to both genes suggest an inhibitory effect of WUS on HaL1L in sunflower zygotic embryos. In Arabidopsis, a group of transcription factors implicated in the earliest events of embryogenesis is the WUSCHEL-RELATED HOMEOBOX (WOX) protein family including WUSCHEL (WUS) and other 14 WOX protein, some of which contain a conserved WUS-box domain in addition to the homeodomain. WUS transcripts appear very early in embryogenesis, at the 16-cell embryo stage, but gradually become restricted to the center of the developing shoot apical meristem (SAM) primordium and continues to be expressed in cells of the niche/organizing center of SAM and floral meristems to maintain stem cell population. Moreover, WUS has decisive roles in the embryonic program presumably promoting the vegetative-to-embryonic transition and/or maintaining the identity of the embryonic stem cells. However, data on the direct interaction between WUS and key genes for seed development (as LEC1 and L1L) are not collected. The novelty of this report consists in the characterization of Helianthus annuus WUS (HaWUS) gene and in its analysis regarding the pattern of the methylated lysine 4 (K4) of the Histone H3 and of the acetylated histone H3 during the zygotic embryo development. Also, a parallel investigation was performed for HaL1L gene since two copies of the WUS-binding site (WUSATA), previously identified on HaL1L nucleotide sequence, were able to be bound by the HaWUS recombinant protein suggesting a not described effect of HaWUS on HaL1L transcription.
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Affiliation(s)
- Mariangela Salvini
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy.
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy.
| | - Marco Fambrini
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Lucia Giorgetti
- Institute of Agricultural Biology and Biotechnology (IBBA), Italian National Research Council (CNR), Via Moruzzi 1, 56124, Pisa, Italy
| | - Claudio Pugliesi
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
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Takatsuka H, Umeda M. Epigenetic Control of Cell Division and Cell Differentiation in the Root Apex. FRONTIERS IN PLANT SCIENCE 2015; 6:1178. [PMID: 26734056 PMCID: PMC4689806 DOI: 10.3389/fpls.2015.01178] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 12/09/2015] [Indexed: 05/25/2023]
Abstract
Epigenetics is defined as heritable changes in gene expression and genome integrity that are accompanied by no alteration in DNA sequence. Throughout plant life cycle, many processes, including genome imprinting, stress responses, and cellular differentiation, are known to be determined by epigenetic regulation. The root apex is also considered to be under the control of epigenetic regulation for optimal growth under variable environments. Recent reports reveal that epigenetic control is especially important in the stem cell niche and the meristematic zone where both cell production and cell specification occur. DNA methylation, histone methylation, and histone acetylation are well-known epigenetic modifications, and each epigenetic modification has distinct roles in roots. Here, we review the updated findings that demonstrate the significance of epigenetic regulation in root apex of Arabidopsis.
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Affiliation(s)
- Hirotomo Takatsuka
- Graduate School of Biological Sciences, Nara Institute of Science and TechnologyNara, Japan
| | - Masaaki Umeda
- Graduate School of Biological Sciences, Nara Institute of Science and TechnologyNara, Japan
- Japan Science and Technology, Core Research for Evolutional Science and Technology AgencyIkoma, Japan
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Guo W, Yang H, Liu Y, Gao Y, Ni Z, Peng H, Xin M, Hu Z, Sun Q, Yao Y. The wheat transcription factor TaGAMyb recruits histone acetyltransferase and activates the expression of a high-molecular-weight glutenin subunit gene. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:347-59. [PMID: 26332346 DOI: 10.1111/tpj.13003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 08/12/2015] [Accepted: 08/25/2015] [Indexed: 05/23/2023]
Abstract
Glutenin proteins in wheat (Triticum aestivum L.) flour confer unique viscoelastic properties to dough products and, therefore, the concentration and composition of the glutenin proteins determine its end-use value. However, the mechanisms governing the glutenin gene expression remain elusive. In this study, we report that wheat TaGAMyb activates the high-molecular-weight glutenin subunit genes (TaGLU) through recruiting the histone acetyltransferase GCN5. By sequencing the promoters of TaGLU-1 genes from 40 modern wheat cultivars, we identified eight types of TaGAMyb binding motifs and verified these by electrophoretic mobility shift assays. The number of TaGAMyb binding motifs in TaGLU-1 genes is correlated with the abundance of glutenin in different cultivars. Chromatin immunoprecipitation plus polymerase chain reaction (ChIP-PCR) analysis reveals that TaGCN5 directly targets the promoters of TaGLU-1 genes in wheat endosperm. We find that TaGAMyb physically interacts with the wheat histone acetyltransferase TaGCN5 and also interacts with Arabidopsis thaliana AtGCN5. TaGAMyb ectopically expressed in Arabidopsis binds to the TaGLU-1Dy promoter on a TaGLU-1Dy transgene and activates its expression. AtGCN5 also targets the TaGLU-1Dy transgene and is involved in the establishment of acetylation at H3K9 and H3K14. These results demonstrate that TaGAMyb plays a dual role in activating expression of glutenin gene by directly binding to the TaGLU promoter and by recruiting GCN5 to modulate histone acetylation during wheat endosperm development.
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Affiliation(s)
- Weiwei Guo
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Hua Yang
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Yongqiang Liu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Yujiao Gao
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
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Spt-Ada-Gcn5-Acetyltransferase (SAGA) Complex in Plants: Genome Wide Identification, Evolutionary Conservation and Functional Determination. PLoS One 2015; 10:e0134709. [PMID: 26263547 PMCID: PMC4532415 DOI: 10.1371/journal.pone.0134709] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Accepted: 07/13/2015] [Indexed: 01/17/2023] Open
Abstract
The recruitment of RNA polymerase II on a promoter is assisted by the assembly of basal transcriptional machinery in eukaryotes. The Spt-Ada-Gcn5-Acetyltransferase (SAGA) complex plays an important role in transcription regulation in eukaryotes. However, even in the advent of genome sequencing of various plants, SAGA complex has been poorly defined for their components and roles in plant development and physiological functions. Computational analysis of Arabidopsis thaliana and Oryza sativa genomes for SAGA complex resulted in the identification of 17 to 18 potential candidates for SAGA subunits. We have further classified the SAGA complex based on the conserved domains. Phylogenetic analysis revealed that the SAGA complex proteins are evolutionary conserved between plants, yeast and mammals. Functional annotation showed that they participate not only in chromatin remodeling and gene regulation, but also in different biological processes, which could be indirect and possibly mediated via the regulation of gene expression. The in silico expression analysis of the SAGA components in Arabidopsis and O. sativa clearly indicates that its components have a distinct expression profile at different developmental stages. The co-expression analysis of the SAGA components suggests that many of these subunits co-express at different developmental stages, during hormonal interaction and in response to stress conditions. Quantitative real-time PCR analysis of SAGA component genes further confirmed their expression in different plant tissues and stresses. The expression of representative salt, heat and light inducible genes were affected in mutant lines of SAGA subunits in Arabidopsis. Altogether, the present study reveals expedient evidences of involvement of the SAGA complex in plant gene regulation and stress responses.
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