1
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Tian H, Lyu R, Yi P. Crosstalk between Rho of Plants GTPase signalling and plant hormones. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:3778-3796. [PMID: 38616410 DOI: 10.1093/jxb/erae162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/12/2024] [Indexed: 04/16/2024]
Abstract
Rho of Plants (ROPs) constitute a plant-specific subset of small guanine nucleotide-binding proteins within the Cdc42/Rho/Rac family. These versatile proteins regulate diverse cellular processes, including cell growth, cell division, cell morphogenesis, organ development, and stress responses. In recent years, the dynamic cellular and subcellular behaviours orchestrated by ROPs have unveiled a notable connection to hormone-mediated organ development and physiological responses, thereby expanding our knowledge of the functions and regulatory mechanisms of this signalling pathway. This review delineates advancements in understanding the interplay between plant hormones and the ROP signalling cascade, focusing primarily on the connections with auxin and abscisic acid pathways, alongside preliminary discoveries in cytokinin, brassinosteroid, and salicylic acid responses. It endeavours to shed light on the intricate, coordinated mechanisms bridging cell- and tissue-level signals that underlie plant cell behaviour, organ development, and physiological processes, and highlights future research prospects and challenges in this rapidly developing field.
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Affiliation(s)
- Haoyu Tian
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, P. R. China
| | - Ruohan Lyu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, P. R. China
| | - Peishan Yi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, P. R. China
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2
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Xu D, Leister D, Kleine T. Identification of a highly drought-resistant pp7l hda6 mutant. FRONTIERS IN PLANT SCIENCE 2024; 15:1341576. [PMID: 38887464 PMCID: PMC11180769 DOI: 10.3389/fpls.2024.1341576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 05/09/2024] [Indexed: 06/20/2024]
Abstract
Plants have developed efficient strategies to counteract drought stress, including stomata closure, significant changes in nuclear gene expression, and epigenetic mechanisms. Previously, we identified Arabidopsis thaliana PROTEIN PHOSPHATASE7-LIKE (PP7L) as an extrachloroplastic protein that promotes chloroplast development. In addition, it was shown that PP7L is involved in high light and salt tolerance. Here, we demonstrate that the pp7l mutant can withstand prolonged periods of drought stress. Interestingly, despite impaired growth under standard growth conditions, photosynthetic efficiency recovers in pp7l mutant plants experiencing drought conditions. To assess the (post)transcriptional changes occurring in the pp7l mutant under different durations of drought exposure, we used an RNA-sequencing technique that allows the simultaneous detection of organellar and nuclear transcripts. Compared with the previously reported drought-responsive changes in the wild type, the drought-responsive changes in organellar and nuclear transcripts detected in the pp7l mutant were negligible. Our analysis of the data generated in this study and review and analysis of previous literature motivated us to create a pp7l hda6 (histone deacetylase 6) mutant, which exhibits remarkable drought resistance. Notably, the growth penalty associated with pp7l was alleviated in the double mutant, ruling out a dwarf effect on the drought-tolerant trait of this genotype. Future studies may consider that multiple loci and factors are involved in stress resistance and explore combinations of these factors to create even more resilient plants.
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Affiliation(s)
| | | | - Tatjana Kleine
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
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3
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Lee K, Yoon H, Park OS, Seo PJ. ENHANCER OF SHOOT REGENERATION1 promotes de novo root organogenesis after wounding in Arabidopsis leaf explants. THE PLANT CELL 2024; 36:2359-2374. [PMID: 38445764 PMCID: PMC11132873 DOI: 10.1093/plcell/koae074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 01/25/2024] [Accepted: 03/01/2024] [Indexed: 03/07/2024]
Abstract
Plants have an astonishing ability to regenerate new organs after wounding. Here, we report that the wound-inducible transcription factor ENHANCER OF SHOOT REGENERATION1 (ESR1) has a dual mode of action in activating ANTHRANILATE SYNTHASE ALPHA SUBUNIT1 (ASA1) expression to ensure auxin-dependent de novo root organogenesis locally at wound sites of Arabidopsis (Arabidopsis thaliana) leaf explants. In the first mode, ESR1 interacts with HISTONE DEACETYLASE6 (HDA6), and the ESR1-HDA6 complex directly binds to the JASMONATE-ZIM DOMAIN5 (JAZ5) locus, inhibiting JAZ5 expression through histone H3 deacetylation. As JAZ5 interferes with the action of ETHYLENE RESPONSE FACTOR109 (ERF109), the transcriptional repression of JAZ5 at the wound site allows ERF109 to activate ASA1 expression. In the second mode, the ESR1 transcriptional activator directly binds to the ASA1 promoter to enhance its expression. Overall, our findings indicate that the dual biochemical function of ESR1, which specifically occurs near wound sites of leaf explants, maximizes local auxin biosynthesis and de novo root organogenesis in Arabidopsis.
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Affiliation(s)
- Kyounghee Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
- Research Institute of Basic Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Hobin Yoon
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Ok-Sun Park
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
- Research Institute of Basic Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Republic of Korea
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4
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Ren Z, Gou R, Zhuo W, Chen Z, Yin X, Cao Y, Wang Y, Mi Y, Liu Y, Wang Y, Fan LM, Deng XW, Qian W. The MBD-ACD DNA methylation reader complex recruits MICRORCHIDIA6 to regulate ribosomal RNA gene expression in Arabidopsis. THE PLANT CELL 2024; 36:1098-1118. [PMID: 38092516 PMCID: PMC10980342 DOI: 10.1093/plcell/koad313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 12/11/2023] [Indexed: 04/01/2024]
Abstract
DNA methylation is an important epigenetic mark implicated in selective rRNA gene expression, but the DNA methylation readers and effectors remain largely unknown. Here, we report a protein complex that reads DNA methylation to regulate variant-specific 45S ribosomal RNA (rRNA) gene expression in Arabidopsis (Arabidopsis thaliana). The complex, consisting of METHYL-CpG-BINDING DOMAIN PROTEIN5 (MBD5), MBD6, ALPHA-CRYSTALLIN DOMAIN PROTEIN15.5 (ACD15.5), and ACD21.4, directly binds to 45S rDNA. While MBD5 and MBD6 function redundantly, ACD15.5 and ACD21.4 are indispensable for variant-specific rRNA gene expression. These 4 proteins undergo phase separation in vitro and in vivo and are interdependent for their phase separation. The α-crystallin domain of ACD15.5 and ACD21.4, which is essential for their function, enables phase separation of the complex, likely by mediating multivalent protein interactions. The effector MICRORCHIDIA6 directly interacts with ACD15.5 and ACD21.4, but not with MBD5 and MBD6, and is recruited to 45S rDNA by the MBD-ACD complex to regulate variant-specific 45S rRNA expression. Our study reveals a pathway in Arabidopsis through which certain 45S rRNA gene variants are silenced, while others are activated.
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Affiliation(s)
- Zhitong Ren
- National Key Laboratory of Wheat Improvement, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Peking University Institute of advanced Agricultural Sciences, Weifang, Shandong 261325, China
- College of Agronomy, Sichuan Agriculture University, Chengdu 611130, China
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Runyu Gou
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Wanqing Zhuo
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Zhiyu Chen
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiaochang Yin
- National Key Laboratory of Wheat Improvement, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Peking University Institute of advanced Agricultural Sciences, Weifang, Shandong 261325, China
| | - Yuxin Cao
- National Key Laboratory of Wheat Improvement, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Peking University Institute of advanced Agricultural Sciences, Weifang, Shandong 261325, China
| | - Yue Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yingjie Mi
- National Key Laboratory of Wheat Improvement, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Peking University Institute of advanced Agricultural Sciences, Weifang, Shandong 261325, China
| | - Yannan Liu
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Yingxiang Wang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
- College of Life Sciences, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Liu-Min Fan
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xing Wang Deng
- National Key Laboratory of Wheat Improvement, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Peking University Institute of advanced Agricultural Sciences, Weifang, Shandong 261325, China
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Weiqiang Qian
- National Key Laboratory of Wheat Improvement, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Peking University Institute of advanced Agricultural Sciences, Weifang, Shandong 261325, China
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
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5
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Du X, Gao Y, Zhang H, Xu X, Li Y, Zhao L, Luo M, Wang H. HDA6 modulates Arabidopsis pavement cell morphogenesis through epigenetic suppression of ROP6 GTPase expression and signaling. THE NEW PHYTOLOGIST 2024; 241:2523-2539. [PMID: 38214469 DOI: 10.1111/nph.19532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 01/01/2024] [Indexed: 01/13/2024]
Abstract
The transcriptional regulation of Rho-related GTPase from plants (ROPs), which determine cell polarity formation and maintenance during plant development, still remains enigmatic. In this study, we elucidated the epigenetic mechanism of histone deacetylase HDA6 in transcriptional repression of ROP6 and its impact on cell polarity and morphogenesis in Arabidopsis leaf epidermal pavement cells (PCs). We found that the hda6 mutant axe1-4 exhibited impaired jigsaw-shaped PCs and convoluted leaves. This correlated with disruptions in the spatial organizations of cortical microtubules and filamentous actin, which is integral to PC indentation and lobe formation. Further transcriptional analyses and chromatin immunoprecipitation assay revealed that HDA6 specifically represses ROP6 expression through histone H3K9K14 deacetylation. Importantly, overexpression of dominant negative-rop6 in axe1-4 restored interdigitated cell morphology. Our study unveils HDA6 as a key regulator in Arabidopsis PC morphogenesis through epigenetic suppression of ROP6. It reveals the pivotal role of HDA6 in the transcriptional regulation of ROP6 and provides compelling evidence for the functional interplay between histone deacetylation and ROP6-mediated cytoskeletal arrangement in the development of interdigitated PCs.
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Affiliation(s)
- Xiaojuan Du
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yingmiao Gao
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hao Zhang
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaoyu Xu
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Ying Li
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Lifeng Zhao
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Ming Luo
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hao Wang
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
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Hung FY, Feng YR, Hsin KT, Shih YH, Chang CH, Zhong W, Lai YC, Xu Y, Yang S, Sugimoto K, Cheng YS, Wu K. Arabidopsis histone H3 lysine 9 methyltransferases KYP/SUVH5/6 are involved in leaf development by interacting with AS1-AS2 to repress KNAT1 and KNAT2. Commun Biol 2023; 6:219. [PMID: 36828846 PMCID: PMC9958104 DOI: 10.1038/s42003-023-04607-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 02/16/2023] [Indexed: 02/26/2023] Open
Abstract
The Arabidopsis H3K9 methyltransferases KRYPTONITE/SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG 4 (KYP/SUVH4), SUVH5 and SUVH6 are redundantly involved in silencing of transposable elements (TEs). Our recent study indicated that KYP/SUVH5/6 can directly interact with the histone deacetylase HDA6 to synergistically regulate TE expression. However, the function of KYP/SUVH5/6 in plant development is still unclear. The transcriptional factors ASYMMETRIC LEAVES1 (AS1) and AS2 form a transcription complex, which is involved in leaf development by repressing the homeobox genes KNOTTED-LIKE FROM ARABIDOPSIS THALIANA 1 (KNAT1) and KNAT2. In this study, we found that KYP and SUVH5/6 directly interact with AS1-AS2 to repress KNAT1 and KNAT2 by altering histone H3 acetylation and H3K9 dimethylation levels. In addition, KYP can directly target the promoters of KNAT1 and KNAT2, and the binding of KYP depends on AS1. Furthermore, the genome-wide occupancy profile of KYP indicated that KYP is enriched in the promoter regions of coding genes, and the binding of KYP is positively correlated with that of AS1 and HDA6. Together, these results indicate that Arabidopsis H3K9 methyltransferases KYP/SUVH5/6 are involved in leaf development by interacting with AS1-AS2 to alter histone H3 acetylation and H3K9 dimethylation from KNAT1 and KNAT2 loci.
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Affiliation(s)
- Fu-Yu Hung
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
- RIKEN, Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Yun-Ru Feng
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Kuan-Ting Hsin
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Yuan-Hsin Shih
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Chung-Han Chang
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Wenjian Zhong
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - You-Cheng Lai
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Yingchao Xu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Songguang Yang
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Keiko Sugimoto
- RIKEN, Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Yi-Sheng Cheng
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Keqiang Wu
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan.
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Sen MK, Hamouzová K, Košnarová P, Roy A, Soukup J. Herbicide resistance in grass weeds: Epigenetic regulation matters too. FRONTIERS IN PLANT SCIENCE 2022; 13:1040958. [PMID: 36438151 PMCID: PMC9685620 DOI: 10.3389/fpls.2022.1040958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Although herbicides have been successfully used for controlling weeds, their continuous use has developed in the evolution of resistance to all major herbicide modes of action worldwide. Reports suggest that the members of Poaceae family are more prone to developing herbicide resistance than other families. In plants, epigenetic mechanisms play critical roles by increasing their stress-adaptive potential in a rapidly changing environment. Epigenetic mechanisms involve alteration of the expression of genetic elements, but without any changes in the DNA sequence. Although the possible roles of epigenetic mechanisms in contributing to survival and fitness under various stresses are well documented in model plants and crops, their contribution to herbicide resistance in weeds is still in its infancy. A few studies with herbicides have shown differential expression of DNA methyltransferases, histone methyltransferases and DNA demethylases in response to the herbicides; however, no further studies were conducted. In the case of herbicide stress, exploring how these epigenetic processes affect the gene expression pattern in individual plants subjected to recurrent selection would be exciting. Hence, our mini-review will focus on the potential contributions of epigenetic mechanisms to the adaptive responses of grass-weedy species to herbicide stress. A better understanding of these epigenetic changes will add novel perceptions to our knowledge of herbicide resistance evolution in weeds enabling the development of herbicides with novel targets.
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Affiliation(s)
- Madhab Kumar Sen
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
| | - Katerina Hamouzová
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
| | - Pavlína Košnarová
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
| | - Amit Roy
- Excellent Team for Mitigation (E.T.M.), Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Praha, Czechia
| | - Josef Soukup
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
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8
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An C, Deng L, Zhai H, You Y, Wu F, Zhai Q, Goossens A, Li C. Regulation of jasmonate signaling by reversible acetylation of TOPLESS in Arabidopsis. MOLECULAR PLANT 2022; 15:1329-1346. [PMID: 35780296 DOI: 10.1016/j.molp.2022.06.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 04/28/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
The plant hormone jasmonate (JA) regulates plant immunity and adaptive growth by orchestrating a genome-wide transcriptional program. Key regulators of JA-responsive gene expression include the master transcription factor MYC2, which is repressed by the conserved Groucho/Tup1-like corepressor TOPLESS (TPL) in the resting state. However, the mechanisms underlying TPL-mediated transcriptional repression of MYC2 activity and hormone-dependent switching between repression and de-repression remain enigmatic. Here, we report the regulation of TPL activity and JA signaling by reversible acetylation of TPL. We found that the histone acetyltransferase GCN5 could mediate TPL acetylation, which enhances its interaction with the NOVEL-INTERACTOR-OF-JAZ (NINJA) adaptor and promotes its recruitment to MYC2 target promoters, facilitating transcriptional repression. Conversely, TPL deacetylation by the histone deacetylase HDA6 weakens TPL-NINJA interaction and inhibits TPL recruitment to MYC2 target promoters, facilitating transcriptional activation. In the resting state, the opposing activities of GCN5 and HDA6 maintain TPL acetylation homeostasis, promoting transcriptional repression activity of TPL. In response to JA elicitation, HDA6 expression is transiently induced, resulted in decreased TPL acetylation and repressor activity, thereby transcriptional activation of MYC2 target genes. Thus, the GCN5-TPL-HDA6 module maintains the homeostasis of acetylated TPL, thereby determining the transcriptional state of JA-responsive genes. Our findings uncovered a mechanism by which the TPL corepressor activity in JA signaling is actively tuned in a rapid and reversible manner.
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Affiliation(s)
- Chunpeng An
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Deng
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huawei Zhai
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, China
| | - Yanrong You
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangming Wu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingzhe Zhai
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Chuanyou Li
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, China.
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9
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Hou Y, Lu Q, Su J, Jin X, Jia C, An L, Tian Y, Song Y. Genome-Wide Analysis of the HDAC Gene Family and Its Functional Characterization at Low Temperatures in Tartary Buckwheat ( Fagopyrum tataricum). Int J Mol Sci 2022; 23:ijms23147622. [PMID: 35886971 PMCID: PMC9319316 DOI: 10.3390/ijms23147622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/02/2022] [Accepted: 07/05/2022] [Indexed: 02/04/2023] Open
Abstract
Histone deacetylases (HDACs), widely found in various types of eukaryotic cells, play crucial roles in biological process, including the biotic and abiotic stress responses in plants. However, no research on the HDACs of Fagopyrum tataricum has been reported. Here, 14 putative FtHDAC genes were identified and annotated in Fagopyrum tataricum. Their gene structure, motif composition, cis-acting elements, phylogenetic relationships, protein structure, alternative splicing events, subcellular localization and gene expression pattern were investigated. The gene structure showed FtHDACs were classified into three subfamilies. The promoter analysis revealed the presence of various cis-acting elements responsible for hormone, abiotic stress and developmental regulation for the specific induction of FtHDACs. Two duplication events were identified in FtHDA6-1, FtHDA6-2, and FtHDA19. The expression patterns of FtHDACs showed their correlation with the flavonoid synthesis pathway genes. In addition, alternative splicing, mRNA enrichment profiles and transgenic analysis showed the potential role of FtHDACs in cold responses. Our study characterized FtHDACs, providing a candidate gene family for agricultural breeding and crop improvement.
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Affiliation(s)
- Yukang Hou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730030, China; (Y.H.); (Q.L.); (J.S.); (X.J.); (L.A.)
| | - Qi Lu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730030, China; (Y.H.); (Q.L.); (J.S.); (X.J.); (L.A.)
| | - Jianxun Su
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730030, China; (Y.H.); (Q.L.); (J.S.); (X.J.); (L.A.)
| | - Xing Jin
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730030, China; (Y.H.); (Q.L.); (J.S.); (X.J.); (L.A.)
| | - Changfu Jia
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu 610017, China;
| | - Lizhe An
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730030, China; (Y.H.); (Q.L.); (J.S.); (X.J.); (L.A.)
| | - Yongke Tian
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730030, China; (Y.H.); (Q.L.); (J.S.); (X.J.); (L.A.)
- Correspondence: (Y.T.); (Y.S.)
| | - Yuan Song
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730030, China; (Y.H.); (Q.L.); (J.S.); (X.J.); (L.A.)
- Correspondence: (Y.T.); (Y.S.)
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10
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Onosato H, Fujimoto G, Higami T, Sakamoto T, Yamada A, Suzuki T, Ozawa R, Matsunaga S, Seki M, Ueda M, Sako K, Galis I, Arimura GI. Sustained defense response via volatile signaling and its epigenetic transcriptional regulation. PLANT PHYSIOLOGY 2022; 189:922-933. [PMID: 35201346 PMCID: PMC9157098 DOI: 10.1093/plphys/kiac077] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/29/2022] [Indexed: 05/11/2023]
Abstract
Plants perceive volatiles emitted from herbivore-damaged neighboring plants to urgently adapt or prime their defense responses to prepare for forthcoming herbivores. Mechanistically, these volatiles can induce epigenetic regulation based on histone modifications that alter the transcriptional status of defense genes, but little is known about the underlying mechanisms. To understand the roles of such epigenetic regulation of plant volatile signaling, we explored the response of Arabidopsis (Arabidopsis thaliana) plants to the volatile β-ocimene. Defense traits of Arabidopsis plants toward larvae of Spodoptera litura were induced in response to β-ocimene, through enriched histone acetylation and elevated transcriptional levels of defense gene regulators, including ethylene response factor genes (ERF8 and ERF104) in leaves. The enhanced defense ability of the plants was maintained for 5 d but not over 10 d after exposure to β-ocimene, and this coincided with elevated expression of those ERFs in their leaves. An array of histone acetyltransferases, including HAC1, HAC5, and HAM1, were responsible for the induction and maintenance of the anti-herbivore property. HDA6, a histone deacetylase, played a role in the reverse histone remodeling. Collectively, our findings illuminate the role of epigenetic regulation in plant volatile signaling.
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Affiliation(s)
- Haruki Onosato
- Department of Biological Science and Technology, Faculty of Advanced Engineering, Tokyo University of Science, Tokyo 125-8585, Japan
| | - Genya Fujimoto
- Department of Biological Science and Technology, Faculty of Advanced Engineering, Tokyo University of Science, Tokyo 125-8585, Japan
| | - Tomota Higami
- Department of Biological Science and Technology, Faculty of Advanced Engineering, Tokyo University of Science, Tokyo 125-8585, Japan
| | - Takuya Sakamoto
- Department of Applied Biological Science, Graduate School of Science and Technology, Tokyo University of Science, Noda 278-8510, Japan
| | - Ayaka Yamada
- Department of Biological Science and Technology, Faculty of Advanced Engineering, Tokyo University of Science, Tokyo 125-8585, Japan
| | - Takamasa Suzuki
- College of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Japan
| | - Rika Ozawa
- Center for Ecological Research, Kyoto University, Otsu 520-2113, Japan
| | - Sachihiro Matsunaga
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8562, Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, Wako 351-0198, Japan
| | - Minoru Ueda
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
| | - Kaori Sako
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, Wako 351-0198, Japan
| | - Ivan Galis
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
| | - Gen-ichiro Arimura
- Department of Biological Science and Technology, Faculty of Advanced Engineering, Tokyo University of Science, Tokyo 125-8585, Japan
- Author for correspondence:
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11
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Vincent SA, Kim JM, Pérez-Salamó I, To TK, Torii C, Ishida J, Tanaka M, Endo TA, Bhat P, Devlin PF, Seki M, Devoto A. Jasmonates and Histone deacetylase 6 activate Arabidopsis genome-wide histone acetylation and methylation during the early acute stress response. BMC Biol 2022; 20:83. [PMID: 35399062 PMCID: PMC8996529 DOI: 10.1186/s12915-022-01273-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/07/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Jasmonates (JAs) mediate trade-off between responses to both biotic and abiotic stress and growth in plants. The Arabidopsis thaliana HISTONE DEACETYLASE 6 is part of the CORONATINE INSENSITIVE1 receptor complex, co-repressing the HDA6/COI1-dependent acetic acid-JA pathway that confers plant drought tolerance. The decrease in HDA6 binding to target DNA mirrors histone H4 acetylation (H4Ac) changes during JA-mediated drought response, and mutations in HDA6 also cause depletion in the constitutive repressive marker H3 lysine 27 trimethylation (H3K27me3). However, the genome-wide effect of HDA6 on H4Ac and much of the impact of JAs on histone modifications and chromatin remodelling remain elusive. RESULTS We performed high-throughput ChIP-Seq on the HDA6 mutant, axe1-5, and wild-type plants with or without methyl jasmonate (MeJA) treatment to assess changes in active H4ac and repressive H3K27me3 histone markers. Transcriptional regulation was investigated in parallel by microarray analysis in the same conditions. MeJA- and HDA6-dependent histone modifications on genes for specialized metabolism; linolenic acid and phenylpropanoid pathways; and abiotic and biotic stress responses were identified. H4ac and H3K27me3 enrichment also differentially affects JAs and HDA6-mediated genome integrity and gene regulatory networks, substantiating the role of HDA6 interacting with specific families of transposable elements in planta and highlighting further specificity of action as well as novel targets of HDA6 in the context of JA signalling for abiotic and biotic stress responses. CONCLUSIONS The findings demonstrate functional overlap for MeJA and HDA6 in tuning plant developmental plasticity and response to stress at the histone modification level. MeJA and HDA6, nonetheless, maintain distinct activities on histone modifications to modulate genetic variability and to allow adaptation to environmental challenges.
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Affiliation(s)
- Stacey A Vincent
- Plant Molecular Science and Centre of Systems and Synthetic Biology, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Jong-Myong Kim
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Present address: Ac-Planta Inc., 2-16-9 Yushima, Bunkyo-ku, Tokyo, 113-0034, Japan
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Imma Pérez-Salamó
- Plant Molecular Science and Centre of Systems and Synthetic Biology, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Taiko Kim To
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Present address: Department of Biological Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Chieko Torii
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Junko Ishida
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Maho Tanaka
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Takaho A Endo
- Bioinformatics and Systems Engineering Division, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Present address: Center for Integrative Medical Sciences, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Prajwal Bhat
- Plant Molecular Science and Centre of Systems and Synthetic Biology, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Paul F Devlin
- Plant Molecular Science and Centre of Systems and Synthetic Biology, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Motoaki Seki
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.
- Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
| | - Alessandra Devoto
- Plant Molecular Science and Centre of Systems and Synthetic Biology, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK.
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12
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An Efficient and Universal Protoplast Isolation Protocol Suitable for Transient Gene Expression Analysis and Single-Cell RNA Sequencing. Int J Mol Sci 2022; 23:ijms23073419. [PMID: 35408780 PMCID: PMC8998730 DOI: 10.3390/ijms23073419] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 03/17/2022] [Accepted: 03/17/2022] [Indexed: 02/06/2023] Open
Abstract
The recent advent of single-cell RNA sequencing (scRNA-seq) has enabled access to the developmental landscape of a complex organ by monitoring the differentiation trajectory of every specialized cell type at the single-cell level. A main challenge in this endeavor is dissociating plant cells from the rigid cell walls and some species are recalcitrant to such cellular isolation. Here, we describe the establishment of a simple and efficient protocol for protoplast preparation in Chirita pumila, which includes two consecutive digestion processes with different enzymatic buffers. Using this protocol, we generated viable cell suspensions suitable for an array of expression analyses, including scRNA-seq. The universal application of this protocol was further tested by successfully isolating high-quality protoplasts from multiple organs (petals, fruits, tuberous roots, and gynophores) from representative species on the key branches of the angiosperm lineage. This work provides a robust method in plant science, overcoming barriers to isolating protoplasts in diverse plant species and opens a new avenue to study cell type specification, tissue function, and organ diversification in plants.
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13
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Ageeva-Kieferle A, Georgii E, Winkler B, Ghirardo A, Albert A, Hüther P, Mengel A, Becker C, Schnitzler JP, Durner J, Lindermayr C. Nitric oxide coordinates growth, development, and stress response via histone modification and gene expression. PLANT PHYSIOLOGY 2021; 187:336-360. [PMID: 34003928 PMCID: PMC8418403 DOI: 10.1093/plphys/kiab222] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/18/2021] [Indexed: 05/02/2023]
Abstract
Nitric oxide (NO) is a signaling molecule with multiple regulatory functions in plant physiology and stress response. In addition to direct effects on transcriptional machinery, NO executes its signaling function via epigenetic mechanisms. We report that light intensity-dependent changes in NO correspond to changes in global histone acetylation (H3, H3K9, and H3K9/K14) in Arabidopsis (Arabidopsis thaliana) wild-type leaves, and that this relationship depends on S-nitrosoglutathione reductase and histone deacetylase 6 (HDA6). The activity of HDA6 was sensitive to NO, demonstrating that NO participates in regulation of histone acetylation. Chromatin immunoprecipitation sequencing and RNA-seq analyses revealed that NO participates in the metabolic switch from growth and development to stress response. This coordinating function of NO might be particularly important in plant ability to adapt to a changing environment, and is therefore a promising foundation for mitigating the negative effects of climate change on plant productivity.
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Affiliation(s)
| | - Elisabeth Georgii
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Barbro Winkler
- Research Unit Environmental Simulation, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Andrea Ghirardo
- Research Unit Environmental Simulation, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Andreas Albert
- Research Unit Environmental Simulation, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Patrick Hüther
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna 1030, Austria
| | - Alexander Mengel
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Claude Becker
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna 1030, Austria
- Faculty of Biology, Ludwig-Maximilians-University Munich, LMU Biocenter, Martinsried 82152, Germany
| | - Jörg-Peter Schnitzler
- Research Unit Environmental Simulation, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Jörg Durner
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Neuherberg 85764, Germany
- Chair of Biochemical Plant Pathology, Technische Universität München, Freising 85354, Germany
| | - Christian Lindermayr
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Neuherberg 85764, Germany
- Author for communication:
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14
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Wang Q, Bao X, Chen S, Zhong H, Liu Y, Zhang L, Xia Y, Kragler F, Luo M, Li XD, Lam HM, Zhang S. AtHDA6 functions as an H3K18ac eraser to maintain pericentromeric CHG methylation in Arabidopsis thaliana. Nucleic Acids Res 2021; 49:9755-9767. [PMID: 34403482 PMCID: PMC8464031 DOI: 10.1093/nar/gkab706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/26/2021] [Accepted: 08/01/2021] [Indexed: 01/06/2023] Open
Abstract
Pericentromeric DNA, consisting of high-copy-number tandem repeats and transposable elements, is normally silenced through DNA methylation and histone modifications to maintain chromosomal integrity and stability. Although histone deacetylase 6 (HDA6) has been known to participate in pericentromeric silencing, the mechanism is still yet unclear. Here, using whole genome bisulfite sequencing (WGBS) and chromatin immunoprecipitation-sequencing (ChIP-Seq), we mapped the genome-wide patterns of differential DNA methylation and histone H3 lysine 18 acetylation (H3K18ac) in wild-type and hda6 mutant strains. Results show pericentromeric CHG hypomethylation in hda6 mutants was mediated by DNA demethylases, not by DNA methyltransferases as previously thought. DNA demethylases can recognize H3K18ac mark and then be recruited to the chromatin. Using biochemical assays, we found that HDA6 could function as an ‘eraser’ enzyme for H3K18ac mark to prevent DNA demethylation. Oxford Nanopore Technology Direct RNA Sequencing (ONT DRS) also revealed that hda6 mutants with H3K18ac accumulation and CHG hypomethylation were shown to have transcriptionally active pericentromeric DNA.
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Affiliation(s)
- Qianwen Wang
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region.,Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region
| | - Xiucong Bao
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Shengjie Chen
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region.,Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region
| | - Huan Zhong
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong Special Administrative Region
| | - Yaqin Liu
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region.,Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region
| | - Li Zhang
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region.,Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region
| | - Yiji Xia
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region.,Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong Special Administrative Region.,State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Kowloon, Hong Kong Special Administrative Region
| | - Friedrich Kragler
- Max-Planck-Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, 14476 Golm, Germany
| | - Ming Luo
- Agriculture and Biotechnology Research Center, Guangdong Provincial Key Laboratory of Applied Botany, Center of Economic Botany, Core Botanical Gardens, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Hon-Ming Lam
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region.,Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region
| | - Shoudong Zhang
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region.,Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region
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15
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Arabidopsis RPD3-like histone deacetylases form multiple complexes involved in stress response. J Genet Genomics 2021; 48:369-383. [PMID: 34144927 DOI: 10.1016/j.jgg.2021.04.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/31/2021] [Accepted: 04/15/2021] [Indexed: 12/13/2022]
Abstract
The Arabidopsis thaliana RPD3-type histone deacetylases have been known to form conserved SIN3-type histone deacetylase complexes, but whether they form other types of complexes is unknown. Here, we perform affinity purification followed by mass spectrometry and demonstrate that the Arabidopsis RPD3-type histone deacetylases HDA6 and HDA19 interact with several previously uncharacterized proteins, thereby forming three types of plant-specific histone deacetylase complexes, which we named SANT, ESANT, and ARID. RNA-seq indicates that the newly identified components function together with HDA6 and HDA19 and coregulate the expression of a number of genes. HDA6 and HDA19 were previously thought to repress gene transcription by histone deacetylation. We find that the histone deacetylase complexes can repress gene expression via both histone deacetylation-dependent and -independent mechanisms. In the mutants of histone deacetylase complexes, the expression of a number of stress-induced genes is up-regulated, and several mutants of the histone deacetylase complexes show severe retardation in growth. Considering that growth retardation is thought to be a trade-off for an increase in stress tolerance, we infer that the histone deacetylase complexes identified in this study prevent overexpression of stress-induced genes and thereby ensure normal growth of plants under nonstress conditions.
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16
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Su L, Liu S, Liu X, Zhang B, Li M, Zeng L, Li L. Transcriptome profiling reveals histone deacetylase 1 gene overexpression improves flavonoid, isoflavonoid, and phenylpropanoid metabolism in Arachis hypogaea hairy roots. PeerJ 2021; 9:e10976. [PMID: 33777524 PMCID: PMC7977374 DOI: 10.7717/peerj.10976] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 01/29/2021] [Indexed: 11/20/2022] Open
Abstract
Background The peanut (Arachis hypogaea) is a crop plant of high economic importance, but the epigenetic regulation of its root growth and development has not received sufficient attention. Research on Arabidopsis thaliana has shown that histone deacetylases (HDACs) are involved in cell growth, cell differentiation, and stress response. Few studies have focused on the role of HDACs in the root development of other plants, particularly crop plants. In earlier studies, we found large accumulations of A. hypogaea histone deacetylase 1 (AhHDA1) mRNA in peanut roots. However, we did not explore the role of AhHDA1 in peanut root development. Methods In this paper, we investigated the role of the peanut AhHDA1 gene and focused on the effect of altered AhHDA1 expression in hairy roots at both the phenotypic and transcriptional levels. We analyzed the transformation of A. hypogaea hairy roots using Agrobacterium rhizogenes and RNA sequencing to identify differentially expressed genes that were assigned to specific metabolic pathways. Transgenic hairy roots were used as experimental material to analyze the downstream genes expression and histone acetylation levels. To thoroughly understand AhHDA1 function, we also simultaneously screened the AhHDA1-interacting proteins using a yeast two-hybrid system. Results AhHDA1-overexpressing hairy roots were growth-retarded after 20 d in vitro cultivation, and they had a greater accumulation of superoxide anions and hydrogen peroxide than the control and RNAi groups. AhHDA1 overexpression in hairy roots accelerated flux through various secondary synthetic metabolic pathways, as well as inhibited the primary metabolism process. AhHDA1 overexpression also caused a significant upregulation of genes encoding the critical enzyme chalcone synthase (Araip.B8TJ0, CHS) in the flavonoid biosynthesis pathway, hydroxyisoflavanone synthase (Araip.0P3RJ) in the isoflavonoid biosynthesis pathway, and caffeoyl-CoA O-methyltransferase (Aradu.M62BY, CCoAOMT) in the phenylpropanoid biosynthesis pathway. In contrast, ferredoxin 1 (Araip.327XS), the polypeptide of the oxygen-evolving complex of photosystem II (Araip.N6ZTJ), and ribulose bisphosphate carboxylase (Aradu.5IY98) in the photosynthetic pathway were significantly downregulated by AhHDA1 overexpression. The expression levels of these genes had a positive correlation with histone acetylation levels. Conclusion Our results revealed that the relationship between altered gene metabolism activities and AhHDA1 overexpression was mainly reflected in flavonoid, isoflavonoid, and phenylpropanoid metabolism. AhHDA1 overexpression retarded the growth of transgenic hairy roots and may be associated with cell metabolism status. Future studies should focus on the function of AhHDA1-interacting proteins and their effect on root development.
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Affiliation(s)
- Liangchen Su
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, South China Normal University, Guangzhou, Guangdong, China.,Department of Bioengineering, Zunyi Medical University, Zhuhai, Guangdong, China
| | - Shuai Liu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, South China Normal University, Guangzhou, Guangdong, China
| | - Xing Liu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, South China Normal University, Guangzhou, Guangdong, China
| | - Baihong Zhang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, South China Normal University, Guangzhou, Guangdong, China
| | - Meijuan Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, South China Normal University, Guangzhou, Guangdong, China
| | - Lidan Zeng
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, South China Normal University, Guangzhou, Guangdong, China
| | - Ling Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, South China Normal University, Guangzhou, Guangdong, China
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17
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Zarreen F, Chakraborty S. Epigenetic regulation of geminivirus pathogenesis: a case of relentless recalibration of defence responses in plants. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:6890-6906. [PMID: 32869846 DOI: 10.1093/jxb/eraa406] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 08/27/2020] [Indexed: 06/11/2023]
Abstract
Geminiviruses constitute one of the largest families of plant viruses and they infect many economically important crops. The proteins encoded by the single-stranded DNA genome of these viruses interact with a wide range of host proteins to cause global dysregulation of cellular processes and help establish infection in the host. Geminiviruses have evolved numerous mechanisms to exploit host epigenetic processes to ensure the replication and survival of the viral genome. Here, we review our current knowledge of diverse epigenetic processes that have been implicated in the regulation of geminivirus pathogenesis, including DNA methylation, histone post-transcriptional modification, chromatin remodelling, and nucleosome repositioning. In addition, we discuss the currently limited evidence of host epigenetic defence responses that are aimed at counteracting geminivirus infection, and the potential for exploiting these responses for the generation of resistance against geminiviruses in crop species.
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Affiliation(s)
- Fauzia Zarreen
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Supriya Chakraborty
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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18
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Lee HJ, Park JS, Shin SY, Kim SG, Lee G, Kim HS, Jeon JH, Cho HS. Submergence deactivates wound-induced plant defence against herbivores. Commun Biol 2020; 3:651. [PMID: 33159149 PMCID: PMC7648080 DOI: 10.1038/s42003-020-01376-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 10/13/2020] [Indexed: 01/01/2023] Open
Abstract
Flooding is a common and critical disaster in agriculture, because it causes defects in plant growth and even crop loss. An increase in herbivore populations is often observed after floods, which leads to additional damage to the plants. Although molecular mechanisms underlying the plant responses to flooding have been identified, how plant defence systems are affected by flooding remains poorly understood. Herein, we show that submergence deactivates wound-induced defence against herbivore attack in Arabidopsis thaliana. Submergence rapidly suppressed the wound-induced expression of jasmonic acid (JA) biosynthesis genes, resulting in reduced JA accumulation. While plants exposed to hypoxia in argon gas exhibited similar reduced wound responses, the inhibitory effects were initiated after short-term submergence without signs for lack of oxygen. Instead, expression of ethylene-responsive genes was increased after short-term submergence. Blocking ethylene signalling by ein2-1 mutation partially restored suppressed expression of several wound-responsive genes by submergence. In addition, submergence rapidly removed active markers of histone modifications at a gene locus involved in JA biosynthesis. Our findings suggest that submergence inactivates defence systems of plants, which would explain the proliferation of herbivores after flooding. Hyo-Jun Lee et al. show that submergence in Arabidopsis deactivates wound-induced defence against herbivore attack by suppressing the expression of jasmonic acid biosynthesis genes and increasing expression of ethylene-responsive genes. These results shed light on how flooding may impact plant defence systems.
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Affiliation(s)
- Hyo-Jun Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea. .,Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, Daejeon, 34113, Korea.
| | - Ji-Sun Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea
| | - Seung Yong Shin
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea
| | - Sang-Gyu Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Korea
| | - Gisuk Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Korea
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Korea
| | - Jae Heung Jeon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea
| | - Hye Sun Cho
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Korea
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19
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Pagano A, L'Andolina C, Sabatini ME, de Sousa Araújo S, Balestrazzi A, Macovei A. Sodium butyrate induces genotoxic stress in function of photoperiod variations and differentially modulates the expression of genes involved in chromatin modification and DNA repair in Petunia hybrida seedlings. PLANTA 2020; 251:102. [PMID: 32350684 DOI: 10.1007/s00425-020-03392-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 04/16/2020] [Indexed: 06/11/2023]
Abstract
Sodium butyrate applied to Petunia hybrida seeds under a long-day photoperiod has a negative impact (reduced seedling length, decreased production of photosynthetic pigments, and accumulation of DNA damage) on early seedling development, whereas its administration under dark/light conditions (complete dark conditions for 5 days followed by exposure to long-day photoperiod for 5 days) bypasses some of the adverse effects. Genotoxic stress impairs plant development. To circumvent DNA damage, plants activate DNA repair pathways in concert with chromatin dynamics. These are essential during seed germination and seedling establishment, and may be influenced by photoperiod variations. To assess this interplay, an experimental design was developed in Petunia hybrida, a relevant horticultural crop and model species. Seeds were treated with different doses of sodium butyrate (NaB, 1 mM and 5 mM) as a stress agent applied under different light/dark conditions throughout a time period of 10 days. Phenotypic (germination percentage and speed, seedling length, and photosynthetic pigments) and molecular (DNA damage and gene expression profiles) analyses were performed to monitor the response to the imposed conditions. Seed germination was not affected by the treatments. Seedling development was hampered by increasing NaB concentrations applied under a long-day photoperiod (L) as reflected by the decreased seedling length accompanied by increased DNA damage. When seedlings were grown under dark conditions for 5 days and then exposed to long-day photoperiod for the remaining 5 days (D/L), the damaging effects of NaB were circumvented. NaB exposure under L conditions resulted in enhanced expression of HAT/HDAC (HISTONE ACETYLTRANSFERASES/HISTONE DEACTEYLASES) genes along with repression of genes involved in DNA repair. Differently, under D/L conditions, the expression of DNA repair genes was increased by NaB treatment and this was associated with lower levels of DNA damage. The observed DNA damage and gene expression profiles suggest the involvement of chromatin modification- and DNA repair-associated pathways in response to NaB and dark/light exposure during seedling development.
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Affiliation(s)
- Andrea Pagano
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Corrado L'Andolina
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Maria Elisa Sabatini
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy
- Viral Control of Cellular Pathways and Biology of Tumorigenesis Unit, European Institute of Oncology (IFOM-IEO), via Adamello 16, 20139, Milano, Italy
| | - Susana de Sousa Araújo
- Instituto de Tecnologia Química E Biológica António Xavier (ITQB-NOVA), Avenida da República, Estação Agronómica Nacional, 2780-157, Oeiras, Portugal
| | - Alma Balestrazzi
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Anca Macovei
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy.
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20
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Chen X, Ding AB, Zhong X. Functions and mechanisms of plant histone deacetylases. SCIENCE CHINA-LIFE SCIENCES 2019; 63:206-216. [PMID: 31879846 DOI: 10.1007/s11427-019-1587-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 11/13/2019] [Indexed: 12/31/2022]
Abstract
Lysine acetylation, one of the major types of post-translational modifications, plays critical roles in regulating gene expression and protein function. Histone deacetylases (HDACs) are responsible for removing acetyl groups from lysines of both histone and non-histone proteins. While tremendous progress has been made in understanding the function and mechanism of HDACs in animals in the past two decades, nearly half of the HDAC studies in plants were reported within the past five years. In this review, we summarize the major findings on plant HDACs, with a focus on the model plant Arabidopsis thaliana, and highlight the components, regulatory mechanisms, and biological functions of HDAC complexes.
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Affiliation(s)
- Xiangsong Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| | - Adeline B Ding
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Xuehua Zhong
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.
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21
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Zhu G, Chang Y, Xu X, Tang K, Chen C, Lei M, Zhu JK, Duan CG. EXPORTIN 1A prevents transgene silencing in Arabidopsis by modulating nucleo-cytoplasmic partitioning of HDA6. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:1243-1254. [PMID: 30697937 DOI: 10.1111/jipb.12787] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 01/25/2019] [Indexed: 05/28/2023]
Abstract
In eukaryotic cells, transport of macromolecules across the nuclear envelope is an essential process that ensures rapid exchange of cellular components, including protein and RNA molecules. Chromatin regulators involved in epigenetic control are among the molecules exported across the nuclear envelope, but the significance of this nucleo-cytoplasmic trafficking is not well understood. Here, we use a forward screen to isolate XPO1A (a nuclear export receptor in Arabidopsis) as an anti-silencing factor that protects transgenes from transcriptional silencing. Loss-of-function of XPO1A leads to locus-specific DNA hypermethylation at transgene promoters and some endogenous loci. We found that XPO1A directly interacts with histone deacetylase HDA6 in vivo and that the xpo1a mutation causes increased nuclear retention of HDA6 protein and results in reduced histone acetylation and enhanced transgene silencing. Our results reveal a new mechanism of epigenetic regulation through the modulation of XPO1A-dependent nucleo-cytoplasm partitioning of a chromatin regulator.
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Affiliation(s)
- Guohui Zhu
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yanan Chang
- Shanghai Center for Plant Stress Biology and Center of Excellence for Molecular Plant Sciences, the Chinese Academy of Sciences, Shanghai, 201602, China
- The University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuezhong Xu
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Kai Tang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
- Shanghai Center for Plant Stress Biology and Center of Excellence for Molecular Plant Sciences, the Chinese Academy of Sciences, Shanghai, 201602, China
| | - Chunxiang Chen
- Shanghai Center for Plant Stress Biology and Center of Excellence for Molecular Plant Sciences, the Chinese Academy of Sciences, Shanghai, 201602, China
- The University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mingguang Lei
- Shanghai Center for Plant Stress Biology and Center of Excellence for Molecular Plant Sciences, the Chinese Academy of Sciences, Shanghai, 201602, China
| | - Jian-Kang Zhu
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
- Shanghai Center for Plant Stress Biology and Center of Excellence for Molecular Plant Sciences, the Chinese Academy of Sciences, Shanghai, 201602, China
| | - Cheng-Guo Duan
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
- Shanghai Center for Plant Stress Biology and Center of Excellence for Molecular Plant Sciences, the Chinese Academy of Sciences, Shanghai, 201602, China
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22
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Cloning and expression analysis of an endo-1,3-β-D-glucosidase from Phytophthora cinnamomi. Mol Biol Rep 2019; 47:935-942. [PMID: 31741259 DOI: 10.1007/s11033-019-05185-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 11/07/2019] [Indexed: 10/25/2022]
Abstract
Phytophthora is considered one of the most destructive genus for many agricultural plant species worldwide, with a strong environmental and economic impact. Phytophthora cinnamomi is a highly aggressive Phytophthora species associated with the forest decline and responsible for the ink disease in chestnut trees (Castanea sativa Miller), a culture which is extremely important in Europe. This pathogenicity occurs due to the action of several enzymes like the hydrolysis of 1,3-β-glucans at specific sites by the enzyme endo-1,3-β-D-glucosidase. The aim of this work to analyze the heterologous expression in two microorganisms, Escherichia coli and Pichia pastoris, of an endo-1,3-β-D-glucosidase encoded by the gene ENDO1 (AM259651) from P. cinnamomi. Different plasmids were used to clone the gene on each organism and the real-time quantitative polymerase chain reaction was used to determine its level of expression. Homologous expression was also analyzed during growth in different carbon sources (glucose, cellulose, and sawdust) and time-course experiments were used for endo-1,3-β-D-glucosidase production. The highest expression of the endo-1,3-β-D-glucosidase gene occurred in glucose after 8 h of induction. In vivo infection of C. sativa by P. cinnamomi revealed an increase in endo-1,3-β-D-glucosidase expression after 12 h. At 24 h its expression decreased and at 48 h there was again a slight increase in expression, and more experiments in order to further explain this fact are underway.
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23
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Lochmanová G, Ihnatová I, Kuchaříková H, Brabencová S, Zachová D, Fajkus J, Zdráhal Z, Fojtová M. Different Modes of Action of Genetic and Chemical Downregulation of Histone Deacetylases with Respect to Plant Development and Histone Modifications. Int J Mol Sci 2019; 20:ijms20205093. [PMID: 31615119 PMCID: PMC6829310 DOI: 10.3390/ijms20205093] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/09/2019] [Accepted: 10/10/2019] [Indexed: 02/02/2023] Open
Abstract
A high degree of developmental plasticity enables plants to adapt to continuous, often unfavorable and unpredictable changes in their environment. At the molecular level, adaptive advantages for plants are primarily provided by epigenetic machinery including DNA methylation, histone modifications, and the activity of noncoding RNA molecules. Using a mass spectrometry-based proteomic approach, we examined the levels of acetylated histone peptide forms in Arabidopsis plants with a loss of function of histone deacetylase 6 (HDA6), and in plants germinated in the presence of HDA inhibitors trichostatin A (TSA) and sodium butyrate (NaB). Our analyses revealed particular lysine sites at histone sequences targeted by the HDA6 enzyme, and by TSA- and NaB-sensitive HDAs. Compared with plants exposed to drugs, more dramatic changes in the overall profiles of histone post-translational modifications were identified in hda6 mutants. However, loss of HDA6 was not sufficient by itself to induce hyperacetylation to the maximum degree, implying complementary activities of other HDAs. In contrast to hda6 mutants that did not exhibit any obvious phenotypic defects, the phenotypes of seedlings exposed to HDA inhibitors were markedly affected, showing that the effect of these drugs on early plant development is not limited to the modulation of histone acetylation levels.
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Affiliation(s)
- Gabriela Lochmanová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic.
| | - Ivana Ihnatová
- RECETOX, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic.
| | - Hana Kuchaříková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic.
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic.
| | - Sylva Brabencová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic.
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic.
| | - Dagmar Zachová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic.
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic.
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic.
| | - Zbyněk Zdráhal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic.
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic.
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic.
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24
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Sims J, Copenhaver GP, Schlögelhofer P. Meiotic DNA Repair in the Nucleolus Employs a Nonhomologous End-Joining Mechanism. THE PLANT CELL 2019; 31:2259-2275. [PMID: 31266898 PMCID: PMC6751124 DOI: 10.1105/tpc.19.00367] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/12/2019] [Accepted: 06/28/2019] [Indexed: 05/03/2023]
Abstract
Ribosomal RNA genes are arranged in large arrays with hundreds of rDNA units in tandem. These highly repetitive DNA elements pose a risk to genome stability since they can undergo nonallelic exchanges. During meiosis, DNA double-strand breaks (DSBs) are induced as part of the regular program to generate gametes. Meiotic DSBs initiate homologous recombination (HR), which subsequently ensures genetic exchange and chromosome disjunction. In Arabidopsis (Arabidopsis thaliana), we demonstrate that all 45S rDNA arrays become transcriptionally active and are recruited into the nucleolus early in meiosis. This shields the rDNA from acquiring canonical meiotic chromatin modifications and meiotic cohesin and allows only very limited meiosis-specific DSB formation. DNA lesions within the rDNA arrays are repaired in an RAD51-independent but LIG4-dependent manner, establishing that nonhomologous end-joining maintains rDNA integrity during meiosis. Utilizing ectopically integrated rDNA repeats, we validate our findings and demonstrate that the rDNA constitutes an HR-refractory genome environment.
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Affiliation(s)
- Jason Sims
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, 1030 Vienna, Austria
| | - Gregory P Copenhaver
- Department of Biology and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Peter Schlögelhofer
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, 1030 Vienna, Austria
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25
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Hung FY, Chen FF, Li C, Chen C, Lai YC, Chen JH, Cui Y, Wu K. The Arabidopsis LDL1/2-HDA6 histone modification complex is functionally associated with CCA1/LHY in regulation of circadian clock genes. Nucleic Acids Res 2019; 46:10669-10681. [PMID: 30124938 PMCID: PMC6237806 DOI: 10.1093/nar/gky749] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 08/07/2018] [Indexed: 12/27/2022] Open
Abstract
In Arabidopsis, the circadian clock central oscillator genes are important cellular components to generate and maintain circadian rhythms. There is a negative feedback loop between the morning expressed CCA1 (CIRCADIAN CLOCK ASSOCIATED 1)/LHY (LATE ELONGATED HYPOCOTYL) and evening expressed TOC1 (TIMING OF CAB EXPRESSION 1). CCA1 and LHY negatively regulate the expression of TOC1, while TOC1 also binds to the promoters of CCA1 and LHY to repress their expression. Recent studies indicate that histone modifications play an important role in the regulation of the central oscillators. However, the regulatory relationship between histone modifications and the circadian clock genes remains largely unclear. In this study, we found that the Lysine-Specific Demethylase 1 (LSD1)-like histone demethylases, LDL1 and LDL2, can interact with CCA1/LHY to repress the expression of TOC1. ChIP-Seq analysis indicated that LDL1 targets a subset of genes involved in the circadian rhythm regulated by CCA1. Furthermore, LDL1 and LDL2 interact with the histone deacetylase HDA6 and co-regulate TOC1 by histone demetylation and deacetylaion. These results provide new insight into the molecular mechanism of how the circadian clock central oscillator genes are regulated through histone modifications.
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Affiliation(s)
- Fu-Yu Hung
- Institute of Plant Biology, National Taiwan University, Taipei 10617, Taiwan.,Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario N5V 4T3, Canada
| | - Fang-Fang Chen
- Institute of Plant Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Chenlong Li
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario N5V 4T3, Canada.,Department of Biology, Western University, London, Ontario N6A 3K7, Canada.,State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Chen Chen
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario N5V 4T3, Canada.,Department of Biology, Western University, London, Ontario N6A 3K7, Canada
| | - You-Cheng Lai
- Institute of Plant Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Jian-Hao Chen
- Institute of Plant Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Yuhai Cui
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario N5V 4T3, Canada.,Department of Biology, Western University, London, Ontario N6A 3K7, Canada
| | - Keqiang Wu
- Institute of Plant Biology, National Taiwan University, Taipei 10617, Taiwan
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26
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Ning YQ, Chen Q, Lin RN, Li YQ, Li L, Chen S, He XJ. The HDA19 histone deacetylase complex is involved in the regulation of flowering time in a photoperiod-dependent manner. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:448-464. [PMID: 30828924 DOI: 10.1111/tpj.14229] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 12/08/2018] [Accepted: 12/19/2018] [Indexed: 05/22/2023]
Abstract
Chromatin modifications are known to affect flowering time in plants, but little is known about how these modifications regulate flowering time in response to environmental signals like photoperiod. In Arabidopsis thaliana, HDC1, a conserved subunit of the RPD3-like histone deacetylase (HDAC) complex, was previously reported to regulate flowering time via the same mechanism as does the HDAC HDA6. Here, we demonstrate that HDC1, SNLs and MSI1 are shared subunits of the HDA6 and HDA19 HDAC complexes. While the late-flowering phenotype of the hda6 mutant is independent of photoperiod, the hda19, hdc1 and snl2/3/4 mutants flower later than or at a similar time to the wild-type in long-day conditions but flower earlier than the wild-type in short-day conditions. Our genome-wide analyses indicate that the effect of hdc1 on histone acetylation and transcription is comparable with that of hda19 but is different from that of hda6. Especially, we demonstrate that the HDA19 complex directly regulates the expression of two flowering repressor genes related to the gibberellin signaling pathway. Thus, the study reveals a photoperiod-dependent role of the HDA19 HDAC complex in the regulation of flowering time.
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Affiliation(s)
- Yong-Qiang Ning
- College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Qing Chen
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Rong-Nan Lin
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Yong-Qiang Li
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing, 102206, China
| | - She Chen
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, 102206, China
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27
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Lee HG, Hong C, Seo PJ. The Arabidopsis Sin3-HDAC Complex Facilitates Temporal Histone Deacetylation at the CCA1 and PRR9 Loci for Robust Circadian Oscillation. FRONTIERS IN PLANT SCIENCE 2019; 10:171. [PMID: 30833956 PMCID: PMC6387943 DOI: 10.3389/fpls.2019.00171] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 02/01/2019] [Indexed: 06/09/2023]
Abstract
The circadian clock synchronizes endogenous rhythmic processes with environmental cycles and maximizes plant fitness. Multiple regulatory layers shape circadian oscillation, and chromatin modification is emerging as an important scheme for precise circadian waveforms. Here, we report the role of an evolutionarily conserved Sin3-histone deacetylase complex (HDAC) in circadian oscillation in Arabidopsis. SAP30 FUNCTION-RELATED 1 (AFR1) and AFR2, which are key components of Sin3-HDAC complex, are circadianly-regulated and possibly facilitate the temporal formation of the Arabidopsis Sin3-HDAC complex at dusk. The evening-expressed AFR proteins bind directly to the CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and PSEUDO-RESPONSE REGULATOR 9 (PRR9) promoters and catalyze histone 3 (H3) deacetylation at the cognate regions to repress expression, allowing the declining phase of their expression at dusk. In support, the CCA1 and PRR9 genes were de-repressed around dusk in the afr1-1afr2-1 double mutant. These findings indicate that periodic histone deacetylation at the morning genes by the Sin3-HDAC complex contributes to robust circadian maintenance in higher plants.
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Affiliation(s)
- Hong Gil Lee
- Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Cheljong Hong
- Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul, South Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
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28
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Hung FY, Chen FF, Li C, Chen C, Chen JH, Cui Y, Wu K. The LDL1/2-HDA6 Histone Modification Complex Interacts With TOC1 and Regulates the Core Circadian Clock Components in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2019; 10:233. [PMID: 30863422 PMCID: PMC6399392 DOI: 10.3389/fpls.2019.00233] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 02/12/2019] [Indexed: 05/18/2023]
Abstract
In Arabidopsis, the circadian rhythm is associated with multiple important biological processes and maintained by multiple interconnected loops that generate robust rhythms. The circadian clock central loop is a negative feedback loop composed of the core circadian clock components. TOC1 (TIMING OF CAB EXPRESSION 1) is highly expressed in the evening and negatively regulates the expression of CCA1 (CIRCADIAN CLOCK ASSOCIATED 1)/LHY (LATE ELONGATED HYPOCOTYL). CCA1/LHY also binds to the promoter of TOC1 and represses the TOC1 expression. Our recent research revealed that the histone modification complex comprising of LYSINE-SPECIFIC DEMETHYLASE 1 (LSD1)-LIKE 1/2 (LDL1/2) and HISTONE DEACETYLASE 6 (HDA6) can be recruited by CCA1/LHY to repress TOC1 expression. In this study, we found that HDA6, LDL1, and LDL2 can interact with TOC1, and the LDL1/2-HDA6 complex is associate with TOC1 to repress the CCA1/LHY expression. Furthermore, LDL1/2-HDA6 and TOC1 co-target a subset of genes involved in the circadian rhythm. Collectively, our results indicate that the LDL1/2-HDA6 histone modification complex is important for the regulation of the core circadian clock components.
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Affiliation(s)
- Fu-Yu Hung
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON, Canada
| | - Fang-Fang Chen
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
| | - Chenlong Li
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON, Canada
- Department of Biology, Western University, London, ON, Canada
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Chen Chen
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON, Canada
- Department of Biology, Western University, London, ON, Canada
| | - Jian-Hao Chen
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
| | - Yuhai Cui
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON, Canada
- Department of Biology, Western University, London, ON, Canada
- *Correspondence: Yuhai Cui, Keqiang Wu,
| | - Keqiang Wu
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
- *Correspondence: Yuhai Cui, Keqiang Wu,
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29
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Lateral Inhibition by a Peptide Hormone-Receptor Cascade during Arabidopsis Lateral Root Founder Cell Formation. Dev Cell 2019; 48:64-75.e5. [DOI: 10.1016/j.devcel.2018.11.031] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 10/30/2018] [Accepted: 11/15/2018] [Indexed: 11/20/2022]
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30
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Yuan L, Chen X, Chen H, Wu K, Huang S. Histone deacetylases HDA6 and HDA9 coordinately regulate valve cell elongation through affecting auxin signaling in Arabidopsis. Biochem Biophys Res Commun 2018; 508:695-700. [PMID: 30527808 DOI: 10.1016/j.bbrc.2018.11.082] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 11/13/2018] [Indexed: 10/27/2022]
Abstract
Both Histone Deacetylases HDA6 and HDA9 belong to class I subfamily of RPD3/HDA1 HDACs. Loss-of-function mutants of HDA9 form slightly blunt siliques. However, the involvement of HDA6 in regulating silique tip growth is unclear. In this study, we show that HDA6 acts redundantly with HDA9 in regulating the elongation of valve cells in the silique tip. Although the hda6 single mutant does not exhibit a detectable silique phenotype, the silique tip of hda6 hda9 double mutant displays a more severe bulge, a morphology we termed as "nock-shaped". The valve cells of the silique tip of hda9 are longer than wild-type, and loss of HDA6 in hda9 enhances the valve cell elongation phenotype. The transcript levels of auxin-signaling-related genes are mis-regulated in hda9 and hda6 hda9 siliques, and the GFP reporter driven by the auxin response promoter DR5 is weaker in hda9 or hda6 hda9 than wild-type or hda6. Thus, our findings reveal that HDA6 and HDA9 coordinately control the elongation of silique valve cells through regulating the expression of auxin-related genes in silique tips.
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Affiliation(s)
- Liangbing Yuan
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Xue Chen
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Huhui Chen
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Keqiang Wu
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, 106, Taiwan
| | - Shangzhi Huang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.
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Micol-Ponce R, Sarmiento-Mañús R, Ruiz-Bayón A, Montacié C, Sáez-Vasquez J, Ponce MR. Arabidopsis RIBOSOMAL RNA PROCESSING7 Is Required for 18S rRNA Maturation. THE PLANT CELL 2018; 30:2855-2872. [PMID: 30361235 PMCID: PMC6305980 DOI: 10.1105/tpc.18.00245] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 09/04/2018] [Accepted: 10/24/2018] [Indexed: 05/24/2023]
Abstract
Ribosome biogenesis is fundamental to growth and development in eukaryotes and is linked to human diseases and cancer. Arabidopsis thaliana MORPHOLOGY OF ARGONAUTE1-52 SUPPRESSED 2 (MAS2) participates in splicing and 45S ribosomal DNA (rDNA) expression. In a screen for MAS2 interactors, we identified RIBOSOMAL RNA PROCESSING 7 (RRP7), an ortholog of yeast rRNA processing protein 7 (Rrp7), which is required for 18S ribosomal RNA (rRNA) maturation. Arabidopsis rrp7 mutants exhibit a pleiotropic phenotype including slow growth, altered shoot phyllotaxy, aberrant venation in lateral organs, partial infertility, and abscisic acid hypersensitivity in seedlings. In Arabidopsis, RRP7 localizes mainly to the nucleolus, the site of the 45S rDNA transcription that produces a 45S pre-rRNA primary transcript, precursor of the 25S, 18S and 5.8S rRNAs. Lack of RRP7 function perturbs 18S rRNA maturation, causes nucleolar hypertrophy, and results in an increased 25S/18S rRNA ratio. Arabidopsis contains hundreds of 45S rDNA genes whose expression is epigenetically regulated, and deregulated, in rrp7 mutants. Double mutant analysis revealed synergistic interactions between RRP7 alleles and alleles of MAS2, NUCLEOLIN1 (NUC1), and HISTONE DEACETYLASE 6 (HDA6), which encode epigenetic regulators of 45S rDNA transcription. Our results reveal the evolutionarily conserved but divergent roles of RRP7 as a ribosome biogenesis factor.
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Affiliation(s)
- Rosa Micol-Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Alicante, Spain
| | - Raquel Sarmiento-Mañús
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Alicante, Spain
| | - Alejandro Ruiz-Bayón
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Alicante, Spain
| | - Charlotte Montacié
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, 66860, Perpignan, France
- Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, 66860, Perpignan, France
| | - Julio Sáez-Vasquez
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, 66860, Perpignan, France
- Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, 66860, Perpignan, France
| | - María Rosa Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Alicante, Spain.
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Vijayapalani P, Hewezi T, Pontvianne F, Baum TJ. An Effector from the Cyst Nematode Heterodera schachtii Derepresses Host rRNA Genes by Altering Histone Acetylation. THE PLANT CELL 2018; 30:2795-2812. [PMID: 30333146 PMCID: PMC6305986 DOI: 10.1105/tpc.18.00570] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/25/2018] [Accepted: 10/14/2018] [Indexed: 05/04/2023]
Abstract
Cyst nematodes are plant-pathogenic animals that secrete effector proteins into plant root cells to alter host gene expression and reprogram these cells to form specialized feeding sites, known as syncytia. The molecular mechanisms of these effectors are mostly unknown. We determined that the sugar beet cyst nematode (Heterodera schachtii) 32E03 effector protein strongly inhibits the activities of Arabidopsis thaliana histone deacetylases including the HDT1 enzyme, which has a known function in the regulation of rRNA gene expression through chromatin modifications. We determined that plants expressing the 32E03 coding sequence exhibited increased acetylation of histone H3 along the rDNA chromatin. At low 32E03 expression levels, these chromatin changes triggered the derepression of a subset of rRNA genes, which were conducive to H. schachtii parasitism. By contrast, high levels of 32E03 caused profound bidirectional transcription along the rDNA, which triggered rDNA-specific small RNA production leading to RNA-directed DNA methylation and silencing of rDNA, which inhibited nematode development. Our data show that the 32E03 effector alters plant rRNA gene expression by modulating rDNA chromatin in a dose-dependent manner. Thus, the 32E03 effector epigenetically regulates plant gene expression to promote cyst nematode parasitism.
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Affiliation(s)
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996
| | - Frederic Pontvianne
- Université de Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR5096, F-66860 Perpignan, France
- Université de Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR5096, F-66860, Perpignan, France
| | - Thomas J. Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011
- Address correspondence to
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33
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Wang B, Yang X, Wang Y, Xie Y, Zhou X. Tomato Yellow Leaf Curl Virus V2 Interacts with Host Histone Deacetylase 6 To Suppress Methylation-Mediated Transcriptional Gene Silencing in Plants. J Virol 2018; 92:e00036-18. [PMID: 29950418 PMCID: PMC6146709 DOI: 10.1128/jvi.00036-18] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 06/22/2018] [Indexed: 12/12/2022] Open
Abstract
Cytosine DNA methylation is a conserved epigenetic silencing mechanism that defends against biotic stresses such as geminivirus infection. As a countermeasure, geminiviruses encode proteins that inhibit methylation and transcriptional gene silencing (TGS). Previous studies showed that V2 protein of Tomato yellow leaf curl virus (TYLCV) functions as a TGS suppressor. However, how V2 mediates TGS suppression remains unknown. Here we show that V2 interacts directly with a Nicotiana benthamiana histone deacetylase 6 (NbHDA6), a homolog of Arabidopsis HDA6 (AtHDA6), known to be involved in gene silencing in cooperation with methyltransferase 1 (MET1). NbHDA6 genetically complemented a late-flowering phenotype and restored histone deacetylation of an AtHDA6 mutant. Furthermore, our investigation showed that NbHDA6 displayed histone deacetylase enzymatic activity, which was not inhibited by V2. Genetic analysis revealed that silencing of NbHDA6 expression resulted in enhanced susceptibility to TYLCV infection. In addition, methylation-sensitive PCR and bisulfite sequencing analysis showed that silencing of NbHDA6 expression caused reduced DNA methylation of the viral genome in infected plants. HDA6 was previously shown to recruit and physically interact with MET1 to function in gene silencing. Using competitive pulldown and coimmunoprecipitation assays, we demonstrated that V2 did not interact but competed with NbMET1 for direct binding to NbHDA6. These findings suggest that V2 interacts with host HDA6 and interferes with the recruitment of MET1 by HDA6, resulting in decreased methylation of the viral DNA genome by TGS with a concomitant increase in host susceptibility to TYLCV infection.IMPORTANCE Plants employ repressive viral genome methylation as an epigenetic defense against geminiviruses. In turn, geminiviruses encode proteins that inhibit methylation by TGS. Previous studies showed that TYLCV V2 can efficiently suppress TGS, but the mechanism remains unknown. We showed that V2 interacted with NbHDA6 but did not inhibit its enzymatic activity. As HDA6 is known to be involved in gene silencing in cooperation with MET1, we explored the relationship between V2, NbMET1, and NbHDA6. Our investigation showed that V2 did not interact but competed with NbMET1 for direct binding to NbHDA6. To our knowledge, this is the first report that viral proteins inhibit TGS by interacting with histone deacetylase but not by blocking the methyl cycle. This work provides an additional mechanism for TGS suppression by geminiviruses.
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Affiliation(s)
- Bi Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, People's Republic of China
| | - Xiuling Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Yaqin Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Yan Xie
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
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Forestan C, Farinati S, Rouster J, Lassagne H, Lauria M, Dal Ferro N, Varotto S. Control of Maize Vegetative and Reproductive Development, Fertility, and rRNAs Silencing by HISTONE DEACETYLASE 108. Genetics 2018; 208:1443-1466. [PMID: 29382649 DOI: 10.1534/genetics.117.300625/-/dc1.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 01/28/2018] [Indexed: 05/28/2023] Open
Abstract
Histone deacetylases (HDACs) catalyze the removal of acetyl groups from acetylated histone tails that consequently interact more closely with DNA, leading to chromatin state refractory to transcription. Zea mays HDA108 belongs to the Rpd3/HDA1 HDAC family and is ubiquitously expressed during development. The newly isolated hda108/hda108 insertional mutant exhibited many developmental defects: significant reduction in plant height, alterations of shoot and leaf development, and alterations of inflorescence patterning and fertility. Western blot analyses and immunolocalization experiments revealed an evident increase in histone acetylation, accompanied by a marked reduction in H3K9 dimethylation, in mutant nuclei. The DNA methylation status, in the CHG sequence context, and the transcript level of ribosomal sequences were also affected in hda108 mutants, while enrichment in H3 and H4 acetylation characterizes both repetitive and nonrepetitive transcriptional up-regulated loci. RNA-Seq of both young leaf and anthers indicated that transcription factor expression is highly affected and that the pollen developmental program is disrupted in hda108 mutants. Crosses between hda108/hda108 and epiregulator mutants did not produce any double mutant progeny indicating possible genetic interactions of HDA108 with distinct epigenetic pathways. Our findings indicate that HDA108 is directly involved in regulation of maize development, fertility, and epigenetic regulation of genome activity.
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Affiliation(s)
- Cristian Forestan
- Department of Agronomy Food Natural Resources, Animals and Environment (DAFNAE) Agripolis, University of Padova, 35020 Legnaro (PD), Italy
| | - Silvia Farinati
- Department of Agronomy Food Natural Resources, Animals and Environment (DAFNAE) Agripolis, University of Padova, 35020 Legnaro (PD), Italy
| | - Jacques Rouster
- GM Trait Cereals, Biogemma, Centre de Research de Chappes, 63720 Chappes, France
| | - Hervé Lassagne
- GM Trait Cereals, Biogemma, Centre de Research de Chappes, 63720 Chappes, France
| | - Massimiliano Lauria
- The Institute of Agricultural Biology and Biotechnology (IBBA), Consiglio Nazionale delle Ricerche (CNR), 20133 Milano, Italy
| | - Nicola Dal Ferro
- Department of Agronomy Food Natural Resources, Animals and Environment (DAFNAE) Agripolis, University of Padova, 35020 Legnaro (PD), Italy
| | - Serena Varotto
- Department of Agronomy Food Natural Resources, Animals and Environment (DAFNAE) Agripolis, University of Padova, 35020 Legnaro (PD), Italy
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35
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Control of Maize Vegetative and Reproductive Development, Fertility, and rRNAs Silencing by HISTONE DEACETYLASE 108. Genetics 2018; 208:1443-1466. [PMID: 29382649 PMCID: PMC5887141 DOI: 10.1534/genetics.117.300625] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 01/28/2018] [Indexed: 12/27/2022] Open
Abstract
Histone deacetylases (HDACs) catalyze the removal of acetyl groups from acetylated histone tails that consequently interact more closely with DNA, leading to chromatin state refractory to transcription. Zea mays HDA108 belongs to the Rpd3/HDA1 HDAC family and is ubiquitously expressed during development. The newly isolated hda108/hda108 insertional mutant exhibited many developmental defects: significant reduction in plant height, alterations of shoot and leaf development, and alterations of inflorescence patterning and fertility. Western blot analyses and immunolocalization experiments revealed an evident increase in histone acetylation, accompanied by a marked reduction in H3K9 dimethylation, in mutant nuclei. The DNA methylation status, in the CHG sequence context, and the transcript level of ribosomal sequences were also affected in hda108 mutants, while enrichment in H3 and H4 acetylation characterizes both repetitive and nonrepetitive transcriptional up-regulated loci. RNA-Seq of both young leaf and anthers indicated that transcription factor expression is highly affected and that the pollen developmental program is disrupted in hda108 mutants. Crosses between hda108/hda108 and epiregulator mutants did not produce any double mutant progeny indicating possible genetic interactions of HDA108 with distinct epigenetic pathways. Our findings indicate that HDA108 is directly involved in regulation of maize development, fertility, and epigenetic regulation of genome activity.
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36
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Suzuki M, Shinozuka N, Hirakata T, Nakata MT, Demura T, Tsukaya H, Horiguchi G. OLIGOCELLULA1/ HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES15 Promotes Cell Proliferation With HISTONE DEACETYLASE9 and POWERDRESS During Leaf Development in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2018; 9:580. [PMID: 29774040 PMCID: PMC5943563 DOI: 10.3389/fpls.2018.00580] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 04/13/2018] [Indexed: 05/18/2023]
Abstract
Organ size regulation is dependent on the precise spatial and temporal regulation of cell proliferation and cell expansion. A number of transcription factors have been identified that play a key role in the determination of aerial lateral organ size, but their functional relationship to various chromatin modifiers has not been well understood. To understand how leaf size is regulated, we previously isolated the oligocellula1 (oli1) mutant of Arabidopsis thaliana that develops smaller first leaves than the wild type (WT) mainly due to a reduction in the cell number. In this study, we further characterized oli1 leaf phenotypes and identified the OLI1 gene as well as interaction partners of OLI1. Detailed characterizations of leaf development suggested that the cell proliferation rate in oli1 leaf primordia is lower than that in the WT. In addition, oli1 was associated with a slight delay of the progression from the juvenile to adult phases of leaf traits. A classical map-based approach demonstrated that OLI1 is identical to HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES15 (HOS15). HOS15/OLI1 encodes a homolog of human transducin β-like protein1 (TBL1). TBL1 forms a transcriptional repression complex with the histone deacetylase (HDAC) HDAC3 and either nuclear receptor co-repressor (N-CoR) or silencing mediator for retinoic acid and thyroid receptor (SMRT). We found that mutations in HISTONE DEACETYLASE9 (HDA9) and a switching-defective protein 3, adaptor 2, N-CoR, and transcription factor IIIB-domain protein gene, POWERDRESS (PWR), showed a small-leaf phenotype similar to oli1. In addition, hda9 and pwr did not further enhance the oli1 small-leaf phenotype, suggesting that these three genes act in the same pathway. Yeast two-hybrid assays suggested physical interactions, wherein PWR probably bridges HOS15/OLI1 and HDA9. Earlier studies suggested the roles of HOS15, HDA9, and PWR in transcriptional repression. Consistently, transcriptome analyses showed several genes commonly upregulated in the three mutants. From these findings, we propose a possibility that HOS15/OLI1, PWR, and HDA9 form an evolutionary conserved transcription repression complex that plays a positive role in the regulation of final leaf size.
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Affiliation(s)
- Marina Suzuki
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Nanae Shinozuka
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Tomohiro Hirakata
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Miyuki T. Nakata
- Research Center for Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Taku Demura
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
| | - Hirokazu Tsukaya
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Okazaki Institute for Integrative Bioscience, Okazaki, Japan
| | - Gorou Horiguchi
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
- Research Center for Life Science, College of Science, Rikkyo University, Tokyo, Japan
- *Correspondence: Gorou Horiguchi,
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37
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Wang Y, Hu Q, Wu Z, Wang H, Han S, Jin Y, Zhou J, Zhang Z, Jiang J, Shen Y, Shi H, Yang W. HISTONE DEACETYLASE 6 represses pathogen defence responses in Arabidopsis thaliana. PLANT, CELL & ENVIRONMENT 2017; 40:2972-2986. [PMID: 28770584 DOI: 10.1111/pce.13047] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 07/23/2017] [Indexed: 05/18/2023]
Abstract
Plant defence mechanisms are suppressed in the absence of pathogen attack to prevent wasted energy and growth inhibition. However, how defence responses are repressed is not well understood. Histone deacetylase 6 (HDA6) is a negative regulator of gene expression, and its role in pathogen defence response in plants is not known. In this study, a novel allele of hda6 (designated as shi5) with spontaneous defence response was isolated from a forward genetics screening in Arabidopsis. The shi5 mutant exhibited increased resistance to hemibiotrophic bacterial pathogen Pst DC3000, constitutively activated expression of pathogen-responsive genes including PR1, PR2, etc. and increased histone acetylation levels at the promoters of most tested genes that were upregulated in shi5. In both wild type and shi5 plants, the expression and histone acetylation of these genes were upregulated by pathogen infection. HDA6 was found to bind to the promoters of these genes under both normal growth conditions and pathogen infection. Our research suggests that HDA6 is a general repressor of pathogen defence response and plays important roles in inhibiting and modulating the expression of pathogen-responsive genes in Arabidopsis.
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Affiliation(s)
- Yizhong Wang
- School of Life Sciences, Central China Normal University, Wuhan, 43009, Hubei, P.R. China
| | - Qin Hu
- School of Life Sciences, Central China Normal University, Wuhan, 43009, Hubei, P.R. China
| | - Zhenjiang Wu
- School of Life Sciences, Central China Normal University, Wuhan, 43009, Hubei, P.R. China
| | - Hui Wang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA
| | - Shiming Han
- School of Life Sciences, Central China Normal University, Wuhan, 43009, Hubei, P.R. China
| | - Ye Jin
- School of Life Sciences, Central China Normal University, Wuhan, 43009, Hubei, P.R. China
| | - Jin Zhou
- School of Life Sciences, Central China Normal University, Wuhan, 43009, Hubei, P.R. China
| | - Zhengfeng Zhang
- School of Life Sciences, Central China Normal University, Wuhan, 43009, Hubei, P.R. China
| | - Jiafu Jiang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA
| | - Yun Shen
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA
| | - Huazhong Shi
- School of Life Sciences, Central China Normal University, Wuhan, 43009, Hubei, P.R. China
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA
| | - Wannian Yang
- School of Life Sciences, Central China Normal University, Wuhan, 43009, Hubei, P.R. China
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38
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Yu CW, Tai R, Wang SC, Yang P, Luo M, Yang S, Cheng K, Wang WC, Cheng YS, Wu K. HISTONE DEACETYLASE6 Acts in Concert with Histone Methyltransferases SUVH4, SUVH5, and SUVH6 to Regulate Transposon Silencing. THE PLANT CELL 2017; 29:1970-1983. [PMID: 28778955 PMCID: PMC5590490 DOI: 10.1105/tpc.16.00570] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 07/20/2017] [Accepted: 08/02/2017] [Indexed: 05/22/2023]
Abstract
Histone deacetylases (HDACs) play important roles in regulating gene expression. In yeast and animals, HDACs act as components of multiprotein complexes that modulate transcription during various biological processes. However, little is known about the interacting proteins of plant HDACs. To identify the plant HDAC complexes and interacting proteins, we developed an optimized workflow using immunopurification coupled to mass spectrometry-based proteomics in Arabidopsis thaliana We found that the histone deacetylase HDA6 can interact with the histone methyltransferases SUVH4, SUVH5, and SUVH6 (SUVH4/5/6). Domain analysis revealed that the C-terminal regions of HDA6 and SUVH5 are important for their interaction. Furthermore, HDA6 interacts with SUVH4/5/6 and coregulates a subset of transposons through histone H3K9 methylation and H3 deacetylation. In addition, two phosphorylated serine residues, S427 and S429, were unambiguously identified in the C-terminal region of HDA6. Phosphomimetics (amino acid substitutions that mimic a phosphorylated protein) of HDA6 resulted in increased enzymatic activity, whereas the mutation of S427 to alanine in HDA6 abolished its interaction with SUVH5 and SUVH6, suggesting that the phosphorylation of HDA6 is important for its activity and function.
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Affiliation(s)
- Chun-Wei Yu
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Ready Tai
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Shen-Chi Wang
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Ping Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Ming Luo
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Songguang Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Kai Cheng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Wen-Chun Wang
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
- Department of Life Science, College of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Yi-Sheng Cheng
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
- Department of Life Science, College of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Keqiang Wu
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
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39
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Kim JM, To TK, Matsui A, Tanoi K, Kobayashi NI, Matsuda F, Habu Y, Ogawa D, Sakamoto T, Matsunaga S, Bashir K, Rasheed S, Ando M, Takeda H, Kawaura K, Kusano M, Fukushima A, Endo TA, Kuromori T, Ishida J, Morosawa T, Tanaka M, Torii C, Takebayashi Y, Sakakibara H, Ogihara Y, Saito K, Shinozaki K, Devoto A, Seki M. Acetate-mediated novel survival strategy against drought in plants. NATURE PLANTS 2017; 3:17097. [PMID: 28650429 DOI: 10.1038/nplants.2017.97] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 05/25/2017] [Indexed: 05/19/2023]
Abstract
Water deficit caused by global climate changes seriously endangers the survival of organisms and crop productivity, and increases environmental deterioration1,2. Plants' resistance to drought involves global reprogramming of transcription, cellular metabolism, hormone signalling and chromatin modification3-8. However, how these regulatory responses are coordinated via the various pathways, and the underlying mechanisms, are largely unknown. Herein, we report an essential drought-responsive network in which plants trigger a dynamic metabolic flux conversion from glycolysis into acetate synthesis to stimulate the jasmonate (JA) signalling pathway to confer drought tolerance. In Arabidopsis, the ON/OFF switching of this whole network is directly dependent on histone deacetylase HDA6. In addition, exogenous acetic acid promotes de novo JA synthesis and enrichment of histone H4 acetylation, which influences the priming of the JA signalling pathway for plant drought tolerance. This novel acetate function is evolutionarily conserved as a survival strategy against environmental changes in plants. Furthermore, the external application of acetic acid successfully enhanced the drought tolerance in Arabidopsis, rapeseed, maize, rice and wheat plants. Our findings highlight a radically new survival strategy that exploits an epigenetic switch of metabolic flux conversion and hormone signalling by which plants adapt to drought.
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Affiliation(s)
- Jong-Myong Kim
- Plant Genomic Network Research Team, RIKEN Centre for Sustainable Resource Science (CSRS), 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
- CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Taiko Kim To
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Akihiro Matsui
- Plant Genomic Network Research Team, RIKEN Centre for Sustainable Resource Science (CSRS), 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Keitaro Tanoi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Natsuko I Kobayashi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Fumio Matsuda
- Metabolic Engineering Laboratory, Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5, Yamadaoka, Suita, Osaka 565-0871, Japan
- Metabolomics Research Group, RIKEN CSRS, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Yoshiki Habu
- Plant Physiology Research Unit, Division of Plant and Microbial Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Daisuke Ogawa
- Breeding Strategies Research Unit, Division of Basic Research, Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Takuya Sakamoto
- Department of Applied Biological Science, Graduate School of Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Sachihiro Matsunaga
- Department of Applied Biological Science, Graduate School of Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Khurram Bashir
- Plant Genomic Network Research Team, RIKEN Centre for Sustainable Resource Science (CSRS), 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Sultana Rasheed
- Plant Genomic Network Research Team, RIKEN Centre for Sustainable Resource Science (CSRS), 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Marina Ando
- Plant Genomic Network Research Team, RIKEN Centre for Sustainable Resource Science (CSRS), 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka, Yokohama 244-0813, Japan
| | - Hiroko Takeda
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka, Yokohama 244-0813, Japan
| | - Kanako Kawaura
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka, Yokohama 244-0813, Japan
| | - Miyako Kusano
- Metabolomics Research Group, RIKEN CSRS, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Atsushi Fukushima
- Metabolome Informatics Research Team, RIKEN CSRS, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Takaho A Endo
- Laboratory for Integrative Genomics, RIKEN Centre for Integrative Medical Sciences, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Takashi Kuromori
- Gene Discovery Research Group, RIKEN CSRS, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Junko Ishida
- Plant Genomic Network Research Team, RIKEN Centre for Sustainable Resource Science (CSRS), 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Taeko Morosawa
- Plant Genomic Network Research Team, RIKEN Centre for Sustainable Resource Science (CSRS), 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Maho Tanaka
- Plant Genomic Network Research Team, RIKEN Centre for Sustainable Resource Science (CSRS), 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Chieko Torii
- Plant Genomic Network Research Team, RIKEN Centre for Sustainable Resource Science (CSRS), 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Yumiko Takebayashi
- Plant Productivity System Research Group, RIKEN CSRS, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Hitoshi Sakakibara
- Plant Productivity System Research Group, RIKEN CSRS, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Yasunari Ogihara
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka, Yokohama 244-0813, Japan
| | - Kazuki Saito
- Metabolomics Research Group, RIKEN CSRS, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN CSRS, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Alessandra Devoto
- School of Biological Sciences, Plant Molecular Sciences, Centre for Systems and Synthetic Biology, Royal Holloway University of London, Egham TW20 0EX, UK
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Centre for Sustainable Resource Science (CSRS), 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
- CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka, Yokohama 244-0813, Japan
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40
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Abstract
Hybrid incompatibility resulting from deleterious gene combinations is thought to be an important step toward reproductive isolation and speciation. Here, we demonstrate involvement of a silent epiallele in hybrid incompatibility. In Arabidopsis thaliana accession Cvi-0, one of the two copies of a duplicated histidine biosynthesis gene, HISN6A, is mutated, making HISN6B essential. In contrast, in accession Col-0, HISN6A is essential because HISN6B is not expressed. Owing to these differences, Cvi-0 × Col-0 hybrid progeny that are homozygous for both Cvi-0 HISN6A and Col-0 HISN6B do not survive. We show that HISN6B of Col-0 is not a defective pseudogene, but a stably silenced epiallele. Mutating HISTONE DEACETYLASE 6 (HDA6), or the cytosine methyltransferase genes MET1 or CMT3, erases HISN6B's silent locus identity, reanimating the gene to circumvent hisn6a lethality and hybrid incompatibility. These results show that HISN6-dependent hybrid lethality is a revertible epigenetic phenomenon and provide additional evidence that epigenetic variation has the potential to limit gene flow between diverging populations of a species.
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41
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Chen X, Lu L, Mayer KS, Scalf M, Qian S, Lomax A, Smith LM, Zhong X. POWERDRESS interacts with HISTONE DEACETYLASE 9 to promote aging in Arabidopsis. eLife 2016; 5. [PMID: 27873573 PMCID: PMC5119886 DOI: 10.7554/elife.17214] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 10/25/2016] [Indexed: 12/27/2022] Open
Abstract
Leaf senescence is an essential part of the plant lifecycle during which nutrients are re-allocated to other tissues. The regulation of leaf senescence is a complex process. However, the underlying mechanism is poorly understood. Here, we uncovered a novel and the pivotal role of Arabidopsis HDA9 (a RPD3-like histone deacetylase) in promoting the onset of leaf senescence. We found that HDA9 acts in complex with a SANT domain-containing protein POWERDRESS (PWR) and transcription factor WRKY53. Our genome-wide profiling of HDA9 occupancy reveals that HDA9 directly binds to the promoters of key negative regulators of senescence and this association requires PWR. Furthermore, we found that PWR is important for HDA9 nuclear accumulation. This study reveals an uncharacterized epigenetic complex involved in leaf senescence and provides mechanistic insights into how a histone deacetylase along with a chromatin-binding protein contribute to a robust regulatory network to modulate the onset of plant aging.
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Affiliation(s)
- Xiangsong Chen
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States.,Wisconsin Institutes for Discovery, University of Wisconsin-Madison, Madison, United States
| | - Li Lu
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States.,Wisconsin Institutes for Discovery, University of Wisconsin-Madison, Madison, United States
| | - Kevin S Mayer
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States.,Wisconsin Institutes for Discovery, University of Wisconsin-Madison, Madison, United States
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin-Madison, Madison, United States
| | - Shuiming Qian
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States.,Wisconsin Institutes for Discovery, University of Wisconsin-Madison, Madison, United States
| | - Aaron Lomax
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, United States
| | - Xuehua Zhong
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States.,Wisconsin Institutes for Discovery, University of Wisconsin-Madison, Madison, United States
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42
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Chen X, Lu L, Mayer KS, Scalf M, Qian S, Lomax A, Smith LM, Zhong X. POWERDRESS interacts with HISTONE DEACETYLASE 9 to promote aging in Arabidopsis. eLife 2016. [PMID: 27873573 DOI: 10.7554/elife.17214.001-10.7554/elife.17214.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Abstract
Leaf senescence is an essential part of the plant lifecycle during which nutrients are re-allocated to other tissues. The regulation of leaf senescence is a complex process. However, the underlying mechanism is poorly understood. Here, we uncovered a novel and the pivotal role of Arabidopsis HDA9 (a RPD3-like histone deacetylase) in promoting the onset of leaf senescence. We found that HDA9 acts in complex with a SANT domain-containing protein POWERDRESS (PWR) and transcription factor WRKY53. Our genome-wide profiling of HDA9 occupancy reveals that HDA9 directly binds to the promoters of key negative regulators of senescence and this association requires PWR. Furthermore, we found that PWR is important for HDA9 nuclear accumulation. This study reveals an uncharacterized epigenetic complex involved in leaf senescence and provides mechanistic insights into how a histone deacetylase along with a chromatin-binding protein contribute to a robust regulatory network to modulate the onset of plant aging.
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Affiliation(s)
- Xiangsong Chen
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States
- Wisconsin Institutes for Discovery, University of Wisconsin-Madison, Madison, United States
| | - Li Lu
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States
- Wisconsin Institutes for Discovery, University of Wisconsin-Madison, Madison, United States
| | - Kevin S Mayer
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States
- Wisconsin Institutes for Discovery, University of Wisconsin-Madison, Madison, United States
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin-Madison, Madison, United States
| | - Shuiming Qian
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States
- Wisconsin Institutes for Discovery, University of Wisconsin-Madison, Madison, United States
| | - Aaron Lomax
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, United States
| | - Xuehua Zhong
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States
- Wisconsin Institutes for Discovery, University of Wisconsin-Madison, Madison, United States
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43
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Abstract
Diverse environmental stimuli largely affect the ionic balance of soil, which have a direct effect on growth and crop yield. Details are fast emerging on the genetic/molecular regulators, at whole-genome levels, of plant responses to mineral deficiencies in model and crop plants. These genetic regulators determine the root architecture and physiological adaptations for better uptake and utilization of minerals from soil. Recent evidence also shows the potential roles of epigenetic mechanisms in gene regulation, driven by minerals imbalance. Mineral deficiency or sufficiency leads to developmental plasticity in plants for adaptation, which is preceded by a change in the pattern of gene expression. Notably, such changes at molecular levels are also influenced by altered chromatin structure and methylation patterns, or involvement of other epigenetic components. Interestingly, many of the changes induced by mineral deficiency are also inheritable in the form of epigenetic memory. Unravelling these mechanisms in response to mineral deficiency would further advance our understanding of this complex plant response. Further studies on such approaches may serve as an exciting interaction model of epigenetic and genetic regulations of mineral homeostasis in plants and designing strategies for crop improvement.
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44
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Histone deacetylase HDA6 enhances brassinosteroid signaling by inhibiting the BIN2 kinase. Proc Natl Acad Sci U S A 2016; 113:10418-23. [PMID: 27562168 DOI: 10.1073/pnas.1521363113] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Glycogen synthase kinase 3 (GSK3)-like kinases play important roles in brassinosteroid (BR), abscisic acid, and auxin signaling to regulate many aspects of plant development and stress responses. The Arabidopsis thaliana GSK3-like kinase BR-INSENSITIVE 2 (BIN2) acts as a key negative regulator in the BR signaling pathway, but the mechanisms regulating BIN2 function remain unclear. Here we report that the histone deacetylase HDA6 can interact with and deacetylate BIN2 to repress its kinase activity. The hda6 mutant showed a BR-repressed phenotype in the dark and was less sensitive to BR biosynthesis inhibitors. Genetic analysis indicated that HDA6 regulates BR signaling through BIN2. Furthermore, we identified K189 of BIN2 as an acetylated site, which can be deacetylated by HDA6 to influence BIN2 activity. Glucose can affect the acetylation level of BIN2 in plants, indicating a connection to cellular energy status. These findings provide significant insights into the regulation of GSK3-like kinases in plant growth and development.
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45
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Chhun T, Chong SY, Park BS, Wong ECC, Yin JL, Kim M, Chua NH. HSI2 Repressor Recruits MED13 and HDA6 to Down-Regulate Seed Maturation Gene Expression Directly During Arabidopsis Early Seedling Growth. PLANT & CELL PHYSIOLOGY 2016; 57:1689-706. [PMID: 27335347 DOI: 10.1093/pcp/pcw095] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 05/01/2016] [Indexed: 05/25/2023]
Abstract
Arabidopsis HSI2 (HIGH-LEVEL EXPRESSION OF SUGAR-INDUCIBLE GENE 2) which carries a EAR (ERF-associated amphiphilic repression) motif acts as a repressor of seed maturation genes and lipid biosynthesis, whereas MEDIATOR (MED) is a conserved multiprotein complex linking DNA-bound transcription factors to RNA polymerase II transcription machinery. How HSI2 executes its repressive function through MED is hitherto unknown. Here, we show that HSI2 and its homolog, HSI2-lik (HSL1), are able to form homo- and heterocomplexes. Both factors bind to the TRAP240 domain of MED13, a subunit of the MED CDK8 module. Mutant alleles of the med13 mutant show elevated seed maturation gene expression and increased lipid accumulation in cotyledons; in contrast, HSI2- or MED13-overexpressing plants display the opposite phenotypes. The overexpression phenotypes of HSI2 and MED13 are abolished in med13 and hsi2 hsl1, respectively, indicating that HSI2 and MED13 together are required for these functions. The HSI2 C-terminal region interacts with HDA6, whose overexpression also reduces seed maturation gene expression and lipid accumulation. Moreover, HSI2, MED13 and HDA6 bind to the proximal promoter and 5'-coding regions of seed maturation genes. Taken together, our results suggest that HSI2 recruits MED13 and HDA6 to suppress directly a subset of seed maturation genes post-germination.
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Affiliation(s)
- Tory Chhun
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Suet Yen Chong
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Bong Soo Park
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Eriko Chi Cheng Wong
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Jun-Lin Yin
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Mijung Kim
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Nam-Hai Chua
- Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065-6399, USA
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46
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Lee WK, Cho MH. Telomere-binding protein regulates the chromosome ends through the interaction with histone deacetylases in Arabidopsis thaliana. Nucleic Acids Res 2016; 44:4610-24. [PMID: 26857545 PMCID: PMC4889915 DOI: 10.1093/nar/gkw067] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 01/20/2016] [Accepted: 01/28/2016] [Indexed: 01/13/2023] Open
Abstract
Telomeres are nucleoprotein complexes at the end of eukaryotic chromosomes. Many telomere-binding proteins bind to telomeric repeat sequences and further generate T-loops in animals. However, it is not clear if they regulate telomere organization using epigenetic mechanisms and how the epigenetic molecules are involved in regulating the telomeres. Here, we show direct interactions between the telomere-binding protein, AtTRB2 and histone deacetylases, HDT4 and HDA6, in vitro and in vivo AtTRB2 mediates the associations of HDT4 and HDA6 with telomeric repeats. Telomere elongation is found in AtTRB2, HDT4 and HDA6 mutants over generations, but also in met1 and cmt3 DNA methyltransferases mutants. We also characterized HDT4 as an Arabidopsis H3K27 histone deacetylase. HDT4 binds to acetylated peptides at residue K27 of histone H3 in vitro, and deacetylates this residue in vivo Our results suggest that AtTRB2 also has a role in the regulation of telomeric chromatin as a possible scaffold protein for recruiting the epigenetic regulators in Arabidopsis, in addition to its telomere binding and length regulation activity. Our data provide evidences that epigenetic molecules associate with telomeres by direct physical interaction with telomere-binding proteins and further regulate homeostasis of telomeres in Arabidopsis thaliana.
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Affiliation(s)
- Won Kyung Lee
- Department of Systems Biology, Yonsei University, Seoul 03722, Republic of Korea
| | - Myeon Haeng Cho
- Department of Systems Biology, Yonsei University, Seoul 03722, Republic of Korea
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47
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Zhang J, Xie S, Cheng J, Lai J, Zhu JK, Gong Z. The Second Subunit of DNA Polymerase Delta Is Required for Genomic Stability and Epigenetic Regulation. PLANT PHYSIOLOGY 2016; 171:1192-208. [PMID: 27208288 PMCID: PMC4902588 DOI: 10.1104/pp.15.01976] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 04/24/2016] [Indexed: 05/08/2023]
Abstract
DNA polymerase δ plays crucial roles in DNA repair and replication as well as maintaining genomic stability. However, the function of POLD2, the second small subunit of DNA polymerase δ, has not been characterized yet in Arabidopsis (Arabidopsis thaliana). During a genetic screen for release of transcriptional gene silencing, we identified a mutation in POLD2. Whole-genome bisulfite sequencing indicated that POLD2 is not involved in the regulation of DNA methylation. POLD2 genetically interacts with Ataxia Telangiectasia-mutated and Rad3-related and DNA polymerase α The pold2-1 mutant exhibits genomic instability with a high frequency of homologous recombination. It also exhibits hypersensitivity to DNA-damaging reagents and short telomere length. Whole-genome chromatin immunoprecipitation sequencing and RNA sequencing analyses suggest that pold2-1 changes H3K27me3 and H3K4me3 modifications, and these changes are correlated with the gene expression levels. Our study suggests that POLD2 is required for maintaining genome integrity and properly establishing the epigenetic markers during DNA replication to modulate gene expression.
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Affiliation(s)
- Jixiang Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China (J.Z., J.C., Z.G.);Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (S.X., J.-K.Z.);Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47906 (S.X., J.-K.Z.); andState Key Laboratory of Agrobiotechnology, China National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China (J.L.)
| | - Shaojun Xie
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China (J.Z., J.C., Z.G.);Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (S.X., J.-K.Z.);Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47906 (S.X., J.-K.Z.); andState Key Laboratory of Agrobiotechnology, China National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China (J.L.)
| | - Jinkui Cheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China (J.Z., J.C., Z.G.);Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (S.X., J.-K.Z.);Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47906 (S.X., J.-K.Z.); andState Key Laboratory of Agrobiotechnology, China National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China (J.L.)
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China (J.Z., J.C., Z.G.);Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (S.X., J.-K.Z.);Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47906 (S.X., J.-K.Z.); andState Key Laboratory of Agrobiotechnology, China National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China (J.L.)
| | - Jian-Kang Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China (J.Z., J.C., Z.G.);Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (S.X., J.-K.Z.);Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47906 (S.X., J.-K.Z.); andState Key Laboratory of Agrobiotechnology, China National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China (J.L.)
| | - Zhizhong Gong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China (J.Z., J.C., Z.G.);Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (S.X., J.-K.Z.);Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47906 (S.X., J.-K.Z.); andState Key Laboratory of Agrobiotechnology, China National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China (J.L.)
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48
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Zhang S, Zhan X, Xu X, Cui P, Zhu JK, Xia Y, Xiong L. Two domain-disrupted hda6 alleles have opposite epigenetic effects on transgenes and some endogenous targets. Sci Rep 2015; 5:17832. [PMID: 26666962 PMCID: PMC4678874 DOI: 10.1038/srep17832] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 11/06/2015] [Indexed: 12/22/2022] Open
Abstract
HDA6 is a RPD3-like histone deacetylase. In Arabidopsis, it mediates transgene and some endogenous target transcriptional gene silencing (TGS) via histone deacetylation and DNA methylation. Here, we characterized two hda6 mutant alleles that were recovered as second-site suppressors of the DNA demethylation mutant ros1-1. Although both alleles derepressed 35S::NPTII and RD29A::LUC in the ros1-1 background, they had distinct effects on the expression of these two transgenes. In accordance to expression profiles of two transgenes, the alleles have distinct opposite methylation profiles on two reporter gene promoters. Furthermore, both alleles could interact in vitro and in vivo with the DNA methyltransferase1 with differential interactive strength and patterns. Although these alleles accumulated different levels of repressive/active histone marks, DNA methylation but not histone modifications in the two transgene promoters was found to correlate with the level of derepression of the reporter genes between the two had6 alleles. Our study reveals that mutations in different domains of HDA6 convey different epigenetic status that in turn controls the expression of the transgenes as well as some endogenous loci.
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Affiliation(s)
- Shoudong Zhang
- Department of Biology, Hong Kong Baptist University, Hong Kong, Hong Kong SAR, China.,Division of Biological and Environmental Sciences &Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Xiangqiang Zhan
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoming Xu
- College of life sciences, Nanjing Agricultural University, Nanjing, China
| | - Peng Cui
- Division of Biological and Environmental Sciences &Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China.,Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
| | - Yiji Xia
- Department of Biology, Hong Kong Baptist University, Hong Kong, Hong Kong SAR, China
| | - Liming Xiong
- Division of Biological and Environmental Sciences &Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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49
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Venturelli S, Belz RG, Kämper A, Berger A, von Horn K, Wegner A, Böcker A, Zabulon G, Langenecker T, Kohlbacher O, Barneche F, Weigel D, Lauer UM, Bitzer M, Becker C. Plants Release Precursors of Histone Deacetylase Inhibitors to Suppress Growth of Competitors. THE PLANT CELL 2015; 27:3175-89. [PMID: 26530086 PMCID: PMC4682303 DOI: 10.1105/tpc.15.00585] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 09/21/2015] [Accepted: 10/15/2015] [Indexed: 05/22/2023]
Abstract
To secure their access to water, light, and nutrients, many plant species have developed allelopathic strategies to suppress competitors. To this end, they release into the rhizosphere phytotoxic substances that inhibit the germination and growth of neighbors. Despite the importance of allelopathy in shaping natural plant communities and for agricultural production, the underlying molecular mechanisms are largely unknown. Here, we report that allelochemicals derived from the common class of cyclic hydroxamic acid root exudates directly affect the chromatin-modifying machinery in Arabidopsis thaliana. These allelochemicals inhibit histone deacetylases both in vitro and in vivo and exert their activity through locus-specific alterations of histone acetylation and associated gene expression. Our multilevel analysis collectively shows how plant-plant interactions interfere with a fundamental cellular process, histone acetylation, by targeting an evolutionarily highly conserved class of enzymes.
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Affiliation(s)
- Sascha Venturelli
- Department of Internal Medicine I, Medical University Clinic, University of Tübingen, 72076 Tübingen, Germany
| | - Regina G Belz
- Agroecology Unit, University of Hohenheim, Institute of Plant Production and Agroecology in the Tropics and Subtropics, 70593 Stuttgart, Germany
| | - Andreas Kämper
- Applied Bioinformatics, University of Tübingen, 72076 Tübingen, Germany
| | - Alexander Berger
- Department of Internal Medicine I, Medical University Clinic, University of Tübingen, 72076 Tübingen, Germany
| | - Kyra von Horn
- Department of Internal Medicine I, Medical University Clinic, University of Tübingen, 72076 Tübingen, Germany
| | - André Wegner
- Applied Bioinformatics, University of Tübingen, 72076 Tübingen, Germany
| | | | - Gérald Zabulon
- Ecology and Evolutionary Biology Section, Institut de Biologie de l'Ecole Normale Supérieure, Ecole Normale Supérieure, Inserm U1024, CNRS UMR 8197, 75005 Paris, France
| | - Tobias Langenecker
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Oliver Kohlbacher
- Applied Bioinformatics, University of Tübingen, 72076 Tübingen, Germany
| | - Fredy Barneche
- Ecology and Evolutionary Biology Section, Institut de Biologie de l'Ecole Normale Supérieure, Ecole Normale Supérieure, Inserm U1024, CNRS UMR 8197, 75005 Paris, France
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Ulrich M Lauer
- Department of Internal Medicine I, Medical University Clinic, University of Tübingen, 72076 Tübingen, Germany
| | - Michael Bitzer
- Department of Internal Medicine I, Medical University Clinic, University of Tübingen, 72076 Tübingen, Germany
| | - Claude Becker
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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50
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Hristova E, Fal K, Klemme L, Windels D, Bucher E. HISTONE DEACETYLASE6 Controls Gene Expression Patterning and DNA Methylation-Independent Euchromatic Silencing. PLANT PHYSIOLOGY 2015; 168:1298-308. [PMID: 25918117 PMCID: PMC4528735 DOI: 10.1104/pp.15.00177] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 04/23/2015] [Indexed: 05/24/2023]
Abstract
To investigate the role of chromatin regulators in patterning gene expression, we employed a unique epigenetically controlled and highly tissue-specific green fluorescent protein reporter line in Arabidopsis (Arabidopsis thaliana). Using a combination of forward and reverse genetic approaches on this line, we show here that distinct epigenetic regulators are involved in silencing the transgene in different tissues. The forward genetic screen led to the identification of a novel HISTONE DEACETYLASE6 (HDA6) mutant allele (epigenetic control1, hda6-8). This allele differs from the previously reported alleles, as it did not affect DNA methylation and only had a very modest effect on the release of transposable elements and other heterochromatic transcripts. Overall, our data shows that HDA6 has at least two clearly separable activities in different genomic regions. In addition, we present an unexpected role for HDA6 in the control of DNA methylation at CG dinucleotides.
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Affiliation(s)
- Emilija Hristova
- Botanical Institute, Zürich-Basel Plant Science Center, University of Basel, CH-4056 Basel, Switzerland (E.H., K.F., L.K., E.B.); andUniversité d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, 49071 Beaucouzé, France (D.W., E.B.)
| | - Kateryna Fal
- Botanical Institute, Zürich-Basel Plant Science Center, University of Basel, CH-4056 Basel, Switzerland (E.H., K.F., L.K., E.B.); andUniversité d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, 49071 Beaucouzé, France (D.W., E.B.)
| | - Laurin Klemme
- Botanical Institute, Zürich-Basel Plant Science Center, University of Basel, CH-4056 Basel, Switzerland (E.H., K.F., L.K., E.B.); andUniversité d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, 49071 Beaucouzé, France (D.W., E.B.)
| | - David Windels
- Botanical Institute, Zürich-Basel Plant Science Center, University of Basel, CH-4056 Basel, Switzerland (E.H., K.F., L.K., E.B.); andUniversité d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, 49071 Beaucouzé, France (D.W., E.B.)
| | - Etienne Bucher
- Botanical Institute, Zürich-Basel Plant Science Center, University of Basel, CH-4056 Basel, Switzerland (E.H., K.F., L.K., E.B.); andUniversité d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, 49071 Beaucouzé, France (D.W., E.B.)
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