1
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Nguyen NH, Sng BJR, Chin HJ, Choi IKY, Yeo HC, Jang IC. HISTONE DEACETYLASE 9 promotes hypocotyl-specific auxin response under shade. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:804-822. [PMID: 37522556 DOI: 10.1111/tpj.16410] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 08/01/2023]
Abstract
Vegetative shade causes an array of morphological changes in plants called shade avoidance syndrome, which includes hypocotyl and petiole elongation, leaf hyponasty, reduced leaf growth, early flowering and rapid senescence. Here, we show that loss-of-function mutations in HISTONE DEACETYLASE 9 (HDA9) attenuated the shade-induced hypocotyl elongation in Arabidopsis. However, the hda9 cotyledons and petioles under shade were not significantly different from those in wild-type, suggesting a specific function of HDA9 in hypocotyl elongation in response to shade. HDA9 expression levels were stable under shade and its protein was ubiquitously detected in cotyledon, hypocotyl and root. Organ-specific transcriptome analysis unraveled that shade induced a set of auxin-responsive genes, such as SMALL AUXIN UPREGULATED RNAs (SAURs) and AUXIN/INDOLE-3-ACETIC ACIDs (AUX/IAAs) and their induction was impaired in hda9-1 hypocotyls. In addition, HDA9 binding to loci of SAUR15/65, IAA5/6/19 and ACS4 was increased under shade. The genetic and organ-specific gene expression analyses further revealed that HDA9 may cooperate with PHYTOCHROME-INTERACTING FACTOR 4/7 in the regulation of shade-induced hypocotyl elongation. Furthermore, HDA9 and PIF7 proteins were found to interact together and thus it is suggested that PIF7 may recruit HDA9 to regulate the shade/auxin responsive genes in response to shade. Overall, our study unravels that HDA9 can work as one component of a hypocotyl-specific transcriptional regulatory machinery that activates the auxin response at the hypocotyl leading to the elongation of this organ under shade.
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Affiliation(s)
- Nguyen Hoai Nguyen
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
| | - Benny Jian Rong Sng
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Hui Jun Chin
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
| | - Ian Kin Yuen Choi
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Hock Chuan Yeo
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
| | - In-Cheol Jang
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
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2
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Bai J, Shi Z, Zheng S. The Role of Histone Modifications in Heat Signal Transduction in Plants. Adv Biol (Weinh) 2023; 7:e2200323. [PMID: 36866515 DOI: 10.1002/adbi.202200323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/27/2023] [Indexed: 03/04/2023]
Abstract
Global warming and the more frequent occurrence of extremly high temperatures seriously affect crop yields. Heat stress (HS) has become a major environmental factor threatening food security worldwide. Understanding how plants sense and respond to HS is of clear interest to plant scientists and crop breeders. However, it is not trivial to elucidate the underlying signaling cascade, as specific cellular responses (ranging from detrimental to systemic effects) must be disentangled. Plants respond and adapt to high temperatures in many ways. In this review, recent progress in understanding heat signal transduction and the role of histone modifications in regulating the expression of genes involved in HS responses are discussed. The outstanding issues that are crucial for understanding the interactions between plants and HS are also discussed. The study of heat signal transduction mechanisms in plants is essential to facilitate the cultivation of heat-resistant crop varieties.
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Affiliation(s)
- Jiaoteng Bai
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Zeyu Shi
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Shuzhi Zheng
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
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3
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Zhao H, Ge Z, Zhou M, Zeng H, Wei Y, Liu G, Yan Y, Reiter RJ, He C, Shi H. Histone deacetylase 9 regulates disease resistance through fine-tuning histone deacetylation of melatonin biosynthetic genes and melatonin accumulation in cassava. J Pineal Res 2023; 74:e12861. [PMID: 36750349 DOI: 10.1111/jpi.12861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/05/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023]
Abstract
Melatonin participates in plant growth and development and biotic and abiotic stress responses. Histone acetylation regulates many plant biological processes via transcriptional reprogramming. However, the direct relationship between melatonin and histone acetylation in plant disease resistance remains unclear. In this study, we identified cassava bacterial blight (CBB) responsive histone deacetylase 9 (HDA9), which negatively regulated disease resistance to CBB by reducing melatonin content. In addition, exogenous melatonin alleviated disease sensitivity of MeHDA9 overexpressed plants to CBB. Importantly, MeHDA9 inhibited the expression of melatonin biosynthetic genes through decreasing lysine 5 of histone 4 (H4K5) acetylation at the promoter regions of melatonin biosynthetic genes, thereby modulating melatonin accumulation in cassava. Furthermore, protein phosphatase 2C 12 (MePP2C12) interacted with MeHDA9 in vivo and in vitro, and it was involved in MeHDA9-mediated disease resistance via melatonin biosynthetic pathway. In summary, this study highlights the direct interaction between histone deacetylation and melatonin biosynthetic genes in cassava disease resistance via histone deacetylation, providing new insights into the genetic improvement of disease resistance via epigenetic regulation of melatonin level in tropical crops.
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Affiliation(s)
- Huiping Zhao
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Sanya Nanfan Research Institute-College of Tropical Crops, Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Sanya and Haikou, Hainan Province, China
| | - Zhongyuan Ge
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Sanya Nanfan Research Institute-College of Tropical Crops, Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Sanya and Haikou, Hainan Province, China
| | - Mengmeng Zhou
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Sanya Nanfan Research Institute-College of Tropical Crops, Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Sanya and Haikou, Hainan Province, China
| | - Hongqiu Zeng
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Sanya Nanfan Research Institute-College of Tropical Crops, Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Sanya and Haikou, Hainan Province, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan Province, China
| | - Yunxie Wei
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Sanya Nanfan Research Institute-College of Tropical Crops, Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Sanya and Haikou, Hainan Province, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan Province, China
| | - Guoyin Liu
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Sanya Nanfan Research Institute-College of Tropical Crops, Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Sanya and Haikou, Hainan Province, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan Province, China
| | - Yu Yan
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Sanya Nanfan Research Institute-College of Tropical Crops, Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Sanya and Haikou, Hainan Province, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan Province, China
| | - Russel J Reiter
- Department of Cellular and Structural Biology, UT Health San Antonio, Long School of Medicine, San Antonio, Texas, USA
| | - Chaozu He
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Sanya Nanfan Research Institute-College of Tropical Crops, Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Sanya and Haikou, Hainan Province, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan Province, China
| | - Haitao Shi
- Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, Sanya Nanfan Research Institute-College of Tropical Crops, Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Sanya and Haikou, Hainan Province, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan Province, China
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4
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Huang LJ, Wang Y, Lin Z, Jiang D, Luo Y, Li N. The role of corepressor HOS15-mediated epigenetic regulation of flowering. FRONTIERS IN PLANT SCIENCE 2023; 13:1101912. [PMID: 36704168 PMCID: PMC9871556 DOI: 10.3389/fpls.2022.1101912] [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: 11/18/2022] [Accepted: 12/21/2022] [Indexed: 06/18/2023]
Abstract
Regulation of gene expression underpins gene function and is essential for regulation of physiological roles. Epigenetic modifications regulate gene transcription by physically facilitating relaxation or condensation of target loci in chromatin. Transcriptional corepressors are involved in chromatin remodeling and regulate gene expression by establishing repressive complexes. Genetic and biochemical studies reveal that a member of the Groucho/Thymidine uptake 1 (Gro/Tup1) corepressor family, HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE 15 (HOS15), is recruited via the evening complex (EC) to the GIGANTEA (GI) promoter to repress gene expression, and modulating flowering time. Therefore, HOS15 connects photoperiodic pathway and epigenetic mechanism to control flowering time in plants. In addition, growing body of evidence support a diverse roles of the epigenetic regulator HOS15 in fine-tuning plant development and growth by integrating intrinsic genetic components and various environmental signals.
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Affiliation(s)
- Li-Jun Huang
- State Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Yukun Wang
- State Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Zeng Lin
- State Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Dong Jiang
- State Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Yong Luo
- School of Chemistry and Environmental Science, Xiangnan University, Chenzhou, China
| | - Ning Li
- State Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, College of Forestry, Central South University of Forestry and Technology, Changsha, China
- Key Laboratory of Forest Bio-resources and Integrated Pest Management for Higher Education in Hunan Province, Central South University of Forestry and Technology, Changsha, China
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5
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Lim CJ, Park KS, Ali A, Park J, Ryou SM, Shen M, Khan HA, Bader ZE, Zareen S, Bae MJ, Choi JH, Xu ZY, Pardo JM, Yun DJ. Negative regulation of floral transition in Arabidopsis by HOS15-PWR-HDA9 complex. FRONTIERS IN PLANT SCIENCE 2023; 13:1105988. [PMID: 36684790 PMCID: PMC9853073 DOI: 10.3389/fpls.2022.1105988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Arabidopsis HOS15/PWR/HDA9 repressor complex, which is similar to the TBL1/NcoR1/HDAC complex in animals, plays a well-known role in epigenetic regulation. PWR and HDA9 have been reported to interact with each other and modulate the flowering time by repressing AGL19 expression, whereas HOS15 and HDA9, together with the photoperiodic evening complex, regulate flowering time through repression of GI transcription. However, the role of the HOS15/PWR/HDA9 core repressor complex as a functional unit in the regulation of flowering time is yet to be explored. In this study, we reported that the loss-of-function hos15-2/pwr/hda9 triple mutant accumulates higher transcript levels of AGL19 and exhibits an early flowering phenotype similar to those of hos15, pwr, and hda9 single mutants. Interestingly, the accumulation of HOS15 in the nucleus was drastically reduced in pwr and hda9 mutants. As a result, HOS15 could not perform its role in histone deacetylation or interaction with H3 in the nucleus. Furthermore, HOS15 is also associated with the same region of the AGL19 promoter known for PWR-HDA9 binding. The acetylation level of the AGL19 promoter was increased in the hos15-2 mutant, similar to the pwr and hda9 mutants. Therefore, our findings reveal that the HOS15/PWR/HDA9 repressor complex deacetylates the promoter region of AGL19, thereby negatively regulating AGL19 transcription, which leads to early flowering in Arabidopsis.
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Affiliation(s)
- Chae Jin Lim
- Institute of Global Disease Control, Konkuk University, Seoul, Republic of Korea
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Ki Suk Park
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Akhtar Ali
- Institute of Global Disease Control, Konkuk University, Seoul, Republic of Korea
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Junghoon Park
- Institute of Global Disease Control, Konkuk University, Seoul, Republic of Korea
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Seung Min Ryou
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Mingzhe Shen
- Department of Agronomy, Agricultural College, Yanbian University, Yanji, China
| | - Haris Ali Khan
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Zein Eddin Bader
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Shah Zareen
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Min Jae Bae
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Jong Hyoo Choi
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Jose M. Pardo
- Institute of Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones 17 Cientificas and Universidad de Sevilla, Seville, Spain
| | - Dae-Jin Yun
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
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6
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Abstract
Heat stress limits plant growth, development, and crop yield, but how plant cells precisely sense and transduce heat stress signals remains elusive. Here, we identified a conserved heat stress response mechanism to elucidate how heat stress signal is transmitted from the cytoplasm into the nucleus for epigenetic modifiers. We demonstrate that HISTONE DEACETYLASE 9 (HDA9) transduces heat signals from the cytoplasm to the nucleus to play a positive regulatory role in heat responses in Arabidopsis. Heat specifically induces HDA9 accumulation in the nucleus. Under heat stress, the phosphatase PP2AB'β directly interacts with and dephosphorylates HDA9 to protect HDA9 from 26S proteasome-mediated degradation, leading to the translocation of nonphosphorylated HDA9 to the nucleus. This heat-induced enrichment of HDA9 in the nucleus depends on the nucleoporin HOS1. In the nucleus, HDA9 binds and deacetylates the target genes related to signaling transduction and plant development to repress gene expression in a transcription factor YIN YANG 1-dependent and -independent manner, resulting in rebalance of plant development and heat response. Therefore, we uncover an HDA9-mediated positive regulatory module in the heat shock signal transduction pathway. More important, this cytoplasm-to-nucleus translocation of HDA9 in response to heat stress is conserved in wheat and rice, which confers the mechanism significant implication potential for crop breeding to cope with global climate warming.
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7
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Lee HG, Jeong YY, Lee H, Seo PJ. Arabidopsis HISTONE DEACETYLASE 9 Stimulates Hypocotyl Cell Elongation by Repressing GIGANTEA Expression Under Short Day Photoperiod. FRONTIERS IN PLANT SCIENCE 2022; 13:950378. [PMID: 35923878 PMCID: PMC9341324 DOI: 10.3389/fpls.2022.950378] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Developmental plasticity contributes to plant adaptation and fitness in a given condition. Hypocotyl elongation is under the tight control of complex genetic networks encompassing light, circadian, and photoperiod signaling. In this study, we demonstrate that HISTONE DEACETYLASE 9 (HDA9) mediates day length-dependent hypocotyl cell elongation. HDA9 binds to the GIGANTEA (GI) locus involved in photoperiodic hypocotyl elongation. The short day (SD)-accumulated HDA9 protein promotes histone H3 deacetylation at the GI locus during the dark period, promoting hypocotyl elongation. Consistently, HDA9-deficient mutants display reduced hypocotyl length, along with an increase in GI gene expression, only under SD conditions. Taken together, our study reveals the genetic basis of day length-dependent cell elongation in plants.
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Affiliation(s)
- Hong Gil Lee
- Department of Chemistry, Seoul National University, Seoul, South Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
| | - Yeong Yeop Jeong
- Research Institute of Basic Sciences, Seoul National University, Seoul, South Korea
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Hongwoo Lee
- 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
- Research Institute of Basic Sciences, Seoul National University, Seoul, South Korea
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
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8
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Chu L, Yang C, Zhuang F, Gao Y, Luo M. The HDA9‐HY5 module epigenetically regulates flowering time in
Arabidopsis thaliana. J Cell Physiol 2022; 237:2961-2968. [DOI: 10.1002/jcp.30761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 04/02/2022] [Accepted: 04/06/2022] [Indexed: 01/20/2023]
Affiliation(s)
- Liutian Chu
- Guangdong Provincial Key Laboratory of Applied Botany & Agriculture and Biotechnology Research Center South China Botanical Garden, Chinese Academy of Sciences Guangzhou China
- University of Chinese Academy of Sciences Beijing China
| | - Chao Yang
- Guangdong Provincial Key Laboratory of Applied Botany & Agriculture and Biotechnology Research Center South China Botanical Garden, Chinese Academy of Sciences Guangzhou China
| | - Feng Zhuang
- Guangdong Provincial Key Laboratory of Applied Botany & Agriculture and Biotechnology Research Center South China Botanical Garden, Chinese Academy of Sciences Guangzhou China
- University of Chinese Academy of Sciences Beijing China
| | - Yingmiao Gao
- Guangdong Provincial Key Laboratory of Applied Botany & Agriculture and Biotechnology Research Center South China Botanical Garden, Chinese Academy of Sciences Guangzhou China
- University of Chinese Academy of Sciences Beijing China
| | - Ming Luo
- Guangdong Provincial Key Laboratory of Applied Botany & Agriculture and Biotechnology Research Center South China Botanical Garden, Chinese Academy of Sciences Guangzhou China
- University of Chinese Academy of Sciences Beijing China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences Guangzhou China
- Guangdong Provincial Key Laboratory of Digital Botanical Garden and Popular Science Guangzhou China
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9
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Sureshkumar S, Balasubramanian S. Complexes and complexities: INO80 takes center stage. MOLECULAR PLANT 2021; 14:1776-1778. [PMID: 34418552 DOI: 10.1016/j.molp.2021.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 08/09/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
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10
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Lim CJ, Ali A, Park J, Shen M, Park KS, Baek D, Yun DJ. HOS15-PWR chromatin remodeling complex positively regulates cold stress in Arabidopsis. PLANT SIGNALING & BEHAVIOR 2021; 16:1893978. [PMID: 33641608 PMCID: PMC8078502 DOI: 10.1080/15592324.2021.1893978] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/18/2021] [Accepted: 02/18/2021] [Indexed: 06/12/2023]
Abstract
Cold stress is a major environmental constraint that restrains plant growth and productivity. To cope with cold stress, plants must be able to perceive a cold signal and regulate the expression of cold-regulated (COR) genes. In our recent study, we showed that Arabidopsis HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE 15 (HOS15) acts as a substrate receptor for CULLIN4-based ubiquitin E3 ligase complex to promote cold-induced histone deacetylase 2 C (HD2C) degradation that allows the activation of COR genes. Additionally, we found that POWERDRESS (PWR), a HOS15-interacting protein, is required for the association of HOS15 with COR gene chromatin and HD2C degradation. The HOS15/PWR complex interacts with and recruits CBF transcription factors to the promoters of COR genes. Collectively, our previous findings suggest that HOS15 and PWR function as positive regulators for the expression of COR genes, and promote cold tolerance. Accordingly, we herein discuss the role of PWR in cold tolerance.
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Affiliation(s)
- Chae Jin Lim
- Institute of Glocal Disease Control, Konkuk University, Seoul, Republic of Korea
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Akhtar Ali
- Institute of Glocal Disease Control, Konkuk University, Seoul, Republic of Korea
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Junghoon Park
- Institute of Glocal Disease Control, Konkuk University, Seoul, Republic of Korea
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Mingzhe Shen
- Division of Applied Life Science (Bk21plus), Plant Molecular Biology and Biotechnology Research Center, Research Institute of Life Sciences, Gyeongsang National University, Jinju, Republic of Korea
| | - Ki Suk Park
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Dongwon Baek
- Division of Applied Life Science (Bk21plus), Plant Molecular Biology and Biotechnology Research Center, Research Institute of Life Sciences, Gyeongsang National University, Jinju, Republic of Korea
| | - Dea-Jin Yun
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
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11
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HOS15 is a transcriptional corepressor of NPR1-mediated gene activation of plant immunity. Proc Natl Acad Sci U S A 2020; 117:30805-30815. [PMID: 33199617 PMCID: PMC7720166 DOI: 10.1073/pnas.2016049117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Immune responses protect organisms against biotic challenges but can also produce deleterious effects, such as inflammation and necrosis. This growth-defense trade-off necessitates fine control of immune responses, including the activation of defense gene expression. The transcriptional coactivator NPR1 is a key regulatory hub of immune activation in plant cells. Surprisingly, full activation of NPR1-activated defense genes requires proteasome-mediated degradation of NPR1 induced by a CUL3-based E3 ubiquitin ligase complex. Our work demonstrates that HOS15 is the specificity determinant of a CUL1-based E3 ubiquitin ligase complex that limits defense gene expression by targeting NPR1 for proteasome-mediated degradation. Thus, distinct ubiquitin-based degradation pathways coordinately modulate the timing and amplitude of transcriptional outputs during plant defense. Transcriptional regulation is a complex and pivotal process in living cells. HOS15 is a transcriptional corepressor. Although transcriptional repressors generally have been associated with inactive genes, increasing evidence indicates that, through poorly understood mechanisms, transcriptional corepressors also associate with actively transcribed genes. Here, we show that HOS15 is the substrate receptor for an SCF/CUL1 E3 ubiquitin ligase complex (SCFHOS15) that negatively regulates plant immunity by destabilizing transcriptional activation complexes containing NPR1 and associated transcriptional activators. In unchallenged conditions, HOS15 continuously eliminates NPR1 to prevent inappropriate defense gene expression. Upon defense activation, HOS15 preferentially associates with phosphorylated NPR1 to stimulate rapid degradation of transcriptionally active NPR1 and thus limit the extent of defense gene expression. Our findings indicate that HOS15-mediated ubiquitination and elimination of NPR1 produce effects contrary to those of CUL3-containing ubiquitin ligase that coactivate defense gene expression. Thus, HOS15 plays a key role in the dynamic regulation of pre- and postactivation host defense.
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12
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de Rooij PGH, Perrella G, Kaiserli E, van Zanten M. The diverse and unanticipated roles of histone deacetylase 9 in coordinating plant development and environmental acclimation. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:6211-6225. [PMID: 32687569 PMCID: PMC7586748 DOI: 10.1093/jxb/eraa335] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 07/15/2020] [Indexed: 05/04/2023]
Abstract
Plants tightly control gene transcription to adapt to environmental conditions and steer growth and development. Different types of epigenetic modifications are instrumental in these processes. In recent years, an important role for the chromatin-modifying RPD3/HDA1 class I HDAC HISTONE DEACETYLASE 9 (HDA9) emerged in the regulation of a multitude of plant traits and responses. HDACs are widely considered transcriptional repressors and are typically part of multiprotein complexes containing co-repressors, DNA, and histone-binding proteins. By catalyzing the removal of acetyl groups from lysine residues of histone protein tails, HDA9 negatively controls gene expression in many cases, in concert with interacting proteins such as POWERDRESS (PWR), HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES 15 (HOS15), WRKY53, ELONGATED HYPOCOTYL 5 (HY5), ABA INSENSITIVE 4 (ABI4), and EARLY FLOWERING 3 (ELF3). However, HDA9 activity has also been directly linked to transcriptional activation. In addition, following the recent breakthrough discovery of mutual negative feedback regulation between HDA9 and its interacting WRKY-domain transcription factor WRKY53, swift progress in gaining understanding of the biology of HDA9 is expected. In this review, we summarize knowledge on this intriguing versatile-and long under-rated-protein and propose novel leads to further unravel HDA9-governed molecular networks underlying plant development and environmental biology.
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Affiliation(s)
- Peter G H de Rooij
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, Padualaan, CH Utrecht, The Netherlands
| | - Giorgio Perrella
- Institute of Molecular, Cell & Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- ENEA - Trisaia Research Centre 75026, Rotondella (Matera), Italy
| | - Eirini Kaiserli
- Institute of Molecular, Cell & Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Martijn van Zanten
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, Padualaan, CH Utrecht, The Netherlands
- Correspondence:
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Ali A, Yun DJ. Chromatin remodeling complex HDA9-PWR-ABI4 epigenetically regulates drought stress response in plants. PLANT SIGNALING & BEHAVIOR 2020; 15:1803568. [PMID: 32752926 PMCID: PMC8550530 DOI: 10.1080/15592324.2020.1803568] [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] [Indexed: 05/03/2023]
Abstract
Among all the major environmental challenges, drought stress causes considerable damage to plant growth and agricultural productivity. Drought stress directly promotes the accumulation of abscisic acid (ABA) via the activation of genes that encode enzymes involved in ABA biosynthesis, which protect the plant against water-limiting conditions. At the same time, the expression of genes that encode ABA-hydroxylases that inactivate the newly synthesized ABA, is repressed by drought stress. These phenomena occur through epigenetic modifications via the reversible processes of histone acetylation and deacetylation, also known as chromatin remodeling, which is an important regulatory mechanism that responds to various environmental stresses. Recently, we had reported that the chromatin remodeling complex HDA9-PWR-ABI4 promotes the development of drought tolerance through the deacetylation of CYP707A1/2 genes that encode the major enzymes involved in ABA catabolism. Here, we discuss the role of HDA9 and PWR in regulating drought stress by modulating the acetylation status of the CYP707A genes.
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Affiliation(s)
- Akhtar Ali
- Institute of Glocal Disease Control, Konkuk University, Seoul, Republic of Korea
- Department of Biomedical Science & Engineering, Konkuk University, Seoul, South Korea
| | - Dae-Jin Yun
- Department of Biomedical Science & Engineering, Konkuk University, Seoul, South Korea
- CONTACT Dae-Jin Yun Department of Biomedical Science & Engineering, Konkuk University, Seoul05029, South Korea
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14
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Lim CJ, Park J, Shen M, Park HJ, Cheong MS, Park KS, Baek D, Bae MJ, Ali A, Jan M, Lee SY, Lee BH, Kim WY, Pardo JM, Yun DJ. The Histone-Modifying Complex PWR/HOS15/HD2C Epigenetically Regulates Cold Tolerance. PLANT PHYSIOLOGY 2020; 184:1097-1111. [PMID: 32732349 PMCID: PMC7536694 DOI: 10.1104/pp.20.00439] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 07/21/2020] [Indexed: 05/04/2023]
Abstract
Cold stress is a major environmental stress that severely affects plant growth and crop productivity. Arabidopsis (Arabidopsis thaliana) HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE15 (HOS15) is a substrate receptor of the CULLIN4-based CLR4 ubiquitin E3 ligase complex, which epigenetically regulates cold tolerance by degrading HISTONE DEACETYLASE2C (HD2C) to switch from repressive to permissive chromatin structure in response to cold stress. In this study, we characterized a HOS15-binding protein, POWERDRESS (PWR), and analyzed its function in the cold stress response. PWR loss-of-function plants (pwr) showed lower expression of cold-regulated (COR) genes and sensitivity to freezing. PWR interacts with HD2C through HOS15, and cold-induced HD2C degradation by HOS15 is diminished in the pwr mutant. The association of HOS15 and HD2C to promoters of cold-responsive COR genes was dependent on PWR. Consistent with these observations, the high acetylation levels of histone H3 by cold-induced and HOS15-mediated HD2C degradation were significantly reduced in pwr under cold stress. PWR also interacts with C-repeat element-binding factor transcription factors to modulate their cold-induced binding to the promoter of COR genes. Collectively, our data signify that the PWR-HOS15-HD2C histone-modifying complex regulates the expression of COR genes and the freezing tolerance of plants.
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Affiliation(s)
- Chae Jin Lim
- Institute of Glocal Disease Control, Konkuk University, Seoul 05029, Republic of Korea
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Junghoon Park
- Institute of Glocal Disease Control, Konkuk University, Seoul 05029, Republic of Korea
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Mingzhe Shen
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Research Institute of Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Hee Jin Park
- Institute of Glocal Disease Control, Konkuk University, Seoul 05029, Republic of Korea
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Mi Sun Cheong
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Research Institute of Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Ki Suk Park
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Dongwon Baek
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Research Institute of Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Min Jae Bae
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Ahktar Ali
- Institute of Glocal Disease Control, Konkuk University, Seoul 05029, Republic of Korea
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Masood Jan
- Institute of Glocal Disease Control, Konkuk University, Seoul 05029, Republic of Korea
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Sang Yeol Lee
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Research Institute of Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Byeong-Ha Lee
- Department of Life Science, Sogang University, Seoul 04107, Republic of Korea
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Research Institute of Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Jose M Pardo
- Institute of Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Cientificas and Universidad de Sevilla, 41092 Seville, Spain
| | - Dea-Jin Yun
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
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15
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Jiang J, Ding AB, Liu F, Zhong X. Linking signaling pathways to histone acetylation dynamics in plants. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5179-5190. [PMID: 32333777 PMCID: PMC7475247 DOI: 10.1093/jxb/eraa202] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 04/22/2020] [Indexed: 05/04/2023]
Abstract
As sessile organisms, plants face versatile environmental challenges and require proper responses at multiple levels for survival. Epigenetic modification of DNA and histones is a conserved gene-regulatory mechanism and plays critical roles in diverse aspects of biological processes, ranging from genome defense and imprinting to development and physiology. In recent years, emerging studies have revealed the interplay between signaling transduction pathways, epigenetic modifications, and chromatin cascades. Specifically, histone acetylation and deacetylation dictate plant responses to environmental cues by modulating chromatin dynamics to regulate downstream gene expression as signaling outputs. In this review, we summarize current understandings of the link between plant signaling pathways and epigenetic modifications with a focus on histone acetylation and deacetylation.
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Affiliation(s)
- Jianjun Jiang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, Jiangsu, China
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - Adeline B Ding
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - Fengquan Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, Jiangsu, China
- Correspondence: or
| | - Xuehua Zhong
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
- Correspondence: or
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Ali A, Yun DJ. HOS15: A missing link that fine-tunes ABA signaling and drought tolerance in Arabidopsis. PLANT SIGNALING & BEHAVIOR 2020; 15:1770964. [PMID: 32425099 PMCID: PMC8570740 DOI: 10.1080/15592324.2020.1770964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Among the phytohormones, abscisic acid (ABA) specifically regulates plant adaptation to osmotic stresses, such as drought and high salinity, by controlling the internal water status in plants. A significant accumulation of ABA occurs in response to conditions of water deficit; this is followed by a sophisticated signaling relay, known as the ABA signaling pathway, which decreases the rate of transpiration through stomatal closure, thereby suppressing photosynthetic activity. Snf1-related kinases (SnRK2s) are the major components regulating the ABA signaling pathway. Of these, SnRK2.6 (OST1) and SnRK2.3 are negatively regulated by HOS15 (HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE15), in an ABA-dependent manner, to cease the signaling relay. HOS15 is a WD40-repeat protein that regulates several physiological processes, including plant growth and development, freezing stress responses, and ABA signaling. Here, we provide a brief overview of the functional importance of HOS15 in the regulation of ABA signaling and drought stress.
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Affiliation(s)
- Akhtar Ali
- Department of Biomedical Science & Engineering, Konkuk University, Seoul, South Korea
| | - Dae-Jin Yun
- Department of Biomedical Science & Engineering, Konkuk University, Seoul, South Korea
- CONTACT Dae-Jin Yun Department of Biomedical Science & Engineering, Konkuk University, Seoul05029, South Korea
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17
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Identification and characterization of the stunted sterile (ss) mutant in rice. Genes Genomics 2020; 42:869-882. [PMID: 32506267 DOI: 10.1007/s13258-020-00954-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 05/19/2020] [Indexed: 10/24/2022]
Abstract
BACKGROUND Proper organ development is pivotal for normal rice growth and production. Many genes are involved in this process, and these genes provide a basis for rice breeding. OBJECTIVE To identify a novel mutation causing developmental defects in rice. METHODS The phenotype of a rice mutant, stunted sterile (ss), identified from the japonica rice cultivar Samkwang treated with N-methyl-N-nitrosourea, was characterized, including anatomical and pollen activity analyses. A genetic analysis and fine mapping were performed to identify a candidate locus, followed by a sequence analysis to determine the causal mutation for the phenotype. RESULTS Compared with wild-type plants, the mutant exhibited a 34% reduction in height, 46% reduction in flag leaf width, and complete panicle sterility. Cell proliferation in the leaf and pollen viability were significantly inhibited in the mutant. The mutant phenotypes were controlled by a single recessive gene that was fine-mapped to an 84 kb region between two SNP markers on the short arm of chromosome 5. A candidate gene analysis determined that the mutant carries an 11 bp insertion in the coding region of LOC_Os05g03550, which encodes a protein containing two SANT domains, resulting in a premature termination codon before the conserved domain. CONCLUSIONS We identified a novel rice gene, Stunted sterile, involved in the regulation of various developmental processes. Our findings improve our understanding of the role of chromatin remodeling in organ development and have implications for breeding owing to the broad effects of the gene on plant growth.
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Yan K, Ran M, Li S, Zhang J, Wang Y, Wang Z, Wei D, Tang Q. The delayed senescence of postharvest buds in salt ions was related to antioxidant activity, HDA9 and CCX1 in broccoli (Brassica oleracea L. var. Italic Planch.). Food Chem 2020; 324:126887. [PMID: 32339788 DOI: 10.1016/j.foodchem.2020.126887] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 03/28/2020] [Accepted: 04/20/2020] [Indexed: 01/07/2023]
Abstract
Epigenetic regulation and salt ions play essential roles in senescence control, but the underlying regulatory mechanism of senescence has not been thoroughly revealed in broccoli postharvest buds. Here, we found 200 mmol·L-1 NaCl, 400 mmol·L-1 KCl, 40 mmol·L-1 CaCl2 and 0.5 μmol·L-1 Trichostatin-A (TSA, a histone deacetylase inhibitor) delayed the bud senescence. They resulted in significantly inhibiting the malondialdehyde (MDA) content, and dramatically promoting the contents of superoxide dismutase (SOD), peroxidase (POD) and Chlorophyll. Furthermore, the expression of PHEOPHYTINASE (PPH) and NONYELLOWING (NYE1), but not SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1), were remarkably repressed by salt ions and TSA. Interestingly, HISTONE DEACETYLASE 9 (HDA9) and CATION/Ca2+ EXCHANGER 1 (CCX1) were down-regulated by NaCl, CaCl2 and TSA. Further assays demonstrated that HDA9 could not interact with CCX1 promoter. It suggested that CCX1 along with HDA9 were involved in inhibiting the senescence of broccoli buds, and regulated aging by indirect interaction.
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Affiliation(s)
- Kai Yan
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China; Chengdu Agricultural College, Chengdu 611130, China; Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing 400715, China
| | - Maolin Ran
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China; Rice and Sorghum Institute, Sichuan Academy of Agricultural Sciences, Sichuan Deyang 618000, China
| | - Shengnan Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China; Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing 400715, China
| | - Junli Zhang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China; Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing 400715, China
| | - Yu Wang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China; Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing 400715, China
| | - Zhimin Wang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China; Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing 400715, China
| | - Dayong Wei
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China; Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing 400715, China.
| | - Qinglin Tang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China; Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing 400715, China.
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19
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Yang L, Chen X, Wang Z, Sun Q, Hong A, Zhang A, Zhong X, Hua J. HOS15 and HDA9 negatively regulate immunity through histone deacetylation of intracellular immune receptor NLR genes in Arabidopsis. THE NEW PHYTOLOGIST 2020; 226:507-522. [PMID: 31854111 PMCID: PMC7080574 DOI: 10.1111/nph.16380] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 12/08/2019] [Indexed: 05/08/2023]
Abstract
Plant immune responses need to be tightly controlled for growth-defense balance. The mechanism underlying this tight control is not fully understood. Here we identify epigenetic regulation of nucleotide-binding leucine rich repeat or Nod-Like Receptor (NLR) genes as an important mechanism for immune responses. Through a sensitized genetic screen and molecular studies, we identified and characterized HOS15 and its associated protein HDA9 as negative regulators of immunity and NLR gene expression. The loss-of-function of HOS15 or HDA9 confers enhanced resistance to pathogen infection accompanied with increased expression of one-third of the 207 NLR genes in Arabidopsis thaliana. HOS15 and HDA9 are physically associated with some of these NLR genes and repress their expression likely through reducing the acetylation of H3K9 at these loci. In addition, these NLR genes are repressed by HOS15 under both pathogenic and nonpathogenic conditions but by HDA9 only under infection condition. Together, this study uncovers a previously uncharacterized histone deacetylase complex in plant immunity and highlights the importance of epigenetic regulation of NLR genes in modulating growth-defense balance.
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Affiliation(s)
- Leiyun Yang
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, 14853, USA
| | - Xiangsong Chen
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, 53706, USA
| | - Zhixue Wang
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, 14853, USA
| | - Qi Sun
- Cornell Computational Biology Service Unit, Cornell University, Ithaca, 14853, USA
| | - Anna Hong
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, 14853, USA
| | - Aiqin Zhang
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, 14853, USA
| | - Xuehua Zhong
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, 53706, USA
- For correspondence: Jian Hua: Tel (+1) 607-255-5554;; Xuehua Zhong: Tel (+1) 608-316-4421;
| | - Jian Hua
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, 14853, USA
- For correspondence: Jian Hua: Tel (+1) 607-255-5554;; Xuehua Zhong: Tel (+1) 608-316-4421;
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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: 47] [Impact Index Per Article: 9.4] [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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HISTONE DEACETYLASE 9 stimulates auxin-dependent thermomorphogenesis in Arabidopsis thaliana by mediating H2A.Z depletion. Proc Natl Acad Sci U S A 2019; 116:25343-25354. [PMID: 31767749 DOI: 10.1073/pnas.1911694116] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many plant species respond to unfavorable high ambient temperatures by adjusting their vegetative body plan to facilitate cooling. This process is known as thermomorphogenesis and is induced by the phytohormone auxin. Here, we demonstrate that the chromatin-modifying enzyme HISTONE DEACETYLASE 9 (HDA9) mediates thermomorphogenesis but does not interfere with hypocotyl elongation during shade avoidance. HDA9 is stabilized in response to high temperature and mediates histone deacetylation at the YUCCA8 locus, a rate-limiting enzyme in auxin biosynthesis, at warm temperatures. We show that HDA9 permits net eviction of the H2A.Z histone variant from nucleosomes associated with YUCCA8, allowing binding and transcriptional activation by PHYTOCHROME INTERACTING FACTOR 4, followed by auxin accumulation and thermomorphogenesis.
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Nakai Y, Horiguchi G, Iwabuchi K, Harada A, Nakai M, Hara-Nishimura I, Yano T. tRNA Wobble Modification Affects Leaf Cell Development in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2019; 60:2026-2039. [PMID: 31076779 DOI: 10.1093/pcp/pcz064] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 04/04/2019] [Indexed: 05/14/2023]
Abstract
The tRNA modification at the wobble position of Lys, Glu and Gln (wobbleU* modification) is responsible for the fine-tuning of protein translation efficiency and translation rate. This modification influences organism function in accordance with growth and environmental changes. However, the effects of wobbleU* modification at the cellular, tissue, or individual level have not yet been elucidated. In this study, we show that sulfur modification of wobbleU* of the tRNAs affects leaf development in Arabidopsis thaliana. The sulfur modification was impaired in the two wobbleU*-modification mutants: the URM1-like protein-defective mutant and the Elongator complex-defective mutants. Analyses of the mutant phenotypes revealed that the deficiency in the wobbleU* modification increased the airspaces in the leaves and the leaf size without affecting the number and the area of palisade mesophyll cells. On the other hand, both mutants exhibited increased number of leaf epidermal pavement cells but with reduced cell size. The deficiency in the wobbleU* modification also delayed the initiation of the endoreduplication processes of mesophyll cells. The phenotype of ASYMMETRIC LEAVES2-defective mutant was enhanced in the Elongator-defective mutants, while it was unchanged in the URM1-like protein-defective mutant. Collectively, the findings of this study suggest that the tRNA wobbleU* modification plays an important role in leaf morphogenesis by balancing the development between epidermal and mesophyll tissues.
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Affiliation(s)
- Yumi Nakai
- Department of Biochemistry, Osaka Medical College, 2-7 Daigakumachi, Takatsuki, Japan
| | - Gorou Horiguchi
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo, Japan
| | - Kosei Iwabuchi
- Faculty of Science and Engineering, Konan University, Kobe, Japan
| | - Akiko Harada
- Department of Biology, Osaka Medical College, 2-7 Daigakumachi, Takatsuki, Japan
| | - Masato Nakai
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Japan
| | | | - Takato Yano
- Department of Biochemistry, Osaka Medical College, 2-7 Daigakumachi, Takatsuki, Japan
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23
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Identification and characterization of WD40 superfamily genes in peach. Gene 2019; 710:291-306. [PMID: 31185283 DOI: 10.1016/j.gene.2019.06.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 04/25/2019] [Accepted: 06/05/2019] [Indexed: 01/16/2023]
Abstract
The WD40 transcription factor family is a superfamily found in all eukaryotes that plays important roles in regulating growth and development. To our knowledge, to date, WD40 superfamily genes have been identified and characterized in several plant species, but little information is available on the WD40 superfamily genes in peach. In this study, we identified 220 members of the WD40 superfamily in the peach genome, and these members were further classified into five subfamilies based on phylogenetic comparison with those in Arabidopsis. The members within each subfamily had conserved motifs and gene structures. The WD40 genes were unevenly distributed on chromosomes 1 to 8 of the peach genome. Additionally, 58 pairs of paralog WD40 members were found on eight chromosomes in peach, and 242 pairs of orthologous WD40 genes in peach and Arabidopsis were matched. The 54 selected putative WD40 genes in peach had diverse expression patterns in red-fleshed and white-fleshed peach fruits at five developmental stages. Prupe.6G211800.1 was located only on the cytomembrane, while Prupe.1G428200.1 and Prupe.I003200.1 were located on both the cytomembrane and in the nucleus; Prupe.1G558700.1 was densely localized around the nuclear rim but relatively faintly localized in the nucleoplasm; Prupe.5G116300.1 was located in the nucleus and cytomembrane with strong signals but showed weak signals in the cytoplasm; and Prupe.8G212400.1 and Prupe.1G053600.1 were located mainly in the nuclear envelope and cytomembrane but relatively faintly in the nucleoplasm. This study provides a foundation for the further functional verification of WD40 genes in peach.
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Fonseca S, Rubio V. Arabidopsis CRL4 Complexes: Surveying Chromatin States and Gene Expression. FRONTIERS IN PLANT SCIENCE 2019; 10:1095. [PMID: 31608079 PMCID: PMC6761389 DOI: 10.3389/fpls.2019.01095] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/09/2019] [Indexed: 05/10/2023]
Abstract
CULLIN4 (CUL4) RING ligase (CRL4) complexes contain a CUL4 scaffold protein, associated to RBX1 and to DDB1 proteins and have traditionally been associated to protein degradation events. Through DDB1, these complexes can associate with numerous DCAF proteins, which directly interact with specific targets promoting their ubiquitination and subsequent degradation by the proteasome. A characteristic feature of the majority of DCAF proteins that associate with DDB1 is the presence of the DWD motif. DWD-containing proteins sum up to 85 in the plant model species Arabidopsis. In the last decade, numerous Arabidopsis DWD proteins have been studied and their molecular functions uncovered. Independently of whether their association with CRL4 has been confirmed or not, DWD proteins are often found as components of additional multimeric protein complexes that play key roles in essential nuclear events. For most of them, the significance of their complex partnership is still unexplored. Here, we summarize recent findings involving both confirmed and putative CRL4-associated DCAF proteins in regulating nuclei architecture remodelling, DNA damage repair, histone post-translational modification, mRNA processing and export, and ribosome biogenesis, that definitely have an impact in gene expression and de novo protein synthesis. We hypothesized that, by maintaining accurate levels of regulatory proteins through targeted degradation and transcriptional control, CRL4 complexes help to surveil nuclear processes essential for plant development and survival.
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25
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Park HJ, Baek D, Cha JY, Liao X, Kang SH, McClung CR, Lee SY, Yun DJ, Kim WY. HOS15 Interacts with the Histone Deacetylase HDA9 and the Evening Complex to Epigenetically Regulate the Floral Activator GIGANTEA. THE PLANT CELL 2019; 31:37-51. [PMID: 30606777 PMCID: PMC6391688 DOI: 10.1105/tpc.18.00721] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 11/26/2018] [Accepted: 12/20/2018] [Indexed: 05/18/2023]
Abstract
In plants, seasonal inputs such as photoperiod and temperature modulate the plant's internal genetic program to regulate the timing of the developmental transition from vegetative to reproductive growth. This regulation of the floral transition involves chromatin remodeling, including covalent modification of histones. Here, we report that HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE 15 (HOS15), a WD40 repeat protein, associates with a histone deacetylase complex to repress transcription of the GIGANTEA (GI)-mediated photoperiodic flowering pathway in Arabidopsis (Arabidopsis thaliana). Loss of function of HOS15 confers early flowering under long-day conditions because elevated GI expression. LUX ARRHYTHMO (LUX), a DNA binding transcription factor and component of the Evening Complex (EC), is important for the binding of HOS15 to the GI promoter. In wild type, HOS15 associates with the EC components LUX, EARLY FLOWERING 3 (ELF3), and ELF4 and the histone deacetylase HDA9 at the GI promoter, resulting in histone deacetylation and reduced GI expression. In the hos15-2 mutant, the levels of histone acetylation are elevated at the GI promoter, resulting in increased GI expression. Our data suggest that the HOS15-EC-HDA9 histone-modifying complex regulates photoperiodic flowering via the transcriptional repression of GI.
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Affiliation(s)
- Hee Jin Park
- Institute of Glocal Disease Control, Konkuk University, Seoul 05029, Republic of Korea
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Research Institute of Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Dongwon Baek
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Research Institute of Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Joon-Yung Cha
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Research Institute of Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Xueji Liao
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Research Institute of Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Sang-Ho Kang
- International Technology Cooperation Center, Rural Development Administration, Jeonju, 54875, Republic of Korea
| | - C Robertson McClung
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755
| | - Sang Yeol Lee
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Research Institute of Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Dae-Jin Yun
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Research Institute of Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
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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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