1
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Wang P, Su L, Cao L, Hu H, Wan H, Wu C, Zheng Y, Bao C, Liu X. AtSRT1 regulates flowering by regulating flowering integrators and energy signals in Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 213:108841. [PMID: 38879987 DOI: 10.1016/j.plaphy.2024.108841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 06/05/2024] [Accepted: 06/13/2024] [Indexed: 06/18/2024]
Abstract
Epigenetic modifications, such as histone alterations, play crucial roles in regulating the flowering process in Arabidopsis, a typical long-day model plant. Histone modifications are notably involved in the intricate regulation of FLC, a key inhibitor of flowering. Although sirtuin-like protein and NAD+-dependent deacetylases play an important role in regulating energy metabolism, plant stress responses, and hormonal signal transduction, the mechanisms underlying their developmental transitions remain unclear. Thus, this study aimed to reveal how Arabidopsis NAD + -dependent deacetylase AtSRT1 affects flowering by regulating the expression of flowering integrators. Genetic and molecular evidence demonstrated that AtSRT1 mediates histone deacetylation by directly binding near the transcriptional start sites (TSS) of the flowering integrator genes FT and SOC1 and negatively regulating their expression by modulating the expression of the downstream gene LFY to inhibit flowering. Additionally, AtSRT1 directly down-regulates the expression of TOR, a glucose-driven central hub of energy signaling, which controls cell metabolism and growth in response to nutritional and environmental factors. This down-regulation occurs through binding near the TSS of TOR, facilitating the addition of H3K27me3 marks on FLC via the TOR-FIE-PRC2 pathway, further repressing flowering. These results uncover a multi-pathway regulatory network involving deacetylase AtSRT1 during the flowering process, highlighting its interaction with TOR as a hub for the coordinated regulation of energy metabolism and flowering initiation. These findings significantly enhance understanding of the complexity of histone modifications in the regulation of flowering.
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Affiliation(s)
- Ping Wang
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Sciences, Jianghan University, Wuhan, 430056, PR China
| | - Lufang Su
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Sciences, Jianghan University, Wuhan, 430056, PR China
| | - Lan Cao
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Sciences, Jianghan University, Wuhan, 430056, PR China
| | - Hanbing Hu
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Sciences, Jianghan University, Wuhan, 430056, PR China
| | - Heping Wan
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Sciences, Jianghan University, Wuhan, 430056, PR China
| | - Chunhong Wu
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Sciences, Jianghan University, Wuhan, 430056, PR China
| | - Yu Zheng
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Sciences, Jianghan University, Wuhan, 430056, PR China
| | - Chun Bao
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Sciences, Jianghan University, Wuhan, 430056, PR China
| | - Xiaoyun Liu
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Sciences, Jianghan University, Wuhan, 430056, PR China.
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2
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Chu Y, Duan R, Song H, Zhang W, Zhou Y, Ma Y, Yin X, Tian L, Ausin I, Han Z. AtHD2D is involved in regulating lateral root development and participates in abiotic stress response in Arabidopsis. JOURNAL OF PLANT PHYSIOLOGY 2024; 297:154242. [PMID: 38614048 DOI: 10.1016/j.jplph.2024.154242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 03/28/2024] [Accepted: 03/28/2024] [Indexed: 04/15/2024]
Abstract
Roots are essential to terrestrial plants, as their growth and morphology are crucial for plant development. The growth of the roots is affected and regulated by several internal and external environmental signals and metabolic pathways. Among them, chromatin modification plays an important regulatory role. In this study, we explore the potential roles of the histone deacetylase AtHD2D in root development and lay the foundation for further research on the biological processes and molecular mechanisms of AtHD2D in the future. Our study indicates that AtHD2D affects the root tip microenvironment homeostasis by affecting the gene transcription levels required to maintain the root tip microenvironment. In addition, we confirmed that AtHD2D is involved in regulating Arabidopsis lateral root development and further explained the possible role of AtHD2D in auxin-mediated lateral root development. AtHD2D can effectively enhance the resistance of Arabidopsis thaliana to abiotic stress. We believe that AtHD2D is involved in coping with abiotic stress by promoting the development of lateral roots. Overexpression of AtHD2D promotes the accumulation of reactive oxygen species (ROS) in roots, indicating that AtHD2D is also involved in developing lateral roots mediated by ROS. Previous studies have shown that the overexpression of AtHD2D can effectively enhance the resistance of Arabidopsis thaliana to abiotic stress. Based on our data, we believe that AtHD2D participates in the response to abiotic stress by promoting the development of lateral roots. AtHD2D-mediated lateral root development provides new ideas for studying the mechanism of HDAC protein in regulating root development.
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Affiliation(s)
- Yueyang Chu
- College of Life Science, Northwest A & F University, Yangling, Shanxi, 712100, China
| | - Ruochen Duan
- College of Life Science, Northwest A & F University, Yangling, Shanxi, 712100, China
| | - Haoran Song
- College of Life Science, Northwest A & F University, Yangling, Shanxi, 712100, China
| | - Wenshuo Zhang
- College of Life Science, Northwest A & F University, Yangling, Shanxi, 712100, China
| | - Yuxuan Zhou
- College of Life Science, Northwest A & F University, Yangling, Shanxi, 712100, China
| | - Yutong Ma
- College of Life Science, Northwest A & F University, Yangling, Shanxi, 712100, China
| | - Xiaotong Yin
- College of Life Science, Northwest A & F University, Yangling, Shanxi, 712100, China
| | - Lining Tian
- London Research and Development Centre, Agriculture and Agri-food Canada, London, Ontario, N5V 4T3, Canada
| | - Israel Ausin
- College of Life Science, Northwest A & F University, Yangling, Shanxi, 712100, China
| | - Zhaofen Han
- College of Life Science, Northwest A & F University, Yangling, Shanxi, 712100, China.
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3
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Luo H, Lu Z, Guan J, Yan M, Liu Z, Wan Y, Zhou G. Gene co-expression network analysis in areca floral organ and the potential role of the AcMADS17 and AcMADS23 in transgenic Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 342:112049. [PMID: 38408509 DOI: 10.1016/j.plantsci.2024.112049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 02/28/2024]
Abstract
Areca catechu L., a monocot belonging to the palm family, is monoecious, with female and male flowers separately distributed on the same inflorescence. To discover the molecular mechanism of flower development in Areca, we sequenced different floral samples to generate tissue-specific transcriptomic profiles. We conducted a comparative analysis of the transcriptomic profiles of apical sections of the inflorescence with male flowers and the basal section of the inflorescence with female flowers. Based on the RNA sequencing dataset, we applied weighted gene co-expression network analysis (WGCNA) to identify sepal, petal, stamen, stigma and other specific modules as well as hub genes involved in specific floral organ development. The syntenic and expression patterns of AcMADS-box genes were analyzed in detail. Furthermore, we analyzed the open chromatin regions and transcription factor PI binding sites in male and female flowers by assay for transposase-accessible chromatin sequencing (ATAC-seq) assay. Heterologous expression revealed the important role of AcMADS17 and AcMADS23 in floral organ development. Our results provide a valuable genomic resource for the functional analysis of floral organ development in Areca.
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Affiliation(s)
- Haifen Luo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Zhongliang Lu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Junqi Guan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Mengyao Yan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Zheng Liu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Yinglang Wan
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, Hainan, China
| | - Guangzhen Zhou
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, Hainan, China.
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4
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Manrique S, Cavalleri A, Guazzotti A, Villarino GH, Simonini S, Bombarely A, Higashiyama T, Grossniklaus U, Mizzotti C, Pereira AM, Coimbra S, Sankaranarayanan S, Onelli E, Masiero S, Franks RG, Colombo L. HISTONE DEACETYLASE19 Controls Ovule Number Determination and Transmitting Tract Differentiation. PLANT PHYSIOLOGY 2024; 194:2117-2135. [PMID: 38060625 PMCID: PMC10980524 DOI: 10.1093/plphys/kiad629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/29/2023] [Indexed: 04/01/2024]
Abstract
The gynoecium is critical for the reproduction of flowering plants as it contains the ovules and the tissues that foster pollen germination, growth, and guidance. These tissues, known as the reproductive tract (ReT), comprise the stigma, style, and transmitting tract (TT). The ReT and ovules originate from the carpel margin meristem (CMM) within the pistil. SHOOT MERISTEMLESS (STM) is a key transcription factor for meristem formation and maintenance. In all above-ground meristems, including the CMM, local STM downregulation is required for organ formation. However, how this downregulation is achieved in the CMM is unknown. Here, we have studied the role of HISTONE DEACETYLASE 19 (HDA19) in Arabidopsis (Arabidopsis thaliana) during ovule and ReT differentiation based on the observation that the hda19-3 mutant displays a reduced ovule number and fails to differentiate the TT properly. Fluorescence-activated cell sorting coupled with RNA-sequencing revealed that in the CMM of hda19-3 mutants, genes promoting organ development are downregulated while meristematic markers, including STM, are upregulated. HDA19 was essential to downregulate STM in the CMM, thereby allowing ovule formation and TT differentiation. STM is ectopically expressed in hda19-3 at intermediate stages of pistil development, and its downregulation by RNA interference alleviated the hda19-3 phenotype. Chromatin immunoprecipitation assays indicated that STM is a direct target of HDA19 during pistil development and that the transcription factor SEEDSTICK is also required to regulate STM via histone acetylation. Thus, we identified factors required for the downregulation of STM in the CMM, which is necessary for organogenesis and tissue differentiation.
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Affiliation(s)
- Silvia Manrique
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Giovanni Celoria 26, Milan 20133, Italy
| | - Alex Cavalleri
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Giovanni Celoria 26, Milan 20133, Italy
| | - Andrea Guazzotti
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Giovanni Celoria 26, Milan 20133, Italy
| | - Gonzalo H Villarino
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27606, USA
| | - Sara Simonini
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, Zurich CH-8008, Switzerland
| | - Aureliano Bombarely
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Giovanni Celoria 26, Milan 20133, Italy
| | - Tetsuya Higashiyama
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, Zurich CH-8008, Switzerland
| | - Chiara Mizzotti
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Giovanni Celoria 26, Milan 20133, Italy
| | - Ana Marta Pereira
- Faculdade de Ciências da Universidade do Porto, Departamento de Biologia, Universidade do Porto, rua do Campo Alegre, Porto 4169-007, Portugal
- LAQV Requimte, Sustainable Chemistry, Universidade do Porto, Porto 4169-007, Portugal
| | - Silvia Coimbra
- Faculdade de Ciências da Universidade do Porto, Departamento de Biologia, Universidade do Porto, rua do Campo Alegre, Porto 4169-007, Portugal
- LAQV Requimte, Sustainable Chemistry, Universidade do Porto, Porto 4169-007, Portugal
| | - Subramanian Sankaranarayanan
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
| | - Elisabetta Onelli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Giovanni Celoria 26, Milan 20133, Italy
| | - Simona Masiero
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Giovanni Celoria 26, Milan 20133, Italy
| | - Robert G Franks
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27606, USA
| | - Lucia Colombo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Giovanni Celoria 26, Milan 20133, Italy
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5
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Chen Y, Guo P, Dong Z. The role of histone acetylation in transcriptional regulation and seed development. PLANT PHYSIOLOGY 2024; 194:1962-1979. [PMID: 37979164 DOI: 10.1093/plphys/kiad614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/09/2023] [Accepted: 10/29/2023] [Indexed: 11/20/2023]
Abstract
Histone acetylation is highly conserved across eukaryotes and has been linked to gene activation since its discovery nearly 60 years ago. Over the past decades, histone acetylation has been evidenced to play crucial roles in plant development and response to various environmental cues. Emerging data indicate that histone acetylation is one of the defining features of "open chromatin," while the role of histone acetylation in transcription remains controversial. In this review, we briefly describe the discovery of histone acetylation, the mechanism of histone acetylation regulating transcription in yeast and mammals, and summarize the research progress of plant histone acetylation. Furthermore, we also emphasize the effect of histone acetylation on seed development and its potential use in plant breeding. A comprehensive knowledge of histone acetylation might provide new and more flexible research perspectives to enhance crop yield and stress resistance.
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Affiliation(s)
- Yan Chen
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Peiguo Guo
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Zhicheng Dong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
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Cai J, Hu F, Yang M, Wu R, Liu X. Genome-wide identification of HDAC members and function analysis of PnHDT1/2 in salt stress response in Phyla nodiflora (L.) Greene. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 208:108442. [PMID: 38382345 DOI: 10.1016/j.plaphy.2024.108442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/28/2024] [Accepted: 02/15/2024] [Indexed: 02/23/2024]
Abstract
Reversible histone acetylation and deacetylation play an essential role in regulating chromatin structure and gene expression. Histone deacetylases (HDACs) catalyze the removal of acetyl groups from lysine residues of core histones, resulting in closed chromatin structure and transcription repression. Although the HDCAs have been extensively studied in model plants, the HDAC members have not been identified in Phyla nodiflora (L.) Greene (P. nodiflora), a salt-tolerant plant species. Here, 17 PnHDAC genes were identified in the genome of P. nodiflora. Phylogenetic analysis displayed that the PnHDACs were classified into three groups, the RPD3/HDA1-group (11 members), the SIR2-group (2 members) and the plant-specific HD2-group (4 members). Transcription analysis displayed that the gene expression patterns of PnHDACs were affected by salt stress in P. nodiflora seedlings. PnHDT1 and PnHDT2, two HD2-type HDAC proteins were found to be subcellular localized in the nucleolus. Furthermore, overexpressing PnHDT1 and PnHDT2 in Arabidopsis decreased the sensitivity to plant hormone abscisic acid whereas reduced the tolerance to salt stress during seed germination and seedling stages. Overall, our work identified the PnHDAC gene family for the first time in P. nodiflora and revealed an involvement of PnHDT1 and PnHDT2 in salt stress tolerance, which may contribute to uncover the mechanism of P. nodiflora in adaption to salt environments.
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Affiliation(s)
- Jiajia Cai
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Feng Hu
- Department of Landscape and Tourism Planning and Design, Guangzhou Urban Planning and Design Survey Research Institute, Guangzhou, 510650, China
| | - Min Yang
- Department of Landscape and Tourism Planning and Design, Guangzhou Urban Planning and Design Survey Research Institute, Guangzhou, 510650, China
| | - Ronghua Wu
- Department of Landscape and Tourism Planning and Design, Guangzhou Urban Planning and Design Survey Research Institute, Guangzhou, 510650, China
| | - Xuncheng Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
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7
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Gao S, Yin M, Xu M, Zhang H, Li S, Han Y, Ji S, Li X, Du G. Transcription factors PuPRE6/PuMYB12 and histone deacetylase PuHDAC9-like regulate sucrose levels in pear. PLANT PHYSIOLOGY 2024; 194:1577-1592. [PMID: 38006319 DOI: 10.1093/plphys/kiad628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/29/2023] [Accepted: 09/29/2023] [Indexed: 11/27/2023]
Abstract
The improvement of fruit quality, in particular sugar content, has been a major goal of plant breeding programmes for many years. Here, 2 varieties of the Ussurian pear (Pyrus ussuriensis), Nanguo, and its high-sucrose accumulation bud sport, Nanhong, were used to study the molecular mechanisms regulating sucrose transport in fruits. Comparative transcriptome analysis showed that in Nanhong fruit, an MYB transcription factor, PuMYB12, and a sucrose transporter protein, PuSUT4-like, were expressed at higher levels, while a paclobutrazol resistance transcription factor, PuPRE6, and a histone deacetylase (HDAC), PuHDAC9-like, were expressed at lower levels in Nanguo fruit. PuSUT4-like silencing and overexpression experiments in Nanguo pear showed that PuSUT4-like is essential for sucrose transportation. PuPRE6 and PuMYB12 act as antagonistic complexes to regulate PuSUT4-like transcription and sucrose accumulation. The histone deacetylation levels of the PuMYB12 and PuSUT4-like promoters were higher in Nanguo fruit than in Nanhong fruit, and Y1H assays showed that HDAC PuHDAC9-like bound directly to the promoters of PuMYB12 and PuSUT4-like. Our results uncovered transcription regulation and epigenetic mechanisms underlying sucrose accumulation in pears.
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Affiliation(s)
- Siyang Gao
- Key Laboratory of Fruit Postharvest Biology, Liaoning Province, College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Mingxin Yin
- Key Laboratory of Fruit Postharvest Biology, Liaoning Province, College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Mingyang Xu
- Key Laboratory of Fruit Postharvest Biology, Liaoning Province, College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - He Zhang
- Key Laboratory of Fruit Postharvest Biology, Liaoning Province, College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Shuai Li
- Key Laboratory of Fruit Postharvest Biology, Liaoning Province, College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Yinxiao Han
- Key Laboratory of Fruit Postharvest Biology, Liaoning Province, College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Shujuan Ji
- Department of Food Science, Shenyang Agricultural University, Shenyang 110866, China
| | - Xinyue Li
- Key Laboratory of Fruit Postharvest Biology, Liaoning Province, College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Department of Food Science, Shenyang Agricultural University, Shenyang 110866, China
| | - Guodong Du
- Key Laboratory of Fruit Postharvest Biology, Liaoning Province, College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
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8
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Perrella G, Fasano C, Donald NA, Daddiego L, Fang W, Martignago D, Carr C, Conti L, Herzyk P, Amtmann A. Histone Deacetylase Complex 1 and histone 1 epigenetically moderate stress responsiveness of Arabidopsis thaliana seedlings. THE NEW PHYTOLOGIST 2024; 241:166-179. [PMID: 37565540 PMCID: PMC10953426 DOI: 10.1111/nph.19165] [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: 03/23/2023] [Accepted: 07/05/2023] [Indexed: 08/12/2023]
Abstract
Early responses of plants to environmental stress factors prevent damage but can delay growth and development in fluctuating conditions. Optimising these trade-offs requires tunability of plant responsiveness to environmental signals. We have previously reported that Histone Deacetylase Complex 1 (HDC1), which interacts with multiple proteins in histone deacetylation complexes, regulates the stress responsiveness of Arabidopsis seedlings, but the underlying mechanism remained elusive. Here, we show that HDC1 attenuates transcriptome re-programming in salt-treated seedlings, and we identify two genes (LEA and MAF5) that inhibit seedling establishment under salt stress downstream of HDC1. HDC1 attenuates their transcriptional induction by salt via a dual mechanism involving H3K9/14 deacetylation and H3K27 trimethylation. The latter, but not the former, was also abolished in a triple knockout mutant of the linker histone H1, which partially mimics the hypersensitivity of the hdc1-1 mutant to salt stress. Although stress-induced H3K27me3 accumulation required both H1 and HDC1, it was not fully recovered by complementing hdc1-1 with a truncated, H1-binding competent HDC1 suggesting other players or independent inputs. The combined findings reveal a dual brake function of HDC1 via regulating both active and repressive epigenetic marks on stress-inducible genes. This natural 'anti-panic' device offers a molecular leaver to tune stress responsiveness in plants.
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Affiliation(s)
- Giorgio Perrella
- Department of BiosciencesUniversità degli Studi di MilanoVia Celoria 26Milan20133Italy
- Plant Science GroupSchool of Molecular Biosciences (SMB), University of GlasgowGlasgowG12 8QQUK
| | - Carlo Fasano
- Italian National Agency for New Technologies, Energy and Sustainable Economic DevelopmentTrisaia Research CentreRotondella (Matera)75026Italy
| | - Naomi A. Donald
- Plant Science GroupSchool of Molecular Biosciences (SMB), University of GlasgowGlasgowG12 8QQUK
| | - Loretta Daddiego
- Italian National Agency for New Technologies, Energy and Sustainable Economic DevelopmentTrisaia Research CentreRotondella (Matera)75026Italy
| | - Weiwei Fang
- Department of BiosciencesUniversità degli Studi di MilanoVia Celoria 26Milan20133Italy
| | - Damiano Martignago
- Department of BiosciencesUniversità degli Studi di MilanoVia Celoria 26Milan20133Italy
| | - Craig Carr
- Plant Science GroupSchool of Molecular Biosciences (SMB), University of GlasgowGlasgowG12 8QQUK
| | - Lucio Conti
- Department of BiosciencesUniversità degli Studi di MilanoVia Celoria 26Milan20133Italy
| | - Pawel Herzyk
- Plant Science GroupSchool of Molecular Biosciences (SMB), University of GlasgowGlasgowG12 8QQUK
- Glasgow Polyomics, Wolfson Wohl Cancer Research CentreUniversity of GlasgowGlasgowG61 1QHUK
| | - Anna Amtmann
- Plant Science GroupSchool of Molecular Biosciences (SMB), University of GlasgowGlasgowG12 8QQUK
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9
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Liu S, He M, Lin X, Kong F. Epigenetic regulation of photoperiodic flowering in plants. THE PLANT GENOME 2023; 16:e20320. [PMID: 37013370 DOI: 10.1002/tpg2.20320] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/12/2023] [Accepted: 01/30/2023] [Indexed: 06/19/2023]
Abstract
In response to changeable season, plants precisely control the initiation of flowering in appropriate time of the year to ensure reproductive success. Day length (photoperiod) acts as the most important external cue to determine flowering time. Epigenetics regulates many major developmental stages in plant life, and emerging molecular genetics and genomics researches reveal their essential roles in floral transition. Here, we summarize the recent advances in epigenetic regulation of photoperiod-mediated flowering in Arabidopsis and rice, and discuss the potential of epigenetic regulation in crops improvement, and give the brief prospect for future study trends.
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Affiliation(s)
- Shuangrong Liu
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Milan He
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Xiaoya Lin
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
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10
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Li J, Li Q, Wang W, Zhang X, Chu C, Tang X, Zhu B, Xiong L, Zhao Y, Zhou D. DELLA-mediated gene repression is maintained by chromatin modification in rice. EMBO J 2023; 42:e114220. [PMID: 37691541 PMCID: PMC10620761 DOI: 10.15252/embj.2023114220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 08/14/2023] [Accepted: 08/21/2023] [Indexed: 09/12/2023] Open
Abstract
DELLA proteins are master regulators of gibberellic acid (GA) signaling through their effects on gene expression. Enhanced DELLA accumulation in rice and wheat varieties has greatly contributed to grain yield increases during the green revolution. However, the molecular basis of DELLA-mediated gene repression remains elusive. In this work, we show that the rice DELLA protein SLENDER RICE1 (SLR1) forms a tripartite complex with Polycomb-repressive complex 2 (PRC2) and the histone deacetylase HDA702 to repress downstream genes by establishing a silent chromatin state. The slr1 mutation and GA signaling resulted in dissociation of PRC2 and HDA702 from GA-inducible genes. Loss-of-function or downregulation of the chromatin regulators impaired SLR1-dependent histone modification and gene repression. Time-resolved analysis of GA signaling revealed that GA-induced transcriptional activation was associated with a rapid increase of H3K9ac followed by H3K27me3 removal. Collectively, these results establish a general epigenetic mechanism for DELLA-mediated gene repression and reveal details of the chromatin dynamics during transcriptional activation stimulated by GA signaling.
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Affiliation(s)
- Junjie Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Qi Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Wentao Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Xinran Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Chen Chu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Xintian Tang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Bo Zhu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Dao‐Xiu Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
- Institute of Plant Science Paris‐Saclay (IPS2), CNRS, INRAEUniversity Paris‐SaclayOrsayFrance
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11
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Paull RE, Ksouri N, Kantar M, Zerpa‐Catanho D, Chen NJ, Uruu G, Yue J, Guo S, Zheng Y, Wai CMJ, Ming R. Differential gene expression during floral transition in pineapple. PLANT DIRECT 2023; 7:e541. [PMID: 38028646 PMCID: PMC10644199 DOI: 10.1002/pld3.541] [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: 12/18/2022] [Revised: 09/20/2023] [Accepted: 09/26/2023] [Indexed: 12/01/2023]
Abstract
Pineapple (Ananas comosus var. comosus) and ornamental bromeliads are commercially induced to flower by treatment with ethylene or its analogs. The apex is transformed from a vegetative to a floral meristem and shows morphological changes in 8 to 10 days, with flowers developing 8 to 10 weeks later. During eight sampling stages ranging from 6 h to 8 days after treatment, 7961 genes were found to exhibit differential expression (DE) after the application of ethylene. In the first 3 days after treatment, there was little change in ethylene synthesis or in the early stages of the ethylene response. Subsequently, three ethylene response transcription factors (ERTF) were up-regulated and the potential gene targets were predicted to be the positive flowering regulator CONSTANS-like 3 (CO), a WUSCHEL gene, two APETALA1/FRUITFULL (AP1/FUL) genes, an epidermal patterning gene, and a jasmonic acid synthesis gene. We confirm that pineapple has lost the flowering repressor FLOWERING LOCUS C. At the initial stages, the SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) was not significantly involved in this transition. Another WUSCHEL gene and a PHD homeobox transcription factor, though not apparent direct targets of ERTF, were up-regulated within a day of treatment, their predicted targets being the up-regulated CO, auxin response factors, SQUAMOSA, and histone H3 genes with suppression of abscisic acid response genes. The FLOWERING LOCUS T (FT), TERMINAL FLOWER (TFL), AGAMOUS-like APETELAR (AP2), and SEPETALA (SEP) increased rapidly within 2 to 3 days after ethylene treatment. Two FT genes were up-regulated at the apex and not at the leaf bases after treatment, suggesting that transport did not occur. These results indicated that the ethylene response in pineapple and possibly most bromeliads act directly to promote the vegetative to flower transition via APETALA1/FRUITFULL (AP1/FUL) and its interaction with SPL, FT, TFL, SEP, and AP2. A model based on AP2/ERTF DE and predicted DE target genes was developed to give focus to future research. The identified candidate genes are potential targets for genetic manipulation to determine their molecular role in flower transition.
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Affiliation(s)
- Robert E. Paull
- Tropical Plant & Soil SciencesUniversity of Hawaii at ManoaHonoluluHawaiiUSA
| | - Najla Ksouri
- Laboratory of Genomics, Genetics and Breeding of Fruits and Grapevine, Experimental Aula Dei‐CSICZaragozaSpain
| | - Michael Kantar
- Tropical Plant & Soil SciencesUniversity of Hawaii at ManoaHonoluluHawaiiUSA
| | | | - Nancy Jung Chen
- Tropical Plant & Soil SciencesUniversity of Hawaii at ManoaHonoluluHawaiiUSA
| | - Gail Uruu
- Tropical Plant & Soil SciencesUniversity of Hawaii at ManoaHonoluluHawaiiUSA
| | - Jingjing Yue
- Center for Genomics and BiotechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Shiyong Guo
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational MedicineKunming University of Science and TechnologyKunmingYunnanChina
| | - Yun Zheng
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational MedicineKunming University of Science and TechnologyKunmingYunnanChina
| | | | - Ray Ming
- Department of Plant BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
- Center for Genomics and BiotechnologyFujian Agriculture and Forestry UniversityFuzhouChina
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12
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Franco-Echevarría E, Nielsen M, Schulten A, Cheema J, Morgan TE, Bienz M, Dean C. Distinct accessory roles of Arabidopsis VEL proteins in Polycomb silencing. Genes Dev 2023; 37:801-817. [PMID: 37734835 PMCID: PMC7615239 DOI: 10.1101/gad.350814.123] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/31/2023] [Indexed: 09/23/2023]
Abstract
Polycomb repressive complex 2 (PRC2) mediates epigenetic silencing of target genes in animals and plants. In Arabidopsis, PRC2 is required for the cold-induced epigenetic silencing of the FLC floral repressor locus to align flowering with spring. During this process, PRC2 relies on VEL accessory factors, including the constitutively expressed VRN5 and the cold-induced VIN3. The VEL proteins are physically associated with PRC2, but their individual functions remain unclear. Here, we show an intimate association between recombinant VRN5 and multiple components within a reconstituted PRC2, dependent on a compact conformation of VRN5 central domains. Key residues mediating this compact conformation are conserved among VRN5 orthologs across the plant kingdom. In contrast, VIN3 interacts with VAL1, a transcriptional repressor that binds directly to FLC These associations differentially affect their role in H3K27me deposition: Both proteins are required for H3K27me3, but only VRN5 is necessary for H3K27me2. Although originally defined as vernalization regulators, VIN3 and VRN5 coassociate with many targets in the Arabidopsis genome that are modified with H3K27me3. Our work therefore reveals the distinct accessory roles for VEL proteins in conferring cold-induced silencing on FLC, with broad relevance for PRC2 targets generally.
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Affiliation(s)
- Elsa Franco-Echevarría
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Mathias Nielsen
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Anna Schulten
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Jitender Cheema
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Tomos E Morgan
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Mariann Bienz
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom;
| | - Caroline Dean
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom;
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
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13
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Patel AB, Qing J, Tam KH, Zaman S, Luiso M, Radhakrishnan I, He Y. Cryo-EM structure of the Saccharomyces cerevisiae Rpd3L histone deacetylase complex. Nat Commun 2023; 14:3061. [PMID: 37244892 PMCID: PMC10224958 DOI: 10.1038/s41467-023-38687-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 05/11/2023] [Indexed: 05/29/2023] Open
Abstract
The Rpd3L histone deacetylase (HDAC) complex is an ancient 12-subunit complex conserved in a broad range of eukaryotes that performs localized deacetylation at or near sites of recruitment by DNA-bound factors. Here we describe the cryo-EM structure of this prototypical HDAC complex that is characterized by as many as seven subunits performing scaffolding roles for the tight integration of the only catalytic subunit, Rpd3. The principal scaffolding protein, Sin3, along with Rpd3 and the histone chaperone, Ume1, are present in two copies, with each copy organized into separate lobes of an asymmetric dimeric molecular assembly. The active site of one Rpd3 is completely occluded by a leucine side chain of Rxt2, while the tips of the two lobes and the more peripherally associated subunits exhibit varying levels of flexibility and positional disorder. The structure reveals unexpected structural homology/analogy between unrelated subunits in the fungal and mammalian complexes and provides a foundation for deeper interrogations of structure, biology, and mechanism of these complexes, as well as for the discovery of HDAC complex-specific inhibitors.
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Affiliation(s)
- Avinash B Patel
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
| | - Jinkang Qing
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - Kelly H Tam
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Sara Zaman
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Maria Luiso
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Ishwar Radhakrishnan
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
| | - Yuan He
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
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14
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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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15
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Tilak P, Kotnik F, Née G, Seidel J, Sindlinger J, Heinkow P, Eirich J, Schwarzer D, Finkemeier I. Proteome-wide lysine acetylation profiling to investigate the involvement of histone deacetylase HDA5 in the salt stress response of Arabidopsis leaves. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023. [PMID: 36961081 DOI: 10.1111/tpj.16206] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 03/15/2023] [Accepted: 03/20/2023] [Indexed: 05/09/2023]
Abstract
Post-translational modifications (PTMs) of proteins play important roles in the acclimation of plants to environmental stress. Lysine acetylation is a dynamic and reversible PTM, which can be removed by histone deacetylases. Here we investigated the role of lysine acetylation in the response of Arabidopsis leaves to 1 week of salt stress. A quantitative mass spectrometry analysis revealed an increase in lysine acetylation of several proteins from cytosol and plastids, which was accompanied by altered histone deacetylase activities in the salt-treated leaves. While activities of HDA14 and HDA15 were decreased upon salt stress, HDA5 showed a mild and HDA19 a strong increase in activity. Since HDA5 is a cytosolic-nuclear enzyme from the class II histone deacetylase family with yet unknown protein substrates, we performed a lysine acetylome analysis on hda5 mutants and characterized its substrate proteins. Next to histone H2B, the salt stress-responsive transcription factor GT2L and the dehydration-related protein ERD7 were identified as HDA5 substrates. In addition, in protein-protein interaction studies, HDA18 was discovered, among other interacting proteins, to work in a complex together with HDA5. Altogether, this study revealed the substrate proteins of HDA5 and identified new lysine acetylation sites which are hyperacetylated upon salt stress. The identification of specific histone deacetylase substrate proteins, apart from histones, will be important to unravel the acclimation response of Arabidopsis to salt stress and their role in plant physiology.
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Affiliation(s)
- Priyadarshini Tilak
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 7, DE-48149, Münster, Germany
| | - Florian Kotnik
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 7, DE-48149, Münster, Germany
| | - Guillaume Née
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 7, DE-48149, Münster, Germany
| | - Julian Seidel
- Interfaculty Institute of Biochemistry (IFIB), University of Tübingen, Auf der Morgenstelle 34, 72076, Tübingen, Germany
| | - Julia Sindlinger
- Interfaculty Institute of Biochemistry (IFIB), University of Tübingen, Auf der Morgenstelle 34, 72076, Tübingen, Germany
| | - Paulina Heinkow
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 7, DE-48149, Münster, Germany
| | - Jürgen Eirich
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 7, DE-48149, Münster, Germany
| | - Dirk Schwarzer
- Interfaculty Institute of Biochemistry (IFIB), University of Tübingen, Auf der Morgenstelle 34, 72076, Tübingen, Germany
| | - Iris Finkemeier
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 7, DE-48149, Münster, Germany
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16
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Zhang Z, Yang W, Chu Y, Yin X, Liang Y, Wang Q, Wang L, Han Z. AtHD2D, a plant-specific histone deacetylase involved in abscisic acid response and lateral root development. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7380-7400. [PMID: 36125085 DOI: 10.1093/jxb/erac381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 09/18/2022] [Indexed: 06/15/2023]
Abstract
In eukaryotes, histone acetylation levels directly regulate downstream gene expression. As a plant-specific histone deacetylase (HDAC), HD2D is involved in plant development and abiotic stress. However, the response of HD2D to drought stress and its interacting proteins, is still unclear. In this study, we analysed HD2D gene expression patterns in Arabidopsis, revealing that HD2D gene was highly expressed in roots and rosette leaves, but poorly expressed in other tissues such as stems, flowers, and young siliques. The HD2D gene expression was induced by d-mannitol. We investigated the responses to drought stress in the wild-type plant, HD2D overexpression lines, and hd2d mutants. HD2D-overexpressing lines showed abscisic acid (ABA) hypersensitivity and drought tolerance, and these phenotypes were not present in hd2d mutants. RNA-seq analysis revealed the transcriptome changes caused by HD2D under drought stress, and showed that HD2D responded to drought stress via the ABA signalling pathway. In addition, we demonstrated that CASEIN KINASE II (CKA4) directly interacted with HD2D. The phosphorylation of Ser residues on HD2D by CKA4 enhanced HD2D enzymatic activity. Furthermore, the phosphorylation of HD2D was shown to contribute to lateral root development and ABA sensing in Arabidopsis, but, these phenotypes could not be reproduced by the overexpression of Ser-phospho-null HD2D lines. Collectively, this study suggests that HD2D responded to drought stress by regulating the ABA signalling pathway, and the expression of drought stress-related genes. The regulatory mechanism of HD2D mediated by CKII phosphorylation provides new insights into the ABA response and lateral root development in Arabidopsis.
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Affiliation(s)
- Zhaochen Zhang
- College of Life Science, Northwest A & F University, Yangling, Shanxi 712100, China
| | - Weixia Yang
- College of Chemistry & Pharmacy, Northwest A & F University, Yangling, Shanxi 712100, China
| | - Yueyang Chu
- College of Life Science, Northwest A & F University, Yangling, Shanxi 712100, China
| | - Xiaotong Yin
- College of Life Science, Northwest A & F University, Yangling, Shanxi 712100, China
| | - Yueqi Liang
- College of Innovation and Experiment, Northwest A & F University, Yangling, Shanxi 712100, China
| | - Qiuping Wang
- College of Life Science, Northwest A & F University, Yangling, Shanxi 712100, China
| | - Lei Wang
- College of Life Science, Northwest A & F University, Yangling, Shanxi 712100, China
| | - Zhaofen Han
- College of Life Science, Northwest A & F University, Yangling, Shanxi 712100, China
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17
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Castro-Camba R, Sánchez C, Vidal N, Vielba JM. Plant Development and Crop Yield: The Role of Gibberellins. PLANTS (BASEL, SWITZERLAND) 2022; 11:2650. [PMID: 36235516 PMCID: PMC9571322 DOI: 10.3390/plants11192650] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 09/29/2022] [Accepted: 10/03/2022] [Indexed: 06/12/2023]
Abstract
Gibberellins have been classically related to a few key developmental processes, thus being essential for the accurate unfolding of plant genetic programs. After more than a century of research, over one hundred different gibberellins have been described. There is a continuously increasing interest in gibberellins research because of their relevant role in the so-called "Green Revolution", as well as their current and possible applications in crop improvement. The functions attributed to gibberellins have been traditionally restricted to the regulation of plant stature, seed germination, and flowering. Nonetheless, research in the last years has shown that these functions extend to many other relevant processes. In this review, the current knowledge on gibberellins homeostasis and mode of action is briefly outlined, while specific attention is focused on the many different responses in which gibberellins take part. Thus, those genes and proteins identified as being involved in the regulation of gibberellin responses in model and non-model species are highlighted. The present review aims to provide a comprehensive picture of the state-of-the-art perception of gibberellins molecular biology and its effects on plant development. This picture might be helpful to enhance our current understanding of gibberellins biology and provide the know-how for the development of more accurate research and breeding programs.
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Affiliation(s)
| | | | | | - Jesús Mª Vielba
- Misión Biológica de Galicia, Consejo Superior de Investigaciones Científicas, 15780 Santiago de Compostela, Spain
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18
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Corcoran ET, LeBlanc C, Huang YC, Arias Tsang M, Sarkiss A, Hu Y, Pedmale UV, Jacob Y. Systematic histone H4 replacement in Arabidopsis thaliana reveals a role for H4R17 in regulating flowering time. THE PLANT CELL 2022; 34:3611-3631. [PMID: 35879829 PMCID: PMC9516085 DOI: 10.1093/plcell/koac211] [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: 01/18/2022] [Accepted: 07/15/2022] [Indexed: 06/13/2023]
Abstract
Despite the broad array of roles for epigenetic mechanisms on regulating diverse processes in eukaryotes, no experimental system is currently available in plants for the direct assessment of histone function. In this work, we present the development of a genetic strategy in Arabidopsis (Arabidopsis thaliana) whereby modified histone H4 transgenes can completely replace the expression of endogenous histone H4 genes. Accordingly, we established a collection of plants expressing different H4 point mutants targeting residues that may be post-translationally modified in vivo. To demonstrate its utility, we screened this new H4 mutant collection to uncover substitutions in H4 that alter flowering time. We identified different mutations in the H4 tail (H4R17A) and the H4 globular domain (H4R36A, H4R39K, H4R39A, and H4K44A) that strongly accelerate the floral transition. Furthermore, we identified a conserved regulatory relationship between H4R17 and the ISWI chromatin remodeling complex in plants: As with other biological systems, H4R17 regulates nucleosome spacing via ISWI. Overall, this work provides a large set of H4 mutants to the plant epigenetics community that can be used to systematically assess histone H4 function in Arabidopsis and a roadmap to replicate this strategy for studying other histone proteins in plants.
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Affiliation(s)
- Emma Tung Corcoran
- Faculty of Arts and Sciences, Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Chantal LeBlanc
- Faculty of Arts and Sciences, Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Yi-Chun Huang
- Faculty of Arts and Sciences, Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Mia Arias Tsang
- Faculty of Arts and Sciences, Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Anthony Sarkiss
- Faculty of Arts and Sciences, Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Yuzhao Hu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Ullas V Pedmale
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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19
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Alves S, Braga Â, Parreira D, Alhinho AT, Silva H, Ramos MJN, Costa MMR, Morais‐Cecílio L. Genome-wide identification, phylogeny, and gene duplication of the epigenetic regulators in Fagaceae. PHYSIOLOGIA PLANTARUM 2022; 174:e13788. [PMID: 36169620 PMCID: PMC9828519 DOI: 10.1111/ppl.13788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 09/16/2022] [Accepted: 09/21/2022] [Indexed: 05/04/2023]
Abstract
Epigenetic regulators are proteins involved in controlling gene expression. Information about the epigenetic regulators within the Fagaceae, a relevant family of trees and shrubs of the northern hemisphere ecosystems, is scarce. With the intent to characterize these proteins in Fagaceae, we searched for orthologs of DNA methyltransferases (DNMTs) and demethylases (DDMEs) and Histone modifiers involved in acetylation (HATs), deacetylation (HDACs), methylation (HMTs), and demethylation (HDMTs) in Fagus, Quercus, and Castanea genera. Blast searches were performed in the available genomes, and freely available RNA-seq data were used to de novo assemble transcriptomes. We identified homologs of seven DNMTs, three DDMEs, six HATs, 11 HDACs, 32 HMTs, and 21 HDMTs proteins. Protein analysis showed that most of them have the putative characteristic domains found in these protein families, which suggests their conserved function. Additionally, to elucidate the evolutionary history of these genes within Fagaceae, paralogs were identified, and phylogenetic analyses were performed with DNA and histone modifiers. We detected duplication events in all species analyzed with higher frequency in Quercus and Castanea and discuss the evidence of transposable elements adjacent to paralogs and their involvement in gene duplication. The knowledge gathered from this work is a steppingstone to upcoming studies concerning epigenetic regulation in this economically important family of Fagaceae.
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Affiliation(s)
- Sofia Alves
- LEAF—Linking Landscape, Environment, Agriculture and FoodInstituto Superior de Agronomia, University of LisbonLisboaPortugal
| | - Ângelo Braga
- Instituto Superior de Agronomia, University of LisbonLisboaPortugal
| | - Denise Parreira
- Instituto Superior de Agronomia, University of LisbonLisboaPortugal
| | - Ana Teresa Alhinho
- Centre of Molecular and Environmental Biology (CBMA)University of MinhoBragaPortugal
| | - Helena Silva
- Centre of Molecular and Environmental Biology (CBMA)University of MinhoBragaPortugal
| | - Miguel Jesus Nunes Ramos
- LEAF—Linking Landscape, Environment, Agriculture and FoodInstituto Superior de Agronomia, University of LisbonLisboaPortugal
- Present address:
GenoMed, Diagnósticos de Medicina MolecularLisboaPortugal
| | | | - Leonor Morais‐Cecílio
- LEAF—Linking Landscape, Environment, Agriculture and FoodInstituto Superior de Agronomia, University of LisbonLisboaPortugal
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20
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Brooker R, Brown LK, George TS, Pakeman RJ, Palmer S, Ramsay L, Schöb C, Schurch N, Wilkinson MJ. Active and adaptive plasticity in a changing climate. TRENDS IN PLANT SCIENCE 2022; 27:717-728. [PMID: 35282996 DOI: 10.1016/j.tplants.2022.02.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 01/24/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Better understanding of the mechanistic basis of plant plasticity will enhance efforts to breed crops resilient to predicted climate change. However, complexity in plasticity's conceptualisation and measurement may hinder fruitful crossover of concepts between disciplines that would enable such advances. We argue active adaptive plasticity is particularly important in shaping the fitness of wild plants, representing the first line of a plant's defence to environmental change. Here, we define how this concept may be applied to crop breeding, suggest appropriate approaches to measure it in crops, and propose a refocussing on active adaptive plasticity to enhance crop resilience. We also discuss how the same concept may have wider utility, such as in ex situ plant conservation and reintroductions.
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Affiliation(s)
- Rob Brooker
- Department of Ecological Sciences, James Hutton Institute, Aberdeen, UK; Department of Ecological Sciences, James Hutton Institute, Dundee, UK.
| | - Lawrie K Brown
- Department of Ecological Sciences, James Hutton Institute, Dundee, UK
| | - Timothy S George
- Department of Ecological Sciences, James Hutton Institute, Dundee, UK
| | - Robin J Pakeman
- Department of Ecological Sciences, James Hutton Institute, Aberdeen, UK
| | - Sarah Palmer
- Institute of Biological, Environmental, and Rural Sciences (IBERS), Aberystwyth University, Plas Gogerddan, Aberystwyth, Ceredigion, UK
| | - Luke Ramsay
- Department of Ecological Sciences, James Hutton Institute, Dundee, UK
| | - Christian Schöb
- Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | | | - Mike J Wilkinson
- Institute of Biological, Environmental, and Rural Sciences (IBERS), Aberystwyth University, Plas Gogerddan, Aberystwyth, Ceredigion, UK
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21
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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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22
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Xu Y, Li Q, Yuan L, Huang Y, Hung FY, Wu K, Yang S. MSI1 and HDA6 function interdependently to control flowering time via chromatin modifications. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:831-843. [PMID: 34807487 DOI: 10.1111/tpj.15596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 10/26/2021] [Accepted: 11/16/2021] [Indexed: 05/14/2023]
Abstract
MULTICOPY SUPPRESSOR OF IRA1 (MSI1) is a conserved subunit of Polycomb Repressive Complex 2 (PRC2), which mediates gene silencing by histone H3 lysine 27 trimethylation (H3K27Me3). Here, we demonstrated that MSI1 interacts with the RPD3-like histone deacetylase HDA6 both in vitro and in vivo. MSI1 and HDA6 are involved in flowering and repress the expression of FLC, MAF4, and MAF5 by removing H3K9 acetylation but adding H3K27Me3. Chromatin immunoprecipitation analysis showed that HDA6 and MSI1 interdependently bind to the chromatin of FLC, MAF4, and MAF5. Furthermore, H3K9 deacetylation mediated by HDA6 is dependent on MSI1, while H3K27Me3 mediated by PRC2 containing MSI1 is also dependent on HDA6. Taken together, these data indicate that MSI1 and HDA6 act interdependently to repress the expression of FLC, MAF4, and MAF5 through histone modifications. Our findings reveal that the HDA6-MSI1 module mediates the interaction between histone H3 deacetylation and H3K27Me3 to repress gene expression involved in flowering time control.
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Affiliation(s)
- Yingchao Xu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049, China
| | - Qing Li
- Guangdong Provincial Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agricultural Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Lianyu Yuan
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- College of Food Science, Southwest University, Chongqing, 400715, China
| | - Yisui Huang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Fu-Yu Hung
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Keqiang Wu
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Songguang Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
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23
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Hirai R, Wang S, Demura T, Ohtani M. Histone Deacetylation Controls Xylem Vessel Cell Differentiation via Transcriptional Regulation of a Transcription Repressor Complex OFP1/4-MYB75-KNAT7-BLH6. FRONTIERS IN PLANT SCIENCE 2022; 12:825810. [PMID: 35154217 PMCID: PMC8829346 DOI: 10.3389/fpls.2021.825810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
Xylem vessels are indispensable tissues in vascular plants that transport water and minerals. The differentiation of xylem vessel cells is characterized by secondary cell wall deposition and programmed cell death. These processes are initiated by a specific set of transcription factors, called VASCULAR-RELATED NAC-DOMAIN (VND) family proteins, through the direct and/or indirectly induction of genes required for secondary cell wall deposition and programmed cell death. In this study, we explored novel regulatory factors for xylem vessel cell differentiation in Arabidopsis thaliana. We tested the effects of cellular stress inducers on VND7-induced differentiation of xylem vessel cells with the VND7-VP16-GR system, in which VND7 activity is post-translationally induced by dexamethasone application. We established that the histone deacetylase (HDAC) inhibitors trichostatin A (TSA) and sirtinol inhibited VND7-induced xylem vessel cell differentiation. The inhibitory effects of TSA and sirtinol treatment were detected only when they were added at the same time as the dexamethasone application, suggesting that TSA and sirtinol mainly influence the early stages of xylem vessel cell differentiation. Expression analysis revealed that these HDAC inhibitors downregulated VND7-downstream genes, including both direct and indirect targets of transcriptional activation. Notably, the HDAC inhibitors upregulated the transcript levels of negative regulators of xylem vessel cells, OVATE FAMILY PROTEIN1 (OFP1), OFP4, and MYB75, which are known to form a protein complex with BEL1-LIKE HOMEODOMAIN6 (BLH6) to repress gene transcription. The KDB system, another in vitro induction system of ectopic xylem vessel cells, demonstrated that TSA and sirtinol also inhibited ectopic formation of xylem vessel cells, and this inhibition was partially suppressed in knat7-1, bhl6-1, knat7-1 bhl6-1, and quintuple ofp1 ofp2 ofp3 ofp4 ofp5 mutants. Thus, the negative effects of HDAC inhibitors on xylem vessel cell differentiation are mediated, at least partly, by the abnormal upregulation of the transcriptional repressor complex OFP1/4-MYB75-KNAT7-BLH6. Collectively, our findings suggest that active regulation of histone deacetylation by HDACs is involved in xylem vessel cell differentiation via the OFP1/4-MYB75-KNAT7-BLH6 complex.
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Affiliation(s)
- Risaku Hirai
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Shumin Wang
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Taku Demura
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Center for Digital Green-Innovation, Nara Institute of Science and Technology, Ikoma, Japan
| | - Misato Ohtani
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
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24
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Zhao L, Li X, Chen W, Xu Z, Chen M, Wang H, Yu D. The emerging role of jasmonate in the control of flowering time. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:11-21. [PMID: 34599804 DOI: 10.1093/jxb/erab418] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/09/2021] [Indexed: 06/13/2023]
Abstract
Plants dynamically synchronize their flowering time with changes in the internal and external environments through a variety of signaling pathways to maximize fitness. In the last two decades, the major pathways associated with flowering, including the photoperiod, vernalization, age, autonomous, gibberellin, and ambient temperature pathways, have been extensively analyzed. In recent years, an increasing number of signals, such as sugar, thermosensory, stress, and certain hormones, have been shown to be involved in fine-tuning flowering time. Among these signals, the jasmonate signaling pathway has a function in the determination of flowering time that has not been systematically summarized. In this review, we present an overview of current knowledge of jasmonate control of flowering and discuss jasmonate crosstalk with other signals (such as gibberellin, defense, and touch) during floral transition.
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Affiliation(s)
- Lirong Zhao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xia Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
| | - Wanqin Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
| | - Zhiyu Xu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
| | - Mifen Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
| | - Houping Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
| | - Diqiu Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
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25
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Baile F, Merini W, Hidalgo I, Calonje M. EAR domain-containing transcription factors trigger PRC2-mediated chromatin marking in Arabidopsis. THE PLANT CELL 2021; 33:2701-2715. [PMID: 34003929 PMCID: PMC8408475 DOI: 10.1093/plcell/koab139] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 05/14/2021] [Indexed: 05/22/2023]
Abstract
Polycomb group (PcG) complexes ensure that every cell in an organism expresses the genes needed at a particular stage, time, or condition. However, it is still not fully understood how PcG complexes PcG-repressive complex 1 (PRC1) and PRC2 are recruited to target genes in plants. Recent findings in Arabidopsis thaliana support the notion that PRC2 recruitment is mediated by different transcription factors (TFs). However, it is unclear how all these TFs interact with PRC2 and whether they also recruit PRC1 activity. Here, by using a system to bind selected TFs to a synthetic promoter lacking the complexity of PcG target promoters in vivo, we show that while binding of the TF VIVIPAROUS1/ABSCISIC ACID-INSENSITIVE3-LIKE1 recapitulates PRC1 and PRC2 marking, the binding of other TFs only renders PRC2 marking. Interestingly, all these TFs contain an Ethylene-responsive element binding factor-associated Amphiphilic Repression (EAR) domain that triggers both HISTONE DEACETYLASE COMPLEX and PRC2 activities, connecting two different repressive mechanisms. Furthermore, we show that different TFs can have an additive effect on PRC2 activity, which may be required to maintain long-term repression of gene expression.
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Affiliation(s)
- Fernando Baile
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC-US), Avenida Américo Vespucio 49, 41092, Seville, Spain
| | - Wiam Merini
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC-US), Avenida Américo Vespucio 49, 41092, Seville, Spain
| | - Inés Hidalgo
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC-US), Avenida Américo Vespucio 49, 41092, Seville, Spain
| | - Myriam Calonje
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC-US), Avenida Américo Vespucio 49, 41092, Seville, Spain
- Author for correspondence:
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26
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Zhou X, He J, Velanis CN, Zhu Y, He Y, Tang K, Zhu M, Graser L, de Leau E, Wang X, Zhang L, Andy Tao W, Goodrich J, Zhu JK, Zhang CJ. A domesticated Harbinger transposase forms a complex with HDA6 and promotes histone H3 deacetylation at genes but not TEs in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1462-1474. [PMID: 33960113 DOI: 10.1111/jipb.13108] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 05/01/2021] [Indexed: 06/12/2023]
Abstract
In eukaryotes, histone acetylation is a major modification on histone N-terminal tails that is tightly connected to transcriptional activation. HDA6 is a histone deacetylase involved in the transcriptional regulation of genes and transposable elements (TEs) in Arabidopsis thaliana. HDA6 has been shown to participate in several complexes in plants, including a conserved SIN3 complex. Here, we uncover a novel protein complex containing HDA6, several Harbinger transposon-derived proteins (HHP1, SANT1, SANT2, SANT3, and SANT4), and MBD domain-containing proteins (MBD1, MBD2, and MBD4). We show that mutations of all four SANT genes in the sant-null mutant cause increased expression of the flowering repressors FLC, MAF4, and MAF5, resulting in a late flowering phenotype. Transcriptome deep sequencing reveals that while the SANT proteins and HDA6 regulate the expression of largely overlapping sets of genes, TE silencing is unaffected in sant-null mutants. Our global histone H3 acetylation profiling shows that SANT proteins and HDA6 modulate gene expression through deacetylation. Collectively, our findings suggest that Harbinger transposon-derived SANT domain-containing proteins are required for histone deacetylation and flowering time control in plants.
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Affiliation(s)
- Xishi Zhou
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Junna He
- College of Horticulture, China Agricultural University, Beijing, 100193, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette,, IN 47907, USA
| | - Christos N Velanis
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Daniel Rutherford Building, Max Born Crescent, Edinburgh, EH9 3BF, United Kingdom
| | - Yiwang Zhu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Yuhan He
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Kai Tang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette,, IN 47907, USA
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Mingku Zhu
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette,, IN 47907, USA
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Lisa Graser
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Daniel Rutherford Building, Max Born Crescent, Edinburgh, EH9 3BF, United Kingdom
- University of Applied Sciences Mannheim, Paul-Wittsack-Str. 10,, Mannheim, 68163, Germany
| | - Erica de Leau
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Daniel Rutherford Building, Max Born Crescent, Edinburgh, EH9 3BF, United Kingdom
| | - Xingang Wang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette,, IN 47907, USA
| | - Lingrui Zhang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette,, IN 47907, USA
| | - W Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette,, IN 47907, USA
| | - Justin Goodrich
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Daniel Rutherford Building, Max Born Crescent, Edinburgh, EH9 3BF, United Kingdom
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Cui-Jun Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
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27
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Zhou JX, Du P, Liu ZW, Feng C, Cai XW, He XJ. FVE promotes RNA-directed DNA methylation by facilitating the association of RNA polymerase V with chromatin. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:467-479. [PMID: 33942410 DOI: 10.1111/tpj.15302] [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: 03/09/2021] [Revised: 04/19/2021] [Accepted: 04/26/2021] [Indexed: 06/12/2023]
Abstract
Association of RNA polymerase V (Pol V) with chromatin is a critical step for RNA- directed DNA methylation (RdDM) in plants. Although the methylated DNA-binding proteins SUVH2 and SUVH9 and the chromatin remodeler-containing complex DRD1-DMS3-RDM1 are known to be required for the association of Pol V with chromatin, the molecular mechanisms underlying the association of Pol V with different chromatin environments remain largely unknown. Here we found that SUVH9 interacts with FVE, a homolog of the mammalian retinoblastoma-associated protein, which has been previously identified as a shared subunit of the histone deacetylase complex and the polycomb-type histone H3K27 trimethyltransferase complex. We demonstrated that FVE facilitates the association of Pol V with chromatin and thus contributes to DNA methylation at a substantial subset of RdDM target loci. Compared with FVE-independent RdDM target loci, FVE-dependent RdDM target loci are more abundant in gene-rich chromosome arms than in pericentromeric heterochromatin regions. This study contributes to our understanding of how the association of Pol V with chromatin is regulated in different chromatin environments.
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Affiliation(s)
- Jin-Xing Zhou
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Ping Du
- National Institute of Biological Sciences, Beijing, 102206, China
- College of Life Sciences, Beijing Normal University, Beijing, China
| | - Zhang-Wei Liu
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Chao Feng
- National Institute of Biological Sciences, Beijing, 102206, China
- College of Life Sciences, Beijing Normal University, Beijing, China
| | - Xue-Wei Cai
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 100084, China
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28
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Yruela I, Moreno-Yruela C, Olsen CA. Zn 2+-Dependent Histone Deacetylases in Plants: Structure and Evolution. TRENDS IN PLANT SCIENCE 2021; 26:741-757. [PMID: 33461867 DOI: 10.1016/j.tplants.2020.12.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/09/2020] [Accepted: 12/18/2020] [Indexed: 06/12/2023]
Abstract
Zn2+-dependent histone deacetylases are widely distributed in archaea, bacteria, and eukaryotes. Through deacetylation of histones and other biomolecules, these enzymes regulate mammalian gene expression, microtubule stability, and polyamine metabolism. In plants, they play essential roles in development and stress response, but little is known about their biochemistry. We provide here a holistic revision of plant histone deacetylase (HDA) phylogeny and translate recent lessons from other organisms. HDA evolution correlates with a gain of structural ductility/disorder, as observed for other proteins. We also highlight two recently identified Brassicaceae-specific HDAs, as well as unprecedented key mutations that would affect the catalytic activity of individual HDAs. This revised phylogeny will contextualize future studies and illuminate research on plant development and adaptation.
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Affiliation(s)
- Inmaculada Yruela
- Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas (CSIC), Avda. Montañana 1005, 50059 Zaragoza, Spain; Group of Biochemistry, Biophysics, and Computational Biology (GBsC), Institute for Biocomputation and Physics of Complex Systems (BIFI) and Universidad de Zaragoza (UNIZAR) Joint Unit to CSIC, Zaragoza, Spain.
| | - Carlos Moreno-Yruela
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
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29
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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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Kumar V, Thakur JK, Prasad M. Histone acetylation dynamics regulating plant development and stress responses. Cell Mol Life Sci 2021; 78:4467-4486. [PMID: 33638653 PMCID: PMC11072255 DOI: 10.1007/s00018-021-03794-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/21/2021] [Accepted: 02/18/2021] [Indexed: 12/17/2022]
Abstract
Crop productivity is directly dependent on the growth and development of plants and their adaptation during different environmental stresses. Histone acetylation is an epigenetic modification that regulates numerous genes essential for various biological processes, including development and stress responses. Here, we have mainly discussed the impact of histone acetylation dynamics on vegetative growth, flower development, fruit ripening, biotic and abiotic stress responses. Besides, we have also emphasized the information gaps which are obligatory to be examined for understanding the complete role of histone acetylation dynamics in plants. A comprehensive knowledge about the histone acetylation dynamics will ultimately help to improve stress resistance and reduce yield losses in different crops due to climate changes.
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Affiliation(s)
- Verandra Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Jitendra K Thakur
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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31
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Jing Y, Guo Q, Lin R. The SNL-HDA19 histone deacetylase complex antagonizes HY5 activity to repress photomorphogenesis in Arabidopsis. THE NEW PHYTOLOGIST 2021; 229:3221-3236. [PMID: 33245784 DOI: 10.1111/nph.17114] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/19/2020] [Indexed: 05/25/2023]
Abstract
Reprogramming of the transcriptome during photomorphogenesis requires dynamic changes in chromatin and distribution of histone modifications. However, the chromatin-based regulation of this process remains to be elucidated. Here, we identify the conserved SWI-INDEPENDENT3 LIKE (SNL)-HISTONE DEACETYLASE19 (HDA19) deacetylase complex, including HDA19 and SNL1-SNL6, as a negative regulator of the light signaling pathway. Light-repression of HDA19 and SNLs expression is mediated by photoreceptors. HDA19 and SNLs are required for histone deacetylation and chromatin inactivation of PHYA gene. We further examined the interaction between SNL-HDA19 complex and ELONGATED HYPOCOTYL5 (HY5), and their antagonistic regulation on the expressions of target genes. The HDA19 deacetylase complex is recruited by HY5 to the chromatin regions of two positive light signaling genes, HY5 and B-BOX CONTAINING PROTEIN 22 (BBX22), thereby reduces the accessibility and histone acetylation and represses their expression. HDA19, SNL1, and HY5 associate with the same regulatory regions of HY5 and BBX22, and HY5 binding to these loci is enhanced upon SNL-HDA19 dysfunction. Our study reveals a crucial role for the HDA19 deacetylase complex in light signaling and demonstrates that the functional interplay between chromatin regulators and transcription factors regulates photomorphogenetic responses to the changing light environments.
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Affiliation(s)
- Yanjun Jing
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Qiang Guo
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rongcheng Lin
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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32
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Hou J, Ren R, Xiao H, Chen Z, Yu J, Zhang H, Shi Q, Hou H, He S, Li L. Characteristic and evolution of HAT and HDAC genes in Gramineae genomes and their expression analysis under diverse stress in Oryza sativa. PLANTA 2021; 253:72. [PMID: 33606144 DOI: 10.1007/s00425-021-03589-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
Comprehensive characterization of Gramineae HATs and HDACs reveals their conservation and variation. The recent WGD/SD gene pairs in the CBP and RPD/HDA1 gene family may confer specific adaptive evolutionary changes. Expression of OsHAT and OsHDAC genes provides a new vision in different aspects of development and response to diverse stress. The histone acetylase (HAT) and histone deacetylase (HDAC) have been proven to be tightly linked to play a crucial role in plant growth, development and response to abiotic stress by regulating histone acetylation levels. However, the evolutionary dynamics and functional differentiation of HATs and HDACs in Gramineae remain largely unclear. In the present study, we identified 37 HAT genes and 110 HDAC genes in seven Gramineae genomes by a detailed analysis. Phylogenetic trees of these HAT and HDAC proteins were constructed to illustrate evolutionary relationship in Gramineae. Gene structure, protein property and protein motif composition illustrated the conservation and variation of HATs and HDACs in Gramineae. Gene duplication analysis suggested that recent whole genome duplication (WGD)/segmental duplication (SD) events contributed to the diversification of the CBP and RPD3/HDA1 gene family in Gramineae. Furthermore, promoter cis-element prediction indicated that OsHATs and OsHDACs were likely functional proteins and involved in various signaling pathways. Expression analysis by RNA-seq data showed that all OsHAT and OsHDAC genes were expressed in different tissues or development stages, revealing that they were ubiquitously expressed. In addition, we found that their expression patterns were altered in response to cold, drought, salt, light, abscisic acid (ABA), and indole-3-acetic acid (IAA) treatments. These findings provide the basis for further identification of candidate OsHAT and OsHDAC genes that may be utilized in regulating growth and development and improving crop tolerance to abiotic stress.
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Affiliation(s)
- Jiaqi Hou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Ruifei Ren
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Huangzhuo Xiao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhenfei Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jinfu Yu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Haorui Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Qipeng Shi
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Haoli Hou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Shibin He
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China.
| | - Lijia Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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Liu C, Zhang Q, Zhu H, Cai C, Li S. Characterization of Mungbean CONSTANS-LIKE Genes and Functional Analysis of CONSTANS-LIKE 2 in the Regulation of Flowering Time in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2021; 12:608603. [PMID: 33613600 PMCID: PMC7890258 DOI: 10.3389/fpls.2021.608603] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 01/11/2021] [Indexed: 05/05/2023]
Abstract
CONSTANS-LIKE (COL) genes play important roles in the regulation of plant growth and development, and they have been analyzed in many plant species. However, few studies have examined COL genes in mungbean (Vigna radiata). In this study, we identified and characterized 31 mungbean genes whose proteins contained B-Box domains. Fourteen were designated as VrCOL genes and were distributed on 7 of the 11 mungbean chromosomes. Based on their phylogenetic relationships, VrCOLs were clustered into three groups (I, II, and III), which contained 4, 6, and 4 members, respectively. The gene structures and conserved motifs of the VrCOL genes were analyzed, and two duplicated gene pairs, VrCOL1/VrCOL2 and VrCOL8/VrCOL9, were identified. A total of 82 cis-acting elements were found in the VrCOL promoter regions, and the numbers and types of cis-acting elements in each VrCOL promoter region differed. As a result, the expression patterns of VrCOLs varied in different tissues and throughout the day under long-day and short-day conditions. Among these VrCOL genes, VrCOL2 showed a close phylogenetic relationship with Arabidopsis thaliana CO and displayed daily oscillations in expression under short-day conditions but not long-day conditions. In addition, overexpression of VrCOL2 accelerated flowering in Arabidopsis under short-day conditions by affecting the expression of the flowering time genes AtFT and AtTSF. Our study lays the foundation for further investigation of VrCOL gene functions.
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Affiliation(s)
- Chenyang Liu
- Key Laboratory of Plant Biotechnology in Universities of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Qianqian Zhang
- Key Laboratory of Plant Biotechnology in Universities of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Hong Zhu
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Chunmei Cai
- Key Laboratory of Plant Biotechnology in Universities of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Shuai Li
- Key Laboratory of Plant Biotechnology in Universities of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
- *Correspondence: Shuai Li,
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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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35
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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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36
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Jing Y, Lin R. Transcriptional regulatory network of the light signaling pathways. THE NEW PHYTOLOGIST 2020; 227:683-697. [PMID: 32289880 DOI: 10.1111/nph.16602] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 03/19/2020] [Indexed: 05/18/2023]
Abstract
The developmental program by which plants respond is tightly controlled by a complex cascade in which photoreceptors perceive and transduce the light signals that drive signaling processes and direct the transcriptional reprogramming, yielding specific cellular responses. The molecular mechanisms involved in the transcriptional regulation include light-regulated nuclear localization (the phytochromes and UVR8) and nuclear accumulation (the cryptochrome, cry2) of photoreceptors. This regulatory cascade also includes master regulatory transcription factors (TFs) that bridge photoreceptor activation with chromatin remodeling and regulate the expression of numerous light-responsive genes. Light signaling-related TFs often function as signal convergence points in concert with TFs in other signaling pathways to integrate complex endogenous and environmental cues that help the plant adapt to the surrounding environment. Increasing evidence suggests that chromatin modifications play a critical role in regulating light-responsive gene expression and provide an additional layer of light signaling regulation. Here, we provide an overview of our current knowledge of the transcriptional regulatory network involved in the light response, particularly the roles of TFs and chromatin in regulating light-responsive gene expression.
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Affiliation(s)
- Yanjun Jing
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Rongcheng Lin
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Beijing, 100093, China
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37
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Leng X, Thomas Q, Rasmussen SH, Marquardt S. A G(enomic)P(ositioning)S(ystem) for Plant RNAPII Transcription. TRENDS IN PLANT SCIENCE 2020; 25:744-764. [PMID: 32673579 DOI: 10.1016/j.tplants.2020.03.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/24/2020] [Accepted: 03/10/2020] [Indexed: 06/11/2023]
Abstract
Post-translational modifications (PTMs) of histone residues shape the landscape of gene expression by modulating the dynamic process of RNA polymerase II (RNAPII) transcription. The contribution of particular histone modifications to the definition of distinct RNAPII transcription stages remains poorly characterized in plants. Chromatin immunoprecipitation combined with next-generation sequencing (ChIP-seq) resolves the genomic distribution of histone modifications. Here, we review histone PTM ChIP-seq data in Arabidopsis thaliana and find support for a Genomic Positioning System (GPS) that guides RNAPII transcription. We review the roles of histone PTM 'readers', 'writers', and 'erasers', with a focus on the regulation of gene expression and biological functions in plants. The distinct functions of RNAPII transcription during the plant transcription cycle may rely, in part, on the characteristic histone PTM profiles that distinguish transcription stages.
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Affiliation(s)
- Xueyuan Leng
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Bülowsvej 34, 1870 Frederiksberg C, Denmark
| | - Quentin Thomas
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Bülowsvej 34, 1870 Frederiksberg C, Denmark
| | - Simon Horskjær Rasmussen
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Bülowsvej 34, 1870 Frederiksberg C, Denmark
| | - Sebastian Marquardt
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Bülowsvej 34, 1870 Frederiksberg C, Denmark.
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38
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Cronk Q, Soolanayakanahally R, Bräutigam K. Gene expression trajectories during male and female reproductive development in balsam poplar (Populus balsamifera L.). Sci Rep 2020; 10:8413. [PMID: 32439903 PMCID: PMC7242425 DOI: 10.1038/s41598-020-64938-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 04/24/2020] [Indexed: 12/19/2022] Open
Abstract
Plant reproductive development from the first appearance of reproductively committed axes through to floral maturation requires massive and rapid remarshalling of gene expression. In dioecious species such as poplar this is further complicated by divergent male and female developmental programs. We used seven time points in male and female balsam poplar (Populus balsamifera L.) buds and catkins representing the full annual flowering cycle, to elucidate the effects of time and sex on gene expression during reproductive development. Time (developmental stage) is dominant in patterning gene expression with the effect of sex nested within this. Here, we find (1) evidence for five successive waves of alterations to the chromatin landscape which may be important in setting the overall reproductive trajectory, regardless of sex. (2) Each individual developmental stage is further characterized by marked sex-differential gene expression. (3) Consistent sexually differentiated gene expression regardless of developmental stage reveal candidates for high-level regulators of sex and include the female-specific poplar ARR17 homologue. There is also consistent male-biased expression of the MADS-box genes PISTILLATA and APETALA3. Our work provides insights into expression trajectories shaping reproductive development, its potential underlying mechanisms, and sex-specific translation of the genome information into reproductive structures in balsam poplar.
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Affiliation(s)
- Quentin Cronk
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
| | - Raju Soolanayakanahally
- Indian Head Research Farm, Agriculture and Agri-Food Canada, Indian Head, SK, S0G 2K0, Canada
| | - Katharina Bräutigam
- Department of Biology, University of Toronto, Mississauga, ON, L5L 1C6, Canada.
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Liu Z, Lei X, Wang P, Wang Y, Lv J, Li X, Gao C. Overexpression of ThSAP30BP from Tamarix hispida improves salt tolerance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 146:124-132. [PMID: 31743857 DOI: 10.1016/j.plaphy.2019.11.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 11/12/2019] [Indexed: 06/10/2023]
Abstract
Histone deacetylases (HDACs) play an important regulatory role in plant response to biotic and abiotic stresses. They improve plant stress resistance by increasing the degree of histone acetylation associated with stress-responsive genes. SAP30BP, a human transcriptional regulatory protein, can increase histone deacetylase activity by regulating the deacetylation levels of lysines 9 and 14 in histone H3. In this study, a ThSAP30BP gene was cloned and characterized from Tamarix hispida (a kind of woody halophyte). The expression patterns of ThSAP30BP under different abiotic stresses and hormone treatments were detected by qRT-PCR. The results showed that ThSAP30BP was significantly upregulated at most time points under various stress treatments, suggesting that ThSAP30BP may be related to the abiotic stress response of T. hispida. To further analyze the salt stress resistance function of the ThSAP30BP gene, the plant overexpression vector pROKII-ThSAP30BP was instantaneously constructed and transformed into T. hispida. Meanwhile, the empty vector pROKII was also transformed as a control. The activities of SOD and POD, the contents of H2O2 and MDA, the relative conductance and the staining of NBT, DAB and Evans blue were analyzed and compared under salt stress. The results showed that the overexpression of ThSAP30BP in T. hispida reduced the accumulation of ROS in plants and the cell death rate under salt stress. These results suggested that ThSAP30BP may play an important physiological role in salt tolerance of T. hispida.
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Affiliation(s)
- Zhongyuan Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Xiaojin Lei
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Peilong Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Yuanyuan Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Jiaxin Lv
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Xinpin Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Caiqiu Gao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China.
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40
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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: 50] [Impact Index Per Article: 10.0] [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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41
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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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Huang F, Yuan W, Tian S, Zheng Q, He Y. SIN3 LIKE genes mediate long-day induction of flowering but inhibit the floral transition in short days through histone deacetylation in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:101-113. [PMID: 31168864 DOI: 10.1111/tpj.14430] [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: 01/07/2019] [Revised: 05/15/2019] [Accepted: 05/20/2019] [Indexed: 05/27/2023]
Abstract
Day length or photoperiod changes are crucial for plants to align the timing of the floral transition with seasonal changes. Through the photoperiod pathway, day length changes induce the expression of the florigenic FLOWERING LOCUS T (FT) to promote flowering. In the facultative long days (LDs) plant Arabidopsis thaliana, LD signals induce flowering, whereas short days (SDs) inhibit flowering. Here, we show that in Arabidopsis SIN3 LIKE (SNL) family genes, encoding a scaffold protein for assembly of histone deacetylase complexes, directly repress the expression of an FT activator and three FT repressors to regulate the transition to flowering in SDs and LDs, respectively. Under inductive LDs, SNLs including SIN3 LIKE 1 (SNL1) to SNL5, function in partial redundancy to repress the expression of three AP2 family transcription factors that repress FT expression, and therefore mediate LD induction of FT expression and promote the transition to flowering. In contrast, under non-inductive SDs SNLs act to inhibit the floral transition, partly through direct repression of a MADS box transcriptional factor that promotes FT expression. Therefore, our results reveal that SNLs, through histone deacetylation, play a dual role for the control of flowering in the LD plant Arabidopsis: inhibiting flowering when the day length is shorter and promoting the floral transition when days become longer than a threshold length.
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Affiliation(s)
- Fei Huang
- Shanghai Center for Plant Stress Biology & National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenya Yuan
- Shanghai Center for Plant Stress Biology & National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai, 201602, China
| | - Shu Tian
- Shanghai Center for Plant Stress Biology & National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qijie Zheng
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Yuehui He
- Shanghai Center for Plant Stress Biology & National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai, 201602, China
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