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Du X, Gao Y, Zhang H, Xu X, Li Y, Zhao L, Luo M, Wang H. HDA6 modulates Arabidopsis pavement cell morphogenesis through epigenetic suppression of ROP6 GTPase expression and signaling. THE NEW PHYTOLOGIST 2024; 241:2523-2539. [PMID: 38214469 DOI: 10.1111/nph.19532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 01/01/2024] [Indexed: 01/13/2024]
Abstract
The transcriptional regulation of Rho-related GTPase from plants (ROPs), which determine cell polarity formation and maintenance during plant development, still remains enigmatic. In this study, we elucidated the epigenetic mechanism of histone deacetylase HDA6 in transcriptional repression of ROP6 and its impact on cell polarity and morphogenesis in Arabidopsis leaf epidermal pavement cells (PCs). We found that the hda6 mutant axe1-4 exhibited impaired jigsaw-shaped PCs and convoluted leaves. This correlated with disruptions in the spatial organizations of cortical microtubules and filamentous actin, which is integral to PC indentation and lobe formation. Further transcriptional analyses and chromatin immunoprecipitation assay revealed that HDA6 specifically represses ROP6 expression through histone H3K9K14 deacetylation. Importantly, overexpression of dominant negative-rop6 in axe1-4 restored interdigitated cell morphology. Our study unveils HDA6 as a key regulator in Arabidopsis PC morphogenesis through epigenetic suppression of ROP6. It reveals the pivotal role of HDA6 in the transcriptional regulation of ROP6 and provides compelling evidence for the functional interplay between histone deacetylation and ROP6-mediated cytoskeletal arrangement in the development of interdigitated PCs.
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Affiliation(s)
- Xiaojuan Du
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yingmiao Gao
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hao Zhang
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaoyu Xu
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Ying Li
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Lifeng Zhao
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Ming Luo
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hao Wang
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
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An C, Deng L, Zhai H, You Y, Wu F, Zhai Q, Goossens A, Li C. Regulation of jasmonate signaling by reversible acetylation of TOPLESS in Arabidopsis. MOLECULAR PLANT 2022; 15:1329-1346. [PMID: 35780296 DOI: 10.1016/j.molp.2022.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 04/28/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
The plant hormone jasmonate (JA) regulates plant immunity and adaptive growth by orchestrating a genome-wide transcriptional program. Key regulators of JA-responsive gene expression include the master transcription factor MYC2, which is repressed by the conserved Groucho/Tup1-like corepressor TOPLESS (TPL) in the resting state. However, the mechanisms underlying TPL-mediated transcriptional repression of MYC2 activity and hormone-dependent switching between repression and de-repression remain enigmatic. Here, we report the regulation of TPL activity and JA signaling by reversible acetylation of TPL. We found that the histone acetyltransferase GCN5 could mediate TPL acetylation, which enhances its interaction with the NOVEL-INTERACTOR-OF-JAZ (NINJA) adaptor and promotes its recruitment to MYC2 target promoters, facilitating transcriptional repression. Conversely, TPL deacetylation by the histone deacetylase HDA6 weakens TPL-NINJA interaction and inhibits TPL recruitment to MYC2 target promoters, facilitating transcriptional activation. In the resting state, the opposing activities of GCN5 and HDA6 maintain TPL acetylation homeostasis, promoting transcriptional repression activity of TPL. In response to JA elicitation, HDA6 expression is transiently induced, resulted in decreased TPL acetylation and repressor activity, thereby transcriptional activation of MYC2 target genes. Thus, the GCN5-TPL-HDA6 module maintains the homeostasis of acetylated TPL, thereby determining the transcriptional state of JA-responsive genes. Our findings uncovered a mechanism by which the TPL corepressor activity in JA signaling is actively tuned in a rapid and reversible manner.
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Affiliation(s)
- Chunpeng An
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Deng
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huawei Zhai
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, China
| | - Yanrong You
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangming Wu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingzhe Zhai
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Chuanyou Li
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, China.
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Su L, Liu S, Liu X, Zhang B, Li M, Zeng L, Li L. Transcriptome profiling reveals histone deacetylase 1 gene overexpression improves flavonoid, isoflavonoid, and phenylpropanoid metabolism in Arachis hypogaea hairy roots. PeerJ 2021; 9:e10976. [PMID: 33777524 PMCID: PMC7977374 DOI: 10.7717/peerj.10976] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 01/29/2021] [Indexed: 11/20/2022] Open
Abstract
Background The peanut (Arachis hypogaea) is a crop plant of high economic importance, but the epigenetic regulation of its root growth and development has not received sufficient attention. Research on Arabidopsis thaliana has shown that histone deacetylases (HDACs) are involved in cell growth, cell differentiation, and stress response. Few studies have focused on the role of HDACs in the root development of other plants, particularly crop plants. In earlier studies, we found large accumulations of A. hypogaea histone deacetylase 1 (AhHDA1) mRNA in peanut roots. However, we did not explore the role of AhHDA1 in peanut root development. Methods In this paper, we investigated the role of the peanut AhHDA1 gene and focused on the effect of altered AhHDA1 expression in hairy roots at both the phenotypic and transcriptional levels. We analyzed the transformation of A. hypogaea hairy roots using Agrobacterium rhizogenes and RNA sequencing to identify differentially expressed genes that were assigned to specific metabolic pathways. Transgenic hairy roots were used as experimental material to analyze the downstream genes expression and histone acetylation levels. To thoroughly understand AhHDA1 function, we also simultaneously screened the AhHDA1-interacting proteins using a yeast two-hybrid system. Results AhHDA1-overexpressing hairy roots were growth-retarded after 20 d in vitro cultivation, and they had a greater accumulation of superoxide anions and hydrogen peroxide than the control and RNAi groups. AhHDA1 overexpression in hairy roots accelerated flux through various secondary synthetic metabolic pathways, as well as inhibited the primary metabolism process. AhHDA1 overexpression also caused a significant upregulation of genes encoding the critical enzyme chalcone synthase (Araip.B8TJ0, CHS) in the flavonoid biosynthesis pathway, hydroxyisoflavanone synthase (Araip.0P3RJ) in the isoflavonoid biosynthesis pathway, and caffeoyl-CoA O-methyltransferase (Aradu.M62BY, CCoAOMT) in the phenylpropanoid biosynthesis pathway. In contrast, ferredoxin 1 (Araip.327XS), the polypeptide of the oxygen-evolving complex of photosystem II (Araip.N6ZTJ), and ribulose bisphosphate carboxylase (Aradu.5IY98) in the photosynthetic pathway were significantly downregulated by AhHDA1 overexpression. The expression levels of these genes had a positive correlation with histone acetylation levels. Conclusion Our results revealed that the relationship between altered gene metabolism activities and AhHDA1 overexpression was mainly reflected in flavonoid, isoflavonoid, and phenylpropanoid metabolism. AhHDA1 overexpression retarded the growth of transgenic hairy roots and may be associated with cell metabolism status. Future studies should focus on the function of AhHDA1-interacting proteins and their effect on root development.
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Affiliation(s)
- Liangchen Su
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, South China Normal University, Guangzhou, Guangdong, China.,Department of Bioengineering, Zunyi Medical University, Zhuhai, Guangdong, China
| | - Shuai Liu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, South China Normal University, Guangzhou, Guangdong, China
| | - Xing Liu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, South China Normal University, Guangzhou, Guangdong, China
| | - Baihong Zhang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, South China Normal University, Guangzhou, Guangdong, China
| | - Meijuan Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, South China Normal University, Guangzhou, Guangdong, China
| | - Lidan Zeng
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, South China Normal University, Guangzhou, Guangdong, China
| | - Ling Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, South China Normal University, Guangzhou, Guangdong, China
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Hung FY, Chen JH, Feng YR, Lai YC, Yang S, Wu K. Arabidopsis JMJ29 is involved in trichome development by regulating the core trichome initiation gene GLABRA3. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1735-1743. [PMID: 32445267 DOI: 10.1111/tpj.14858] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 05/07/2020] [Accepted: 05/18/2020] [Indexed: 06/11/2023]
Abstract
Plant trichomes are large single cells that are organized in a regular pattern and play multiple biological functions. In Arabidopsis, trichome development is mainly governed by the core trichome initiation regulators, including the R2R3 type MYB transcript factor GLABRA 1 (GL1), bHLH transcript factors GLABRA 3/ENHANCER OF GLABRA 3 (GL3/EGL3), and the WD-40 repeat protein TRANSPARENT TESTA GLABRA 1 (TTG1), as well as the downstream trichome regulator GLABRA 2 (GL2). GL1, GL3/EGL3, and TTG1 can form a trimeric activation complex to activate GL2, which is required for the trichome initiation and maintenance during cell differentiation. Arabidopsis JMJ29 is a JmjC domain-containing histone demethylase belonging to the JHDM2/KDM3 group. Members of the JHDM2/KDM3 group histone demethylases are mainly responsible for the H3K9me1/2 demethylation. In the present study, we found that the trichome density on leaves and inflorescence stems is significantly decreased in jmj29 mutants. The expression of the core trichome regulators GL1, GL2, and GL3 is decreased in jmj29 mutants as well. Furthermore, JMJ29 can directly target GL3 and remove H3K9me2 on the GL3 locus. Collectively, we found that Arabidopsis JMJ29 is involved in trichome development by directly regulating GL3 expression. These results provide further insights into the molecular mechanism of epigenetic regulation in Arabidopsis trichome development.
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Affiliation(s)
- Fu-Yu Hung
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Jian-Hao Chen
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Yun-Ru Feng
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - You-Cheng Lai
- 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
| | - Keqiang Wu
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
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Peng Z, Tian J, Luo R, Kang Y, Lu Y, Hu Y, Liu N, Zhang J, Cheng H, Niu S, Zhang J, Yao Y. MiR399d and epigenetic modification comodulate anthocyanin accumulation in Malus leaves suffering from phosphorus deficiency. PLANT, CELL & ENVIRONMENT 2020; 43:1148-1159. [PMID: 31833568 DOI: 10.1111/pce.13697] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 11/17/2019] [Accepted: 12/03/2019] [Indexed: 05/14/2023]
Abstract
Inorganic phosphorus (Pi) deficiency induces anthocyanin accumulation in the leaves of some plant species; however, the molecular mechanisms underlying this phenomenon have not been well characterized. Here, we showed that microRNA399d (miR399d), high-affinity Pi transporter McPHT1;4, and McMYB10 are strongly induced in Malus leaves suffering from Pi deficiency. By culturing explants of transiently transformed plants in MS medium under conditions of Pi sufficiency and Pi deficiency, miR399d and McPHT1;4 were shown to play essential roles in the response to Pi deficiency and to play positive roles in the regulation of anthocyanin biosynthesis. Silencing of McHDA6 expression and treatment with the inhibitor trichostatin A suggested that the low expression of McHDA6 simultaneously reduced the transcription of McMET1 and decreased the methylation level of the McMYB10 promoter; however, the expression of McMYB10 and anthocyanin content were increased. Bimolecular fluorescence complementation and yeast two-hybrid assays revealed that McHDA6 binds directly to McMET1 through its BAH2 and DNMT1-RFD domains. Based on the results of our study, we propose a mechanism for the molecular regulation of anthocyanin biosynthesis, namely, the miR399d and epigenetic modification comodulation model, to explain the phenomenon in which leaves turn red under conditions of Pi deficiency.
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Affiliation(s)
- Zhen Peng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Ji Tian
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Rongli Luo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Yanhui Kang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Yanfen Lu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Yujing Hu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Na Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Jie Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Hao Cheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Shuqing Niu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Jie Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Yuncong Yao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
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Singh S, Singh A, Singh A, Yadav S, Bajaj I, Kumar S, Jain A, Sarkar AK. Role of chromatin modification and remodeling in stem cell regulation and meristem maintenance in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:778-792. [PMID: 31793642 DOI: 10.1093/jxb/erz459] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 09/10/2019] [Indexed: 06/10/2023]
Abstract
In higher plants, pluripotent stem cells reside in the specialized microenvironment called stem cell niches (SCNs) harbored at the shoot apical meristem (SAM) and root apical meristem (RAM), which give rise to the aerial and underground parts of a plant, respectively. The model plant Arabidopsis thaliana (Arabidopsis) has been extensively studied to decipher the intricate regulatory mechanisms involving some key transcriptions factors and phytohormones that play pivotal roles in stem cell homeostasis, meristem maintenance, and organ formation. However, there is increasing evidence to show the epigenetic regulation of the chromatin architecture, gene expression exerting an influence on an innate balance between the self-renewal of stem cells, and differentiation of the progeny cells to a specific tissue type or organ. Post-translational histone modifications, ATP-dependent chromatin remodeling, and chromatin assembly/disassembly are some of the key features involved in the modulation of chromatin architecture. Here, we discuss the major epigenetic regulators and illustrate their roles in the regulation of stem cell activity, meristem maintenance, and related organ patterning in Arabidopsis.
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Affiliation(s)
- Sharmila Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Alka Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Archita Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Sandeep Yadav
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Ishita Bajaj
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Shailendra Kumar
- Amity School of Architecture and Planning, Amity University, Kant Kalwar, Rajasthan, India
| | - Ajay Jain
- Amity Institute of Biotechnology, Amity University, Kant Kalwar, Rajasthan, India
| | - Ananda K Sarkar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
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Chen S, Wang S. GLABRA2, A Common Regulator for Epidermal Cell Fate Determination and Anthocyanin Biosynthesis in Arabidopsis. Int J Mol Sci 2019; 20:ijms20204997. [PMID: 31601032 PMCID: PMC6834157 DOI: 10.3390/ijms20204997] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 09/24/2019] [Accepted: 09/30/2019] [Indexed: 01/18/2023] Open
Abstract
Epidermal cell fate determination—including trichome initiation, root hair formation, and flavonoid and mucilage biosynthesis in Arabidopsis (Arabidopsis thaliana)—are controlled by a similar transcriptional regulatory network. In the network, it has been proposed that the MYB-bHLH-WD40 (MBW) activator complexes formed by an R2R3 MYB transcription factor, a bHLH transcription factor and the WD40-repeat protein TRANSPARENT TESTA GLABRA1 (TTG1) regulate the expression of downstream genes required for cell fate determination, flavonoid or mucilage biosynthesis, respectively. In epidermal cell fate determination and mucilage biosynthesis, the MBW activator complexes activate the expression of GLABRA2 (GL2). GL2 is a homeodomain transcription factor that promotes trichome initiation in shoots, mucilage biosynthesis in seeds, and inhibits root hair formation in roots. The MBW activator complexes also activate several R3 MYB genes. The R3 MYB proteins, in turn, competing with the R2R3 MYBs for binding bHLH transcription factors, therefore inhibiting the formation of the MBW activator complexes, lead to the inhibition of trichome initiation in shoots, and promotion of root hair formation in roots. In flavonoid biosynthesis, the MBW activator complexes activate the expression of the late biosynthesis genes in the flavonoid pathway, resulting in the production of anthocyanins or proanthocyanidins. Research progress in recent years suggests that the transcriptional regulatory network that controls epidermal cell fate determination and anthocyanin biosynthesis in Arabidopsis is far more complicated than previously thought. In particular, more regulators of GL2 have been identified, and GL2 has been shown to be involved in the regulation of anthocyanin biosynthesis. This review focuses on the research progress on the regulation of GL2 expression, and the roles of GL2 in the regulation of epidermal cell fate determination and anthocyanin biosynthesis in Arabidopsis.
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Affiliation(s)
- Siyu Chen
- College of Life Science, Linyi University, Linyi 276005, China.
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, China.
| | - Shucai Wang
- College of Life Science, Linyi University, Linyi 276005, China.
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, China.
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Chen WQ, Drapek C, Li DX, Xu ZH, Benfey PN, Bai SN. Histone Deacetylase HDA19 Affects Root Cortical Cell Fate by Interacting with SCARECROW. PLANT PHYSIOLOGY 2019; 180:276-288. [PMID: 30737268 PMCID: PMC6501111 DOI: 10.1104/pp.19.00056] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 01/27/2019] [Indexed: 05/27/2023]
Abstract
The Arabidopsis (Arabidopsis thaliana) root epidermis is a simple model for investigating cell fate specification and pattern formation. In addition to regulatory networks consisting of transcription factors, histone deacetylases are also involved in the formation of cellular patterns. Here, we report thatHistone Deacetylase19 (HDA19) affects the root epidermal cellular pattern through regulation of cortical cell fate by interacting with SCARECROW (SCR). HDA19 binds to the DNA sequence upstream of SCR, as well as to those of several of SCR's target genes, and regulates their expression. Mutant lines of several SCR target genes show impaired patterns of epidermal differentiation and cortical cell division, similar to that of hda19 This work presents HDA19 and SCR as two further players in the regulation of cortical and epidermal cell specification and describes an additional function for SCR.
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Affiliation(s)
- Wen-Qian Chen
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Colleen Drapek
- Department of Biology and Howard Hughes Medical Institute, Duke University, Durham, North Carolina 27708
| | - Dong-Xu Li
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Zhi-Hong Xu
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Philip N Benfey
- Department of Biology and Howard Hughes Medical Institute, Duke University, Durham, North Carolina 27708
| | - Shu-Nong Bai
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
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Liu S, Yu F, Yang Z, Wang T, Xiong H, Chang C, Yu W, Li N. Establishment of Dimethyl Labeling-based Quantitative Acetylproteomics in Arabidopsis. Mol Cell Proteomics 2018; 17:1010-1027. [PMID: 29440448 DOI: 10.1074/mcp.ra117.000530] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/18/2018] [Indexed: 12/19/2022] Open
Abstract
Protein acetylation, one of many types of post-translational modifications (PTMs), is involved in a variety of biological and cellular processes. In the present study, we applied both CsCl density gradient (CDG) centrifugation-based protein fractionation and a dimethyl-labeling-based 4C quantitative PTM proteomics workflow in the study of dynamic acetylproteomic changes in Arabidopsis. This workflow integrates the dimethyl chemical labeling with chromatography-based acetylpeptide separation and enrichment followed by mass spectrometry (MS) analysis, the extracted ion chromatogram (XIC) quantitation-based computational analysis of mass spectrometry data to measure dynamic changes of acetylpeptide level using an in-house software program, named Stable isotope-based Quantitation-Dimethyl labeling (SQUA-D), and finally the confirmation of ethylene hormone-regulated acetylation using immunoblot analysis. Eventually, using this proteomic approach, 7456 unambiguous acetylation sites were found from 2638 different acetylproteins, and 5250 acetylation sites, including 5233 sites on lysine side chain and 17 sites on protein N termini, were identified repetitively. Out of these repetitively discovered acetylation sites, 4228 sites on lysine side chain (i.e. 80.5%) are novel. These acetylproteins are exemplified by the histone superfamily, ribosomal and heat shock proteins, and proteins related to stress/stimulus responses and energy metabolism. The novel acetylproteins enriched by the CDG centrifugation fractionation contain many cellular trafficking proteins, membrane-bound receptors, and receptor-like kinases, which are mostly involved in brassinosteroid, light, gravity, and development signaling. In addition, we identified 12 highly conserved acetylation site motifs within histones, P-glycoproteins, actin depolymerizing factors, ATPases, transcription factors, and receptor-like kinases. Using SQUA-D software, we have quantified 33 ethylene hormone-enhanced and 31 hormone-suppressed acetylpeptide groups or called unique PTM peptide arrays (UPAs) that share the identical unique PTM site pattern (UPSP). This CDG centrifugation protein fractionation in combination with dimethyl labeling-based quantitative PTM proteomics, and SQUA-D may be applied in the quantitation of any PTM proteins in any model eukaryotes and agricultural crops as well as tissue samples of animals and human beings.
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Affiliation(s)
- Shichang Liu
- From the ‡Division of Life Science, Energy Institute, Institute for the Environment, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Fengchao Yu
- §Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China.,¶Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Zhu Yang
- From the ‡Division of Life Science, Energy Institute, Institute for the Environment, The Hong Kong University of Science and Technology, Hong Kong SAR, China.,‖The Hong Kong University of Science and Technology, Shenzhen Research Institute, Shenzhen, Guangdong, 518057, China
| | - Tingliang Wang
- **Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Hairong Xiong
- ‡‡College of Life Science, South-central University for Nationalities, Wuhan, 430074, China
| | - Caren Chang
- §§Department of Cell Biology and Molecular Genetics, University of Maryland, Maryland 20742-5815
| | - Weichuan Yu
- §Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China; .,¶Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Ning Li
- From the ‡Division of Life Science, Energy Institute, Institute for the Environment, The Hong Kong University of Science and Technology, Hong Kong SAR, China; .,‖The Hong Kong University of Science and Technology, Shenzhen Research Institute, Shenzhen, Guangdong, 518057, China
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10
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Chen DH, Huang Y, Jiang C, Si JP. Chromatin-Based Regulation of Plant Root Development. FRONTIERS IN PLANT SCIENCE 2018; 9:1509. [PMID: 30386363 PMCID: PMC6198463 DOI: 10.3389/fpls.2018.01509] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 09/26/2018] [Indexed: 05/10/2023]
Abstract
Plant is endowed with sessile habit and nutrient acquisition mainly through the root organ, which also provides an excellent model to study stem cell fate and asymmetric division due to well-organized cell layers and relatively simple cell types in root meristem. Besides genetic material DNA wrapped around histone octamer, chromatin structure determined by chromatin modification including DNA methylation, histone modification and chromatin remodeling also contributes greatly to the regulation of gene expression. In this review, we summarize the current progresses on the molecular mechanisms of chromatin modification in regulating root development.
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Affiliation(s)
- Dong-Hong Chen
- State Key Laboratory of Subtropical Silviculture, SFGA Engineering Research Center for Dendrobium Catenatum, Zhejiang A&F University, Hangzhou, China
- *Correspondence: Dong-Hong Chen
| | - Yong Huang
- Key Laboratory of Education Department of Hunan Province on Plant Genetics and Molecular Biology, Hunan Agricultural University, Changsha, China
| | | | - Jin-Ping Si
- State Key Laboratory of Subtropical Silviculture, SFGA Engineering Research Center for Dendrobium Catenatum, Zhejiang A&F University, Hangzhou, China
- Jin-Ping Si
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11
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Wang Y, Hu Q, Wu Z, Wang H, Han S, Jin Y, Zhou J, Zhang Z, Jiang J, Shen Y, Shi H, Yang W. HISTONE DEACETYLASE 6 represses pathogen defence responses in Arabidopsis thaliana. PLANT, CELL & ENVIRONMENT 2017; 40:2972-2986. [PMID: 28770584 DOI: 10.1111/pce.13047] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 07/23/2017] [Indexed: 05/18/2023]
Abstract
Plant defence mechanisms are suppressed in the absence of pathogen attack to prevent wasted energy and growth inhibition. However, how defence responses are repressed is not well understood. Histone deacetylase 6 (HDA6) is a negative regulator of gene expression, and its role in pathogen defence response in plants is not known. In this study, a novel allele of hda6 (designated as shi5) with spontaneous defence response was isolated from a forward genetics screening in Arabidopsis. The shi5 mutant exhibited increased resistance to hemibiotrophic bacterial pathogen Pst DC3000, constitutively activated expression of pathogen-responsive genes including PR1, PR2, etc. and increased histone acetylation levels at the promoters of most tested genes that were upregulated in shi5. In both wild type and shi5 plants, the expression and histone acetylation of these genes were upregulated by pathogen infection. HDA6 was found to bind to the promoters of these genes under both normal growth conditions and pathogen infection. Our research suggests that HDA6 is a general repressor of pathogen defence response and plays important roles in inhibiting and modulating the expression of pathogen-responsive genes in Arabidopsis.
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Affiliation(s)
- Yizhong Wang
- School of Life Sciences, Central China Normal University, Wuhan, 43009, Hubei, P.R. China
| | - Qin Hu
- School of Life Sciences, Central China Normal University, Wuhan, 43009, Hubei, P.R. China
| | - Zhenjiang Wu
- School of Life Sciences, Central China Normal University, Wuhan, 43009, Hubei, P.R. China
| | - Hui Wang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA
| | - Shiming Han
- School of Life Sciences, Central China Normal University, Wuhan, 43009, Hubei, P.R. China
| | - Ye Jin
- School of Life Sciences, Central China Normal University, Wuhan, 43009, Hubei, P.R. China
| | - Jin Zhou
- School of Life Sciences, Central China Normal University, Wuhan, 43009, Hubei, P.R. China
| | - Zhengfeng Zhang
- School of Life Sciences, Central China Normal University, Wuhan, 43009, Hubei, P.R. China
| | - Jiafu Jiang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA
| | - Yun Shen
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA
| | - Huazhong Shi
- School of Life Sciences, Central China Normal University, Wuhan, 43009, Hubei, P.R. China
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA
| | - Wannian Yang
- School of Life Sciences, Central China Normal University, Wuhan, 43009, Hubei, P.R. China
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12
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Adaptor proteins GIR1 and GIR2. II. Interaction with the co-repressor TOPLESS and promotion of histone deacetylation of target chromatin. Biochem Biophys Res Commun 2017; 488:609-613. [PMID: 28526412 DOI: 10.1016/j.bbrc.2017.05.085] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 05/15/2017] [Indexed: 12/31/2022]
Abstract
Understanding how root hair development is controlled is important for understanding of many fundamental aspects of plant biology. Previously, we identified two plant-specific adaptor proteins GIR1 and GIR2 that interact with the major regulator of root hair development GL2 and suppress formation of root hair. Here, we show that GIR1 and GIR2 also interact with the co-repressor TOPLESS (TPL). This interaction required the GIR1 protein EAR motif, and was essential for the transcriptional repressor activity of GIR1. Both GIR1 and GIR2 promoted histone hypoacetylation of their target chromatin. Potentially, GIR1 and GIR2 might may link TPL to and participate in epigenetic regulation of root hair development.
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13
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Palmeros-Suárez PA, Massange-Sánchez JA, Sánchez-Segura L, Martínez-Gallardo NA, Espitia Rangel E, Gómez-Leyva JF, Délano-Frier JP. AhDGR2, an amaranth abiotic stress-induced DUF642 protein gene, modifies cell wall structure and composition and causes salt and ABA hyper-sensibility in transgenic Arabidopsis. PLANTA 2017; 245:623-640. [PMID: 27988887 DOI: 10.1007/s00425-016-2635-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 12/02/2016] [Indexed: 05/26/2023]
Abstract
An amaranth DGR gene, induced under abiotic stress, modifies cell wall structure and causes hypersensitivity to ABA and salt when overexpressed in Arabidopsis. DUF642 is a highly conserved plant-specific family of unknown cell wall-associated proteins. The AhDGR2 gene, coding for a DUF642 protein, was significantly induced in grain amaranth (Amaranthus hypochondriacus) plants subjected to water-deficit and salinity stress, thereby suggesting its participation in abiotic stress tolerance in this plant. A role in development was also inferred from the higher AhDGR2 expression rates detected in young tissues. Subsequent overexpression of AhDGR2 in transgenic Arabidopsis plants (OE-AhDGR2) supported its possible role in development processes. Thus, OE-AhDGR2 plants generated significantly longer roots when grown in normal MS medium. However, they showed a hypersensitivity to increasing concentrations of abscisic acid or NaCl in the medium, as manifested by shorter root length, smaller and slightly chlorotic rosettes, as well as highly reduced germination rates. Contrary to expectations, OE-AhDGR2 plants were intolerant to abiotic stress. Moreover, cell walls in transgenic plants were thinner, in leaves, and more disorganized, in roots, and had significantly modified pectin levels. Lower pectin methylesterase activity detected in leaves of OE-AhDGR2 plants, but not in roots, was contrary to previous reports associating DUF642 proteins and decreased pectin esterification levels in cell walls. Nonetheless, microarray data identified candidate genes whose expression levels explained the phenotypes observed in leaves of OE-AhDGR2 plants, including several involved in cell wall integrity and extension, growth and development, and resistance to abiotic stress. These results support the role of DUF642 proteins in cell wall-related processes and offer novel insights into their possible role(s) in plants.
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Affiliation(s)
- Paola A Palmeros-Suárez
- Laboratorio de Biología Molecular, Instituto Tecnológico de Tlajomulco, Jalisco, km 10 Carretera a San Miguel Cuyutlán, CP 45640, Tlajomulco de Zúñiga, Jalisco, Mexico
| | - Julio A Massange-Sánchez
- Biotechnology and Biochemistry Department, Centro de Investigación y de Estudios Avanzados del I. P. N., Unidad Irapuato, Km 9.6 del Libramiento Norte Carretera Irapuato-León, CP 36821, Irapuato, GTO., Mexico
| | - Lino Sánchez-Segura
- Biotechnology and Biochemistry Department, Centro de Investigación y de Estudios Avanzados del I. P. N., Unidad Irapuato, Km 9.6 del Libramiento Norte Carretera Irapuato-León, CP 36821, Irapuato, GTO., Mexico
| | - Norma A Martínez-Gallardo
- Biotechnology and Biochemistry Department, Centro de Investigación y de Estudios Avanzados del I. P. N., Unidad Irapuato, Km 9.6 del Libramiento Norte Carretera Irapuato-León, CP 36821, Irapuato, GTO., Mexico
| | - Eduardo Espitia Rangel
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Km 13.5 Carrretera Los Reyes-Texcoco, CP 56250, Coatlinchán Texcoco, Estado de México, Mexico
| | - Juan F Gómez-Leyva
- Laboratorio de Biología Molecular, Instituto Tecnológico de Tlajomulco, Jalisco, km 10 Carretera a San Miguel Cuyutlán, CP 45640, Tlajomulco de Zúñiga, Jalisco, Mexico
| | - John P Délano-Frier
- Biotechnology and Biochemistry Department, Centro de Investigación y de Estudios Avanzados del I. P. N., Unidad Irapuato, Km 9.6 del Libramiento Norte Carretera Irapuato-León, CP 36821, Irapuato, GTO., Mexico.
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14
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Zhu Y, Rong L, Luo Q, Wang B, Zhou N, Yang Y, Zhang C, Feng H, Zheng L, Shen WH, Ma J, Dong A. The Histone Chaperone NRP1 Interacts with WEREWOLF to Activate GLABRA2 in Arabidopsis Root Hair Development. THE PLANT CELL 2017; 29:260-276. [PMID: 28138017 PMCID: PMC5354192 DOI: 10.1105/tpc.16.00719] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 01/13/2017] [Accepted: 01/27/2017] [Indexed: 05/10/2023]
Abstract
NUCLEOSOME ASSEMBLY PROTEIN1 (NAP1) defines an evolutionarily conserved family of histone chaperones and loss of function of the Arabidopsis thaliana NAP1 family genes NAP1-RELATED PROTEIN1 (NRP1) and NRP2 causes abnormal root hair formation. Yet, the underlying molecular mechanisms remain unclear. Here, we show that NRP1 interacts with the transcription factor WEREWOLF (WER) in vitro and in vivo and enriches at the GLABRA2 (GL2) promoter in a WER-dependent manner. Crystallographic analysis indicates that NRP1 forms a dimer via its N-terminal α-helix. Mutants of NRP1 that either disrupt the α-helix dimerization or remove the C-terminal acidic tail, impair its binding to histones and WER and concomitantly lead to failure to activate GL2 transcription and to rescue the nrp1-1 nrp2-1 mutant phenotype. Our results further demonstrate that WER-dependent enrichment of NRP1 at the GL2 promoter is involved in local histone eviction and nucleosome loss in vivo. Biochemical competition assays imply that the association between NRP1 and histones may counteract the inhibitory effect of histones on the WER-DNA interaction. Collectively, our study provides important insight into the molecular mechanisms by which histone chaperones are recruited to target chromatin via interaction with a gene-specific transcription factor to moderate chromatin structure for proper root hair development.
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Affiliation(s)
- Yan Zhu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 20043, P.R. China
| | - Liang Rong
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 20043, P.R. China
| | - Qiang Luo
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 20043, P.R. China
| | - Baihui Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 20043, P.R. China
| | - Nana Zhou
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 20043, P.R. China
| | - Yue Yang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 20043, P.R. China
| | - Chi Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 20043, P.R. China
| | - Haiyang Feng
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 20043, P.R. China
| | - Lina Zheng
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 20043, P.R. China
| | - Wen-Hui Shen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 20043, P.R. China
- Institut de Biologie Moléculaire des Plantes, UPR2357 CNRS, Université de Strasbourg, 67084 Strasbourg Cédex, France
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 20043, P.R. China
| | - Aiwu Dong
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 20043, P.R. China
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15
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Abstract
Reversible histone acetylation and deacetylation at the N-terminus of histone tails play a crucial role in regulation of gene activity. Hyperacetylation of histones relaxes chromatin structure and is associated with transcriptional activation, whereas hypoacetylation of histones induces chromatin compaction and gene repression. Histone acetylation and deacetylation are catalyzed by histone acetyltransferases (HATs) and histone deacetylases (HDACs), respectively. Emerging evidences revealed that plant HATs and HDACs play essential roles in regulation of gene expression in plant development and plant responses to environmental stresses. Furthermore, HATs and HDACs were shown to interact with various chromatin-remodeling factors and transcription factors involved in transcriptional regulation of multiple developmental processes.
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Affiliation(s)
- X Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - S Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - C-W Yu
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - C-Y Chen
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - K Wu
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan.
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16
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Salazar-Henao JE, Vélez-Bermúdez IC, Schmidt W. The regulation and plasticity of root hair patterning and morphogenesis. Development 2016; 143:1848-58. [DOI: 10.1242/dev.132845] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Root hairs are highly specialized cells found in the epidermis of plant roots that play a key role in providing the plant with water and mineral nutrients. Root hairs have been used as a model system for understanding both cell fate determination and the morphogenetic plasticity of cell differentiation. Indeed, many studies have shown that the fate of root epidermal cells, which differentiate into either root hair or non-hair cells, is determined by a complex interplay of intrinsic and extrinsic cues that results in a predictable but highly plastic pattern of epidermal cells that can vary in shape, size and function. Here, we review these studies and discuss recent evidence suggesting that environmental information can be integrated at multiple points in the root hair morphogenetic pathway and affects multifaceted processes at the chromatin, transcriptional and post-transcriptional levels.
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Affiliation(s)
| | | | - Wolfgang Schmidt
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
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17
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Salazar-Henao JE, Schmidt W. An Inventory of Nutrient-Responsive Genes in Arabidopsis Root Hairs. FRONTIERS IN PLANT SCIENCE 2016; 7:237. [PMID: 26973680 PMCID: PMC4771725 DOI: 10.3389/fpls.2016.00237] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 02/12/2016] [Indexed: 05/07/2023]
Abstract
Root hairs, single cell extensions of root epidermal cells that are critically involved in the acquisition of mineral nutrients, have proven to be an excellent model system for studying plant cell growth. More recently, omics-based systems biology approaches have extended the model function of root hairs toward functional genomic studies. While such studies are extremely useful to decipher the complex mechanisms underlying root hair morphogenesis, their importance for the performance and fitness of the plant puts root hairs in the spotlight of research aimed at elucidating aspects with more practical implications. Here, we mined transcriptomic and proteomic surveys to catalog genes that are preferentially expressed in root hairs and responsive to nutritional signals. We refer to this group of genes as the root hair trophomorphome. Our analysis shows that the activity of genes within the trophomorphome is regulated at both the transcriptional and post-transcriptional level with the mode of regulation being related to the function of the gene product. A core set of proteins functioning in cell wall modification and protein transport was defined as the backbone of the trophomorphome. In addition, our study shows that homeostasis of reactive oxygen species and redox regulation plays a key role in root hair trophomorphogenesis.
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Affiliation(s)
| | - Wolfgang Schmidt
- Institute of Plant and Microbial Biology, Academia SinicaTaipei, Taiwan
- Biotechnology Center, National Chung-Hsing UniversityTaichung, Taiwan
- Genome and Systems Biology Degree Program, College of Life Science, National Taiwan UniversityTaipei, Taiwan
- *Correspondence: Wolfgang Schmidt
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18
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Chen WQ, Li DX, Zhao F, Xu ZH, Bai SN. One additional histone deacetylase and 2 histone acetyltransferases are involved in cellular patterning of Arabidopsis root epidermis. PLANT SIGNALING & BEHAVIOR 2016; 11:e1131373. [PMID: 26689639 PMCID: PMC4883955 DOI: 10.1080/15592324.2015.1131373] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The cellular patterning of Arabidopsis root epidermis is a well-characterized system for study of how single-layered cells are arranged in a particular spatial order. Previously, we found that histone acetylation plays an important role in regulating epidermal differentiation by relaying positional information. To investigate the underlying mechanisms, we screened all available mutants of both HDAC and HAT families. Analyses of mutants of HDAC family members revealed that among single mutants, only HDA6, HDA18 and HDA19 exhibited ectopic H cells at the N position. Similarly, among HAT family members, only single mutants for GCN5 and HAF2 exhibited altered epidermal phenotypes, which were unexpectedly similar to the phenotypes observed in HDAC mutants. Based on these results, together with the previous findings regarding the regulatory mechanisms of HDA18 and HDA6, we proposed that homeostasis of histone acetylation is important for robustness of the regulatory network responsible for the cellular patterning of the Arabidopsis root epidermis.
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Affiliation(s)
- Wen-Qian Chen
- State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Peking University, Beijing, China
- The National Center of Plant Gene Research, Beijing, China
| | - Dong-Xu Li
- State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Peking University, Beijing, China
- The National Center of Plant Gene Research, Beijing, China
| | - Feng Zhao
- State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Peking University, Beijing, China
- The National Center of Plant Gene Research, Beijing, China
| | - Zhi-Hong Xu
- State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Peking University, Beijing, China
- The National Center of Plant Gene Research, Beijing, China
| | - Shu-Nong Bai
- State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Peking University, Beijing, China
- The National Center of Plant Gene Research, Beijing, China
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19
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Balcerowicz D, Schoenaers S, Vissenberg K. Cell Fate Determination and the Switch from Diffuse Growth to Planar Polarity in Arabidopsis Root Epidermal Cells. FRONTIERS IN PLANT SCIENCE 2015; 6:1163. [PMID: 26779192 PMCID: PMC4688357 DOI: 10.3389/fpls.2015.01163] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 12/07/2015] [Indexed: 05/19/2023]
Abstract
Plant roots fulfill important functions as they serve in water and nutrient uptake, provide anchorage of the plant body in the soil and in some species form the site of symbiotic interactions with soil-living biota. Root hairs, tubular-shaped outgrowths of specific epidermal cells, significantly increase the root's surface area and aid in these processes. In this review we focus on the molecular mechanisms that determine the hair and non-hair cell fate of epidermal cells and that define the site on the epidermal cell where the root hair will be initiated (=planar polarity determination). In the model plant Arabidopsis, trichoblast and atrichoblast cell fate results from intra- and intercellular position-dependent signaling and from complex feedback loops that ultimately regulate GL2 expressing and non-expressing cells. When epidermal cells reach the end of the root expansion zone, root hair promoting transcription factors dictate the establishment of polarity within epidermal cells followed by the selection of the root hair initiation site at the more basal part of the trichoblast. Molecular players in the abovementioned processes as well as the role of phytohormones are discussed, and open areas for future experiments are identified.
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Affiliation(s)
| | | | - Kris Vissenberg
- Integrated Molecular Plant Physiology Research, Department Biology, University of AntwerpAntwerpen, Belgium
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20
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Affiliation(s)
- Anna Amtmann
- Institute of Molecular, Cell and Systems Biology College of Medical, Veterinary and Life Sciences University of Glasgow Glasgow G12 8QQ United Kingdom
| | - Hong Ma
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development School of Life Sciences Fudan University Shanghai 200438, China
| | - Doris Wagner
- Department of Biology University of Pennsylvania Philadelphia, PA 19104
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