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Wu Y, Hou J, Ren R, Chen Z, Yue M, Li L, Hou H, Zheng X, Li L. DNA methylation and lipid metabolism are involved in GA-induced maize aleurone layers PCD as revealed by transcriptome analysis. BMC PLANT BIOLOGY 2023; 23:584. [PMID: 37993774 PMCID: PMC10664605 DOI: 10.1186/s12870-023-04565-5] [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: 07/31/2023] [Accepted: 10/27/2023] [Indexed: 11/24/2023]
Abstract
BACKGROUND The aleurone layer is a part of many plant seeds, and during seed germination, aleurone cells undergo PCD, which is promoted by GA from the embryo. However, the numerous components of the GA signaling pathway that mediate PCD of the aleurone layers remain to be identified. Few genes and transcriptomes have been studied thus far in aleurone layers to improve our understanding of how PCD occurs and how the regulatory mechanism functions during PCD. Our previous studies have shown that histone deacetylases (HDACs) are required in GA-induced PCD of aleurone layer. To further explore the molecular mechanisms by which epigenetic modifications regulate aleurone PCD, we performed a global comparative transcriptome analysis of embryoless aleurones treated with GA or histone acetylase (HAT) inhibitors. RESULTS In this study, a total of 7,919 differentially expressed genes (DEGs) were analyzed, 2,554 DEGs of which were found to be common under two treatments. These identified DEGs were involved in various biological processes, including DNA methylation, lipid metabolism and ROS signaling. Further investigations revealed that inhibition of DNA methyltransferases prevented aleurone PCD, suggesting that active DNA methylation plays a role in regulating aleurone PCD. GA or HAT inhibitor induced lipoxygenase gene expression, leading to lipid degradation, but this process was not affected by DNA methylation. However, DNA methylation inhibitor could regulate ROS-related gene expression and inhibit GA-induced production of hydrogen peroxide (H2O2). CONCLUSION Overall, linking of lipoxygenase, DNA methylation, and H2O2 may indicate that GA-induced higher HDAC activity in aleurones causes breakdown of lipids via regulating lipoxygenase gene expression, and increased DNA methylation positively mediates H2O2 production; thus, DNA methylation and lipid metabolism pathways may represent an important and complex signaling network in maize aleurone PCD.
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Affiliation(s)
- Yequn Wu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - 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
| | - Zhenfei Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Mengxia Yue
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Le Li
- 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
| | - Xueke Zheng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
- College of Food, Xinyang Agriculture and Forestry University, Xinyang, 464000, China.
| | - Lijia Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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Zhang K, Yu L, Pang X, Cao H, Si H, Zang J, Xing J, Dong J. In silico analysis of maize HDACs with an emphasis on their response to biotic and abiotic stresses. PeerJ 2020; 8:e8539. [PMID: 32095360 PMCID: PMC7023831 DOI: 10.7717/peerj.8539] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 01/09/2020] [Indexed: 01/20/2023] Open
Abstract
Histone deacetylases (HDACs) are key epigenetic factors in regulating chromatin structure and gene expression in multiple aspects of plant growth, development, and response to abiotic or biotic stresses. Many studies on systematic analysis and molecular function of HDACs in Arabidopsis and rice have been conducted. However, systematic analysis of HDAC gene family and gene expression in response to abiotic and biotic stresses has not yet been reported. In this study, a systematic analysis of the HDAC gene family in maize was performed and 18 ZmHDACs distributed on nine chromosomes were identified. Phylogenetic analysis of ZmHDACs showed that this gene family could be divided into RPD3/HDA1, SIR2, and HD2 groups. Tissue-specific expression results revealed that ZmHDACs exhibited diverse expression patterns in different tissues, indicating that these genes might have diversified functions in growth and development. Expression pattern of ZmHDACs in hormone treatment and inoculation experiment suggested that several ZmHDACs might be involved in jasmonic acid or salicylic acid signaling pathway and defense response. Interestingly, HDAC genes were downregulated under heat stress, and immunoblotting results demonstrated that histones H3K9ac and H4K5ac levels were increased under heat stress. These results provide insights into ZmHDACs, which could help to reveal their functions in controlling maize development and responses to abiotic or biotic stresses.
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Affiliation(s)
- Kang Zhang
- College of Life Science, Hebei Agricultrual University, Baoding, Hebei, China.,Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultrual University, Baoding, Hebei, China
| | - Lu Yu
- College of Life Science, Hebei Agricultrual University, Baoding, Hebei, China.,Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultrual University, Baoding, Hebei, China
| | - Xi Pang
- College of Life Science, Hebei Agricultrual University, Baoding, Hebei, China.,Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultrual University, Baoding, Hebei, China
| | - Hongzhe Cao
- College of Life Science, Hebei Agricultrual University, Baoding, Hebei, China.,Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultrual University, Baoding, Hebei, China
| | - Helong Si
- College of Life Science, Hebei Agricultrual University, Baoding, Hebei, China.,Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultrual University, Baoding, Hebei, China
| | - Jinping Zang
- College of Life Science, Hebei Agricultrual University, Baoding, Hebei, China.,Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultrual University, Baoding, Hebei, China
| | - Jihong Xing
- College of Life Science, Hebei Agricultrual University, Baoding, Hebei, China.,Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultrual University, Baoding, Hebei, China
| | - Jingao Dong
- College of Life Science, Hebei Agricultrual University, Baoding, Hebei, China.,Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultrual University, Baoding, Hebei, China
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Zhang H, Yue M, Zheng X, Gautam M, He S, Li L. The Role of Promoter-Associated Histone Acetylation of Haem Oxygenase-1 ( HO-1) and Giberellic Acid-Stimulated Like-1 ( GSL-1) Genes in Heat-Induced Lateral Root Primordium Inhibition in Maize. FRONTIERS IN PLANT SCIENCE 2018; 9:1520. [PMID: 30459784 PMCID: PMC6232826 DOI: 10.3389/fpls.2018.01520] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 09/27/2018] [Indexed: 05/21/2023]
Abstract
In plants, lateral roots play a crucial role in the uptake of water and nutrients. Several genes such as Zea mays Haem Oxygenase-1 (ZmHO-1) and Giberellic Acid-Stimulated Like-1 (ZmGSL-1) have been found to be involved in lateral root development. In the present investigation, we observed that heat treatment might be involved in the inhibition of lateral root primordium (LRP) formation in maize, accompanied by an increase in global acetylation levels of histone 3 lysine residue 9 (H3K9) and histone 4 lysine residue 5 (H4K5), suggesting that histone modification was related to LRP inhibition. However, Trichostatin A (TSA), an inhibitor of histone deacetylases (HDACs), apparently did not inhibit the LRP formation, revealing that global hyperacetylation might not be the determining factor in the LRP inhibition induced by heat stress. Furthermore, expression of genes related to lateral root development in maize, ZmHO-1 and ZmGSL-1, was down-regulated and the acetylation levels in the promoter region of these two genes were decreased under heat stress, suggesting that promoter-associated histone acetylation might be associated with the expression of ZmHO-1 and ZmGSL-1 genes which were found to be involved in the heat-induced LRP inhibition in maize.
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Affiliation(s)
- Hao Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Mengxia Yue
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xueke Zheng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Mayank Gautam
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Shibin He
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- State Key Laboratory of Cotton Biology, College of Life Sciences, Henan University, Kaifeng, China
- *Correspondence: Shibin He, Lijia Li,
| | - Lijia Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- *Correspondence: Shibin He, Lijia Li,
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Pagano A, Araújo SDS, Macovei A, Leonetti P, Balestrazzi A. The Seed Repair Response during Germination: Disclosing Correlations between DNA Repair, Antioxidant Response, and Chromatin Remodeling in Medicago truncatula. FRONTIERS IN PLANT SCIENCE 2017; 8:1972. [PMID: 29184569 PMCID: PMC5694548 DOI: 10.3389/fpls.2017.01972] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 11/01/2017] [Indexed: 05/05/2023]
Abstract
This work provides novel insights into the effects caused by the histone deacetylase inhibitor trichostatin A (TSA) during Medicago truncatula seed germination, with emphasis on the seed repair response. Seeds treated with H2O and TSA (10 and 20 μM) were collected during imbibition (8 h) and at the radicle protrusion phase. Biometric data showed delayed germination and impaired seedling growth in TSA-treated samples. Comet assay, performed on radicles at the protrusion phase and 4-days old M. truncatula seedlings, revealed accumulation of DNA strand breaks upon exposure to TSA. Activation of DNA repair toward TSA-mediated genotoxic damage was evidenced by the up-regulation of MtOGG1(8-OXOGUANINE GLYCOSYLASE/LYASE) gene involved in the removal of oxidative DNA lesions, MtLIGIV(LIGASE IV) gene, a key determinant of seed quality, required for the rejoining of DNA double strand breaks and TDP(TYROSYL-DNA PHOSPHODIESTERASE) genes encoding the multipurpose DNA repair enzymes tyrosyl-DNA phosphodiesterases. Since radical scavenging can prevent DNA damage, the specific antioxidant activity (SAA) was measured by DPPH (1,1-diphenyl-2-picrylhydrazyl) and Folin-Ciocalteu reagent assays. Fluctuations of SAA were observed in TSA-treated seeds/seedlings concomitant with the up-regulation of antioxidant genes MtSOD(SUPEROXIDE DISMUTASE, MtAPX(ASCORBATE PEROXIDASE) and MtMT2(TYPE 2 METALLOTHIONEIN). Chromatin remodeling, required to facilitate the access of DNA repair enzymes at the damaged sites, is also part of the multifaceted seed repair response. To address this aspect, still poorly explored in plants, the MtTRRAP(TRANSFORMATION/TRANSACTIVATION DOMAIN-ASSOCIATED PROTEIN) gene was analyzed. TRRAP is a transcriptional adaptor, so far characterized only in human cells where it is needed for the recruitment of histone acetyltransferase complexes to chromatin during DNA repair. The MtTRRAP gene and the predicted interacting partners MtHAM2 (HISTONE ACETYLTRANSFERASE OF THE MYST FAMILY) and MtADA2A (TRANSCRIPTIONAL ADAPTOR) showed tissue- and dose-dependent fluctuations in transcript levels. PCA (Principal Component Analysis) and correlation analyses suggest for a new putative link between DNA repair and chromatin remodeling that involves MtOGG1 and MtTRRAP genes, in the context of seed germination. Interesting correlations also connect DNA repair and chromatin remodeling with antioxidant players and proliferation markers.
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Affiliation(s)
- Andrea Pagano
- Department of Biology and Biotechnology ‘Lazzaro Spallanzani’, University of Pavia, Pavia, Italy
| | - Susana de Sousa Araújo
- Plant Cell Biotechnology, Instituto de Tecnologia Química e Biológica António Xavier (ITQB-NOVA), Oeiras, Portugal
| | - Anca Macovei
- Department of Biology and Biotechnology ‘Lazzaro Spallanzani’, University of Pavia, Pavia, Italy
| | - Paola Leonetti
- Institute for Sustainable Plant Protection, National Research Council (CNR), Bari, Italy
| | - Alma Balestrazzi
- Department of Biology and Biotechnology ‘Lazzaro Spallanzani’, University of Pavia, Pavia, Italy
- *Correspondence: Alma Balestrazzi
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Li Y, Dong XM, Jin F, Shen Z, Chao Q, Wang BC. Histone Acetylation Modifications Affect Tissue-Dependent Expression of Poplar Homologs of C 4 Photosynthetic Enzyme Genes. FRONTIERS IN PLANT SCIENCE 2017; 8:950. [PMID: 28642769 PMCID: PMC5462996 DOI: 10.3389/fpls.2017.00950] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 05/22/2017] [Indexed: 05/18/2023]
Abstract
Histone modifications play important roles in regulating the expression of C4 photosynthetic genes. Given that all enzymes required for the C4 photosynthesis pathway are present in C3 plants, it has been hypothesized that this expression regulatory mechanism has been conserved. However, the relationship between histone modification and the expression of homologs of C4 photosynthetic enzyme genes has not been well determined in C3 plants. In the present study, we cloned nine hybrid poplar (Populus simonii × Populus nigra) homologs of maize (Zea mays) C4 photosynthetic enzyme genes, carbonic anhydrase (CA), pyruvate orthophosphate dikinase (PPDK), phosphoenolpyruvate carboxykinase (PCK), and phosphoenolpyruvate carboxylase (PEPC), and investigated the correlation between the expression levels of these genes and the levels of promoter histone acetylation modifications in four vegetative tissues. We found that poplar homologs of C4 homologous genes had tissue-dependent expression patterns that were mostly well-correlated with the level of histone acetylation modification (H3K9ac and H4K5ac) determined by chromatin immunoprecipitation assays. Treatment with the histone deacetylase inhibitor trichostatin A further confirmed the role of histone acetylation in the regulation of the nine target genes. Collectively, these results suggest that both H3K9ac and H4K5ac positively regulate the tissue-dependent expression pattern of the PsnCAs, PsnPPDKs, PsnPCKs, and PsnPEPCs genes and that this regulatory mechanism seems to be conserved among the C3 and C4 species. Our findings provide new insight that will aid efforts to modify the expression pattern of these homologs of C4 genes to engineer C4 plants from C3 plants.
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Affiliation(s)
- Yuan Li
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of SciencesBeijing, China
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry UniversityHarbin, China
| | - Xiu-Mei Dong
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Feng Jin
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Zhuo Shen
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Qing Chao
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Bai-Chen Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of SciencesBeijing, China
- *Correspondence: Bai-Chen Wang,
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Hashiguchi A, Komatsu S. Impact of Post-Translational Modifications of Crop Proteins under Abiotic Stress. Proteomes 2016; 4:proteomes4040042. [PMID: 28248251 PMCID: PMC5260974 DOI: 10.3390/proteomes4040042] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Revised: 11/30/2016] [Accepted: 12/16/2016] [Indexed: 12/15/2022] Open
Abstract
The efficiency of stress-induced adaptive responses of plants depends on intricate coordination of multiple signal transduction pathways that act coordinately or, in some cases, antagonistically. Protein post-translational modifications (PTMs) can regulate protein activity and localization as well as protein-protein interactions in numerous cellular processes, thus leading to elaborate regulation of plant responses to various external stimuli. Understanding responses of crop plants under field conditions is crucial to design novel stress-tolerant cultivars that maintain robust homeostasis even under extreme conditions. In this review, proteomic studies of PTMs in crops are summarized. Although the research on the roles of crop PTMs in regulating stress response mechanisms is still in its early stage, several novel insights have been retrieved so far. This review covers techniques for detection of PTMs in plants, representative PTMs in plants under abiotic stress, and how PTMs control functions of representative proteins. In addition, because PTMs under abiotic stresses are well described in soybeans under submergence, recent findings in PTMs of soybean proteins under flooding stress are introduced. This review provides information on advances in PTM study in relation to plant adaptations to abiotic stresses, underlining the importance of PTM study to ensure adequate agricultural production in the future.
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Affiliation(s)
- Akiko Hashiguchi
- Faculty of Medicine, University of Tsukuba, Tsukuba 305-8577, Japan.
| | - Setsuko Komatsu
- National Institute of Crop Science, NARO, Tsukuba 305-8518, Japan.
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