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Leal JL, Milesi P, Hodková E, Zhou Q, James J, Eklund DM, Pyhäjärvi T, Salojärvi J, Lascoux M. Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles. Syst Biol 2024; 73:392-418. [PMID: 38613229 PMCID: PMC11282369 DOI: 10.1093/sysbio/syae012] [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: 08/17/2023] [Revised: 12/18/2023] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Introgression allows polyploid species to acquire new genomic content from diploid progenitors or from other unrelated diploid or polyploid lineages, contributing to genetic diversity and facilitating adaptive allele discovery. In some cases, high levels of introgression elicit the replacement of large numbers of alleles inherited from the polyploid's ancestral species, profoundly reshaping the polyploid's genomic composition. In such complex polyploids, it is often difficult to determine which taxa were the progenitor species and which taxa provided additional introgressive blocks through subsequent hybridization. Here, we use population-level genomic data to reconstruct the phylogenetic history of Betula pubescens (downy birch), a tetraploid species often assumed to be of allopolyploid origin and which is known to hybridize with at least four other birch species. This was achieved by modeling polyploidization and introgression events under the multispecies coalescent and then using an approximate Bayesian computation rejection algorithm to evaluate and compare competing polyploidization models. We provide evidence that B. pubescens is the outcome of an autoploid genome doubling event in the common ancestor of B. pendula and its extant sister species, B. platyphylla, that took place approximately 178,000-188,000 generations ago. Extensive hybridization with B. pendula, B. nana, and B. humilis followed in the aftermath of autopolyploidization, with the relative contribution of each of these species to the B. pubescens genome varying markedly across the species' range. Functional analysis of B. pubescens loci containing alleles introgressed from B. nana identified multiple genes involved in climate adaptation, while loci containing alleles derived from B. humilis revealed several genes involved in the regulation of meiotic stability and pollen viability in plant species.
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Affiliation(s)
- J Luis Leal
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Pascal Milesi
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
- Science for Life Laboratory (SciLifeLab), Uppsala University, 75237 Uppsala, Sweden
| | - Eva Hodková
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 16521 Prague, Czech Republic
| | - Qiujie Zhou
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Jennifer James
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - D Magnus Eklund
- Physiology and Environmental Toxicology, Department of Organismal Biology, Uppsala University, Norbyvägen 18A, 75236 Uppsala, Sweden
| | - Tanja Pyhäjärvi
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Centre, University of Helsinki, P.O. Box 65 (Viikinkaari 1), 00014 Helsinki, Finland
- Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Jarkko Salojärvi
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Centre, University of Helsinki, P.O. Box 65 (Viikinkaari 1), 00014 Helsinki, Finland
| | - Martin Lascoux
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
- Science for Life Laboratory (SciLifeLab), Uppsala University, 75237 Uppsala, Sweden
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Hou J, Xiao H, Yao P, Ma X, Shi Q, Yang J, Hou H, Li L. Unveiling the mechanism of broad-spectrum blast resistance in rice: The collaborative role of transcription factor OsGRAS30 and histone deacetylase OsHDAC1. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1740-1756. [PMID: 38294722 PMCID: PMC11123394 DOI: 10.1111/pbi.14299] [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: 08/31/2023] [Revised: 11/15/2023] [Accepted: 01/16/2024] [Indexed: 02/01/2024]
Abstract
Rice blast, caused by Magnaporthe oryzae, significantly impacts grain yield, necessitating the identification of broad-spectrum resistance genes and their functional mechanisms for disease-resistant crop breeding. Here, we report that rice with knockdown OsHDAC1 gene expression displays enhanced broad-spectrum blast resistance without effects on plant height and tiller numbers compared to wild-type rice, while rice overexpressing OsHDAC1 is more susceptible to M. oryzae. We identify a novel blast resistance transcription factor, OsGRAS30, which genetically acts upstream of OsHDAC1 and interacts with OsHDAC1 to suppress its enzymatic activity. This inhibition increases the histone H3K27ac level, thereby boosting broad-spectrum blast resistance. Integrating genome-wide mapping of OsHDAC1 and H3K27ac targets with RNA sequencing analysis unveils how OsHDAC1 mediates the expression of OsSSI2, OsF3H, OsRLR1 and OsRGA5 to regulate blast resistance. Our findings reveal that the OsGRAS30-OsHDAC1 module is critical to rice blast control. Therefore, targeting either OsHDAC1 or OsGRAS30 offers a promising approach for enhancing crop blast resistance.
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Affiliation(s)
- Jiaqi Hou
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
| | - Huangzhuo Xiao
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
| | - Peng Yao
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
| | - Xiaoci Ma
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
| | - Qipeng Shi
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
| | - Jin Yang
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
| | - Haoli Hou
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
| | - Lijia Li
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
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Lv Z, Lan G, Bai B, Yu P, Wang C, Zhang H, Zhong C, Zhao X, Yu H. Identification of candidate genes associated with peanut pod length by combined analysis of QTL-seq and RNA-seq. Genomics 2024; 116:110835. [PMID: 38521201 DOI: 10.1016/j.ygeno.2024.110835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/14/2024] [Accepted: 03/21/2024] [Indexed: 03/25/2024]
Abstract
Pod length (PL) is one of the major traits determining pod size and yield of peanut. Discovering the quantitative trait loci (QTL) and identifying candidate genes associated with PL are essential for breeding high-yield peanut. In this study, quantitative trait loci sequencing (QTL-seq) was performed using the F2 population constructed by a short-pod variety Tifrunner (Tif) and a long-pod line Lps, and a 0.77 Mb genomic region on chromosome 07 was identified as the candidate region for PL. Then, the candidate region was narrowed to a 265.93 kb region by traditional QTL approach. RNA-seq analysis showed that there were four differentially expressed genes (DEGs) in the candidate region, among which Arahy.PF2L6F (AhCDC48) and Arahy.P4LK2T (AhTAA1) were speculated to be PL-related candidate genes. These results were informative for the elucidation of the underlying regulatory mechanism in peanut pod length and would facilitate further identification of valuable target genes.
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Affiliation(s)
- Zhenghao Lv
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Guohu Lan
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Baiyi Bai
- College of Agriculture and Horticulture, Liaoning Agriculture Ovcational and Technical College, Yingkou 115009, China
| | - Penghao Yu
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Chuantang Wang
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; Shandong Peanut Research Institute, Qingdao 266100, China
| | - He Zhang
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Chao Zhong
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Xinhua Zhao
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Haiqiu Yu
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; College of Agriculture and Horticulture, Liaoning Agriculture Ovcational and Technical College, Yingkou 115009, China.
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Hong Y, Liu S, Chen Y, Yao Z, Jiang S, Wang L, Zhu X, Xu W, Zhang J, Li Y. Amyloplast is involved in the MIZ1-modulated root hydrotropism. JOURNAL OF PLANT PHYSIOLOGY 2024; 296:154224. [PMID: 38507925 DOI: 10.1016/j.jplph.2024.154224] [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: 02/28/2024] [Revised: 03/10/2024] [Accepted: 03/10/2024] [Indexed: 03/22/2024]
Abstract
Roots exhibit hydrotropism in response to moisture gradients, with the hydrotropism-related gene Mizu-kussei1 (MIZ1) playing a role in regulating root hydrotropism in an oblique orientation. However, the mechanisms underlying MIZ1-regulated root hydrotropism are not well understood. In this study, we employed obliquely oriented experimental systems to investigate root hydrotropism in Arabidopsis. We found that the miz1 mutant displays reduced root hydrotropism but increased root gravitropism following hydrostimulation, as compared to wild-type plants. Conversely, overexpression of AtMIZ1 leads to enhanced root hydrotropism but decreased root gravitropism following hydrostimulation, as compared to wild-type plants. Using co-immunoprecipitation followed by mass spectrometry (IP-MS), we explored proteins that interact with AtMIZ1, and we identified PGMC1 co-immunoprecipitated with MIZ1 in vivo. Furthermore, the miz1 mutant exhibited higher expression of the PGMC1 gene and increased phosphoglucomutase (PGM) activity, while AtMIZ1 overexpressors resulted in lower expression of the PGMC1 gene, reduced amyloplast amount, and reduced PGM activity in comparison to wild-type roots. In addition, different Arabidopsis natural accessions having difference in their hydrotropic response demonstrated expression level of PGMC1 was negatively correlated with hydrotropic root curvature and AtMIZ1 expression. Our results provide valuable insights into the role of amyloplast in MIZ1-regulated root hydrotropism.
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Affiliation(s)
- Yonghui Hong
- Jiangsu Key Laboratory of Crop Genomics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Siqi Liu
- Jiangsu Key Laboratory of Crop Genomics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Yadi Chen
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China
| | - Zixuan Yao
- Jiangsu Key Laboratory of Crop Genomics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Shuqiu Jiang
- Jiangsu Key Laboratory of Crop Genomics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Lulu Wang
- Jiangsu Key Laboratory of Crop Genomics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Xinkai Zhu
- Jiangsu Key Laboratory of Crop Genomics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Weifeng Xu
- Joint International Research Laboratory of Water and Nutrient in Crops, Center for Plant Water-Use and Nutrition Regulation and College of Resource and Environment, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, Hong Kong, 999077, China; School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, 999077, China.
| | - Ying Li
- Jiangsu Key Laboratory of Crop Genomics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China; Department of Biology, Hong Kong Baptist University, Hong Kong, 999077, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China; Joint International Research Laboratory of Water and Nutrient in Crops, Center for Plant Water-Use and Nutrition Regulation and College of Resource and Environment, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China.
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5
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Liu X, Cheng W, Yao P, Ren K, Wang Y, Sun Y, Hou X, Lu L, Chen X. Conserved serine phosphorylation regulates histone deacetylase activity in Arabidopsis and humans. PLANT PHYSIOLOGY 2024; 194:2017-2021. [PMID: 37966963 DOI: 10.1093/plphys/kiad587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 10/02/2023] [Indexed: 11/17/2023]
Abstract
Conserved serine phosphorylation regulates histone deacetylase activity in Arabidopsis and humans
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Affiliation(s)
- Xiaojing Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Weijia Cheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Peng Yao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Kexin Ren
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Yu Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Yingnan Sun
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Xin Hou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Li Lu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Xiangsong Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
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Kumar V, Singh B, Kumar Singh R, Sharma N, Muthamilarasan M, Sawant SV, Prasad M. Histone deacetylase 9 interacts with SiHAT3.1 and SiHDA19 to repress dehydration responses through H3K9 deacetylation in foxtail millet. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1098-1111. [PMID: 37889853 DOI: 10.1093/jxb/erad425] [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: 09/08/2023] [Accepted: 10/26/2023] [Indexed: 10/29/2023]
Abstract
Climate change inflicts several stresses on plants, of which dehydration stress severely affects growth and productivity. C4 plants possess better adaptability to dehydration stress; however, the role of epigenetic modifications underlying this trait is unclear. In particular, the molecular links between histone modifiers and their regulation remain elusive. In this study, genome-wide H3K9 acetylation (H3K9ac) enrichment using ChIP-sequencing was performed in two foxtail millet cultivars with contrasting dehydration tolerances (IC403579, cv. IC4-tolerant, and IC480117, cv. IC41-sensitive). It revealed that a histone deacetylase, SiHDA9, was significantly up-regulated in the sensitive cultivar. Further characterization indicated that SiHDA9 interacts with SiHAT3.1 and SiHDA19 to form a repressor complex. SiHDA9 might be recruited through the SiHAT3.1 recognition sequence onto the upstream of dehydration-responsive genes to decrease H3K9 acetylation levels. The silencing of SiHDA9 resulted in the up-regulation of crucial genes, namely, SiRAB18, SiRAP2.4, SiP5CS2, SiRD22, SiPIP1;4, and SiLHCB2.3, which imparted dehydration tolerance in the sensitive cultivar (IC41). Overall, the study provides mechanistic insights into SiHDA9-mediated regulation of dehydration stress response in foxtail millet.
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Affiliation(s)
- Verandra Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, Delhi, India
| | - Babita Singh
- Plant Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, Uttar Pradesh, India
| | - Roshan Kumar Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, Delhi, India
| | - Namisha Sharma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, Delhi, India
| | | | - Samir V Sawant
- Plant Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, Uttar Pradesh, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, Delhi, India
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
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7
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Cadena-Ramos AI, De-la-Peña C. Picky eaters: selective autophagy in plant cells. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:364-384. [PMID: 37864806 DOI: 10.1111/tpj.16508] [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: 07/14/2023] [Revised: 09/21/2023] [Accepted: 10/10/2023] [Indexed: 10/23/2023]
Abstract
Autophagy, a fundamental cellular process, plays a vital role in maintaining cellular homeostasis by degrading damaged or unnecessary components. While selective autophagy has been extensively studied in animal cells, its significance in plant cells has only recently gained attention. In this review, we delve into the intriguing realm selective autophagy in plants, with specific focus on its involvement in nutrient recycling, organelle turnover, and stress response. Moreover, recent studies have unveiled the interesting interplay between selective autophagy and epigenetic mechanisms in plants, elucidating the significance of epigenetic regulation in modulating autophagy-related gene expression and finely tuning the selective autophagy process in plants. By synthesizing existing knowledge, this review highlights the emerging field of selective autophagy in plant cells, emphasizing its pivotal role in maintaining nutrient homeostasis, facilitating cellular adaptation, and shedding light on the epigenetic regulation that governs these processes. Our comprehensive study provides the way for a deeper understanding of the dynamic control of cellular responses to nutrient availability and stress conditions, opening new avenues for future research in this field of autophagy in plant physiology.
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Affiliation(s)
- Alexis I Cadena-Ramos
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34 Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
| | - Clelia De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34 Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
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Nguyen NH, Sng BJR, Chin HJ, Choi IKY, Yeo HC, Jang IC. HISTONE DEACETYLASE 9 promotes hypocotyl-specific auxin response under shade. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:804-822. [PMID: 37522556 DOI: 10.1111/tpj.16410] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 08/01/2023]
Abstract
Vegetative shade causes an array of morphological changes in plants called shade avoidance syndrome, which includes hypocotyl and petiole elongation, leaf hyponasty, reduced leaf growth, early flowering and rapid senescence. Here, we show that loss-of-function mutations in HISTONE DEACETYLASE 9 (HDA9) attenuated the shade-induced hypocotyl elongation in Arabidopsis. However, the hda9 cotyledons and petioles under shade were not significantly different from those in wild-type, suggesting a specific function of HDA9 in hypocotyl elongation in response to shade. HDA9 expression levels were stable under shade and its protein was ubiquitously detected in cotyledon, hypocotyl and root. Organ-specific transcriptome analysis unraveled that shade induced a set of auxin-responsive genes, such as SMALL AUXIN UPREGULATED RNAs (SAURs) and AUXIN/INDOLE-3-ACETIC ACIDs (AUX/IAAs) and their induction was impaired in hda9-1 hypocotyls. In addition, HDA9 binding to loci of SAUR15/65, IAA5/6/19 and ACS4 was increased under shade. The genetic and organ-specific gene expression analyses further revealed that HDA9 may cooperate with PHYTOCHROME-INTERACTING FACTOR 4/7 in the regulation of shade-induced hypocotyl elongation. Furthermore, HDA9 and PIF7 proteins were found to interact together and thus it is suggested that PIF7 may recruit HDA9 to regulate the shade/auxin responsive genes in response to shade. Overall, our study unravels that HDA9 can work as one component of a hypocotyl-specific transcriptional regulatory machinery that activates the auxin response at the hypocotyl leading to the elongation of this organ under shade.
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Affiliation(s)
- Nguyen Hoai Nguyen
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
| | - Benny Jian Rong Sng
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Hui Jun Chin
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
| | - Ian Kin Yuen Choi
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Hock Chuan Yeo
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
| | - In-Cheol Jang
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
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Zhang Y, Huang D, Miao Y. Epigenetic control of plant senescence and cell death and its application in crop improvement. FRONTIERS IN PLANT SCIENCE 2023; 14:1258487. [PMID: 37965008 PMCID: PMC10642554 DOI: 10.3389/fpls.2023.1258487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023]
Abstract
Plant senescence is the last stage of plant development and a type of programmed cell death, occurring at a predictable time and cell. It involves the functional conversion from nutrient assimilation to nutrient remobilization, which substantially impacts plant architecture and plant biomass, crop quality, and horticultural ornamental traits. In past two decades, DNA damage was believed to be a main reason for cell senescence. Increasing evidence suggests that the alteration of epigenetic information is a contributing factor to cell senescence in organisms. In this review, we summarize the current research progresses of epigenetic and epitranscriptional mechanism involved in cell senescence of plant, at the regulatory level of DNA methylation, histone methylation and acetylation, chromatin remodeling, non-coding RNAs and RNA methylation. Furthermore, we discuss their molecular genetic manipulation and potential application in agriculture for crop improvement. Finally we point out the prospects of future research topics.
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Affiliation(s)
- Yu Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dongmei Huang
- Department of Biochemistry and Molecular Biology, Xiamen Medical College, Xiamen, China
| | - Ying Miao
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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Agbemafle W, Wong MM, Bassham DC. Transcriptional and post-translational regulation of plant autophagy. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6006-6022. [PMID: 37358252 PMCID: PMC10575704 DOI: 10.1093/jxb/erad211] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/09/2023] [Indexed: 06/27/2023]
Abstract
In response to changing environmental conditions, plants activate cellular responses to enable them to adapt. One such response is autophagy, in which cellular components, for example proteins and organelles, are delivered to the vacuole for degradation. Autophagy is activated by a wide range of conditions, and the regulatory pathways controlling this activation are now being elucidated. However, key aspects of how these factors may function together to properly modulate autophagy in response to specific internal or external signals are yet to be discovered. In this review we discuss mechanisms for regulation of autophagy in response to environmental stress and disruptions in cell homeostasis. These pathways include post-translational modification of proteins required for autophagy activation and progression, control of protein stability of the autophagy machinery, and transcriptional regulation, resulting in changes in transcription of genes involved in autophagy. In particular, we highlight potential connections between the roles of key regulators and explore gaps in research, the filling of which can further our understanding of the autophagy regulatory network in plants.
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Affiliation(s)
- William Agbemafle
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Min May Wong
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Diane C Bassham
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
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Bardani E, Kallemi P, Tselika M, Katsarou K, Kalantidis K. Spotlight on Plant Bromodomain Proteins. BIOLOGY 2023; 12:1076. [PMID: 37626962 PMCID: PMC10451976 DOI: 10.3390/biology12081076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 07/28/2023] [Accepted: 07/30/2023] [Indexed: 08/27/2023]
Abstract
Bromodomain-containing proteins (BRD-proteins) are the "readers" of histone lysine acetylation, translating chromatin state into gene expression. They act alone or as components of larger complexes and exhibit diverse functions to regulate gene expression; they participate in chromatin remodeling complexes, mediate histone modifications, serve as scaffolds to recruit transcriptional regulators or act themselves as transcriptional co-activators or repressors. Human BRD-proteins have been extensively studied and have gained interest as potential drug targets for various diseases, whereas in plants, this group of proteins is still not well investigated. In this review, we aimed to concentrate scientific knowledge on these chromatin "readers" with a focus on Arabidopsis. We organized plant BRD-proteins into groups based on their functions and domain architecture and summarized the published work regarding their interactions, activity and diverse functions. Overall, it seems that plant BRD-proteins are indispensable components and fine-tuners of the complex network plants have built to regulate development, flowering, hormone signaling and response to various biotic or abiotic stresses. This work will facilitate the understanding of their roles in plants and highlight BRD-proteins with yet undiscovered functions.
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Affiliation(s)
- Eirini Bardani
- Department of Biology, University of Crete, Voutes University Campus, 71500 Heraklion, Greece; (E.B.); (P.K.); (M.T.)
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013 Heraklion, Greece
| | - Paraskevi Kallemi
- Department of Biology, University of Crete, Voutes University Campus, 71500 Heraklion, Greece; (E.B.); (P.K.); (M.T.)
| | - Martha Tselika
- Department of Biology, University of Crete, Voutes University Campus, 71500 Heraklion, Greece; (E.B.); (P.K.); (M.T.)
| | - Konstantina Katsarou
- Department of Biology, University of Crete, Voutes University Campus, 71500 Heraklion, Greece; (E.B.); (P.K.); (M.T.)
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013 Heraklion, Greece
| | - Kriton Kalantidis
- Department of Biology, University of Crete, Voutes University Campus, 71500 Heraklion, Greece; (E.B.); (P.K.); (M.T.)
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013 Heraklion, Greece
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12
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Shapulatov U, van Zanten M, van Hoogdalem M, Meisenburg M, van Hall A, Kappers I, Fasano C, Facella P, Loh CC, Perrella G, van der Krol A. The Mediator complex subunit MED25 interacts with HDA9 and PIF4 to regulate thermomorphogenesis. PLANT PHYSIOLOGY 2023; 192:582-600. [PMID: 36537119 PMCID: PMC10152658 DOI: 10.1093/plphys/kiac581] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 10/27/2022] [Accepted: 11/01/2022] [Indexed: 05/03/2023]
Abstract
Thermomorphogenesis is, among other traits, characterized by enhanced hypocotyl elongation due to the induction of auxin biosynthesis genes like YUCCA8 by transcription factors, most notably PHYTOCHROME INTERACTING FACTOR 4 (PIF4). Efficient binding of PIF4 to the YUCCA8 locus under warmth depends on HISTONE DEACETYLASE 9 (HDA9) activity, which mediates histone H2A.Z depletion at the YUCCA8 locus. However, HDA9 lacks intrinsic DNA-binding capacity, and how HDA9 is recruited to YUCCA8, and possibly other PIF4-target sites, is currently not well understood. The Mediator complex functions as a bridge between transcription factors bound to specific promoter sequences and the basal transcription machinery containing RNA polymerase II. Mutants of Mediator component Mediator25 (MED25) exhibit reduced hypocotyl elongation and reduced expression of YUCCA8 at 27°C. In line with a proposed role for MED25 in thermomorphogenesis in Arabidopsis (Arabidopsis thaliana), we demonstrated an enhanced association of MED25 to the YUCCA8 locus under warmth and interaction of MED25 with both PIF4 and HDA9. Genetic analysis confirmed that MED25 and HDA9 operate in the same pathway. Intriguingly, we also showed that MED25 destabilizes HDA9 protein. Based on our findings, we propose that MED25 recruits HDA9 to the YUCCA8 locus by binding to both PIF4 and HDA9.
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Affiliation(s)
- Umidjon Shapulatov
- Laboratory of Plant Physiology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Temasek Life Science Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
| | - Martijn van Zanten
- Plant Stress Resilience, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Mark van Hoogdalem
- Laboratory of Plant Physiology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Mara Meisenburg
- Laboratory of Plant Physiology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Alexander van Hall
- Laboratory of Plant Physiology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Iris Kappers
- Laboratory of Plant Physiology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Carlo Fasano
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Trisaia Research Centre, S.S. Ionica, km 419.5, 75026 Rotondella (Matera), Italy
| | - Paolo Facella
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Trisaia Research Centre, S.S. Ionica, km 419.5, 75026 Rotondella (Matera), Italy
| | - Chi Cheng Loh
- Temasek Life Science Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
| | - Giorgio Perrella
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Trisaia Research Centre, S.S. Ionica, km 419.5, 75026 Rotondella (Matera), Italy
| | - Alexander van der Krol
- Laboratory of Plant Physiology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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Huang LJ, Wang Y, Lin Z, Jiang D, Luo Y, Li N. The role of corepressor HOS15-mediated epigenetic regulation of flowering. FRONTIERS IN PLANT SCIENCE 2023; 13:1101912. [PMID: 36704168 PMCID: PMC9871556 DOI: 10.3389/fpls.2022.1101912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 12/21/2022] [Indexed: 06/18/2023]
Abstract
Regulation of gene expression underpins gene function and is essential for regulation of physiological roles. Epigenetic modifications regulate gene transcription by physically facilitating relaxation or condensation of target loci in chromatin. Transcriptional corepressors are involved in chromatin remodeling and regulate gene expression by establishing repressive complexes. Genetic and biochemical studies reveal that a member of the Groucho/Thymidine uptake 1 (Gro/Tup1) corepressor family, HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE 15 (HOS15), is recruited via the evening complex (EC) to the GIGANTEA (GI) promoter to repress gene expression, and modulating flowering time. Therefore, HOS15 connects photoperiodic pathway and epigenetic mechanism to control flowering time in plants. In addition, growing body of evidence support a diverse roles of the epigenetic regulator HOS15 in fine-tuning plant development and growth by integrating intrinsic genetic components and various environmental signals.
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Affiliation(s)
- Li-Jun Huang
- State Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Yukun Wang
- State Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Zeng Lin
- State Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Dong Jiang
- State Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Yong Luo
- School of Chemistry and Environmental Science, Xiangnan University, Chenzhou, China
| | - Ning Li
- State Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, College of Forestry, Central South University of Forestry and Technology, Changsha, China
- Key Laboratory of Forest Bio-resources and Integrated Pest Management for Higher Education in Hunan Province, Central South University of Forestry and Technology, Changsha, China
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14
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Lim CJ, Park KS, Ali A, Park J, Ryou SM, Shen M, Khan HA, Bader ZE, Zareen S, Bae MJ, Choi JH, Xu ZY, Pardo JM, Yun DJ. Negative regulation of floral transition in Arabidopsis by HOS15-PWR-HDA9 complex. FRONTIERS IN PLANT SCIENCE 2023; 13:1105988. [PMID: 36684790 PMCID: PMC9853073 DOI: 10.3389/fpls.2022.1105988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Arabidopsis HOS15/PWR/HDA9 repressor complex, which is similar to the TBL1/NcoR1/HDAC complex in animals, plays a well-known role in epigenetic regulation. PWR and HDA9 have been reported to interact with each other and modulate the flowering time by repressing AGL19 expression, whereas HOS15 and HDA9, together with the photoperiodic evening complex, regulate flowering time through repression of GI transcription. However, the role of the HOS15/PWR/HDA9 core repressor complex as a functional unit in the regulation of flowering time is yet to be explored. In this study, we reported that the loss-of-function hos15-2/pwr/hda9 triple mutant accumulates higher transcript levels of AGL19 and exhibits an early flowering phenotype similar to those of hos15, pwr, and hda9 single mutants. Interestingly, the accumulation of HOS15 in the nucleus was drastically reduced in pwr and hda9 mutants. As a result, HOS15 could not perform its role in histone deacetylation or interaction with H3 in the nucleus. Furthermore, HOS15 is also associated with the same region of the AGL19 promoter known for PWR-HDA9 binding. The acetylation level of the AGL19 promoter was increased in the hos15-2 mutant, similar to the pwr and hda9 mutants. Therefore, our findings reveal that the HOS15/PWR/HDA9 repressor complex deacetylates the promoter region of AGL19, thereby negatively regulating AGL19 transcription, which leads to early flowering in Arabidopsis.
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Affiliation(s)
- Chae Jin Lim
- Institute of Global Disease Control, Konkuk University, Seoul, Republic of Korea
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Ki Suk Park
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Akhtar Ali
- Institute of Global Disease Control, Konkuk University, Seoul, Republic of Korea
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Junghoon Park
- Institute of Global Disease Control, Konkuk University, Seoul, Republic of Korea
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Seung Min Ryou
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Mingzhe Shen
- Department of Agronomy, Agricultural College, Yanbian University, Yanji, China
| | - Haris Ali Khan
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Zein Eddin Bader
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Shah Zareen
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Min Jae Bae
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Jong Hyoo Choi
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Jose M. Pardo
- Institute of Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones 17 Cientificas and Universidad de Sevilla, Seville, Spain
| | - Dae-Jin Yun
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
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15
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Jia H, Zuo Q, Sadeghnezhad E, Zheng T, Chen X, Dong T, Fang J. HDAC19 recruits ERF4 to the MYB5a promoter and diminishes anthocyanin accumulation during grape ripening. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:127-144. [PMID: 36423230 DOI: 10.1111/tpj.16040] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 11/04/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
DNA acetylation alters the expression of responsive genes during plant development. In grapes (Vitis vinifera), however, little is known about this regulatory mechanism. In the present study, 'Kyoho' grapes treated with trichostatin A (TSA, a deacetylase inhibitor) were used for transcriptome sequencing and quantitative proteomics analysis. We observed that acetylation was associated with anthocyanin accumulation and gene expression. Acetylation positively regulated phenylalanine metabolism and flavonoid biosynthesis pathways. Using omics analysis, we detected an increase in the levels of the AP2/EREBP transcription factor family after TSA treatment, indicating its association with acetylation-deacetylation dynamics in grapes. Furthermore, ethylene response factor 4 (ERF4) physically interacted with VvHDAC19, a histone deacetylase, which synergistically reduced the expression of target genes involved in anthocyanin biosynthesis owing to the binding of VvERF4 to the GCC-box cis-regulatory element in the VvMYB5a promoter. VvHDAC19 and VvERF4 also controlled anthocyanin biosynthesis and accumulation by regulating acetylation levels of histones H3 and H4. Therefore, alterations in histone modification can significantly regulate the expression of genes involved in anthocyanin biosynthesis and affect grape ripening.
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Affiliation(s)
- Haifeng Jia
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
- NJAU (Suqian) Academy of Protected Horticultures, Suqian, China
| | - Qianqian Zuo
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
| | - Ehsan Sadeghnezhad
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
| | - Ting Zheng
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
| | - Xueqin Chen
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
| | - Tianyu Dong
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
| | - JinggGui Fang
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
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16
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Patil V, Nandi AK. POWERDRESS positively regulates systemic acquired resistance in Arabidopsis. PLANT CELL REPORTS 2022; 41:2351-2362. [PMID: 36152035 DOI: 10.1007/s00299-022-02926-2] [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: 06/09/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
PWR, an epigenetic regulator, and PIF4, a transcription factor coordinately regulate both local resistance and systemic acquired resistance in Arabidopsis. A plant that gets infected once becomes resistant to subsequent infections through the development of systemic acquired resistance (SAR). Primary-infected tissues generate mobile signals that travel to systemic tissues and cause epigenetic changes associated with the SAR activation. Epigenetic regulators and the process of infection memory development are largely obscure for plants. POWERDRESS (PWR), a SANT domain-containing histone deacetylation (HDAC) promoting gene, is essential for thermomorphogenesis. Here we show that PWR is required for the SAR activation in Arabidopsis. The pwr mutants in Ler and Col-0 background possess normal local resistance but are defective in SAR. PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) genetically interacts with PWR for flowering and thermomorphogenesis and is a negative regulator of basal immunity. We found a cooperative function for suppressing basal immunity and SAR activation by PIF4 and PWR, respectively. PWR promotes the expression of SA biosynthesis genes and the accumulation of SA in the systemic tissues. RSI1/FLD, which influences histone methylation and acetylation, is essential to infection memory development in Arabidopsis. Our results show that PWR and RSI1 positively regulate each other's expression. Exogenous application of HDAC inhibitor sodium butyrate abolishes SAR-mediated SA accumulation, expression of PR1 gene, and protection against pathogens after challenge inoculation. The results indicate the possibility of the involvement of HDAC activity of PWR in the formation of infection memory development in Arabidopsis.
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Affiliation(s)
- Vishal Patil
- School of Life Sciences, Jawaharlal Nehru University, 415, New Delhi, 110067, India
| | - Ashis Kumar Nandi
- School of Life Sciences, Jawaharlal Nehru University, 415, New Delhi, 110067, India.
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17
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Zhou Q, Sun Y, Zhao X, Yu Y, Cheng W, Lu L, Chu Z, Chen X. Bromodomain-containing factor GTE4 regulates Arabidopsis immune response. BMC Biol 2022; 20:256. [DOI: 10.1186/s12915-022-01454-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 10/31/2022] [Indexed: 11/15/2022] Open
Abstract
Abstract
Background
Plants are continuously challenged with biotic stress from environmental pathogens, and precise regulation of defense responses is critical for plant survival. Defense systems require considerable amounts of energy and resources, impairing plant growth, and plant hormones controlling transcriptional regulation play essential roles in establishing the appropriate balance between defense response to pathogens and growth. Chromatin regulators modulating gene transcription are broadly involved in regulating stress-responsive genes. However, which chromatin factors are involved in coordinating hormone signaling and immune responses in plants, and their functional mechanisms, remains unclear. Here, we identified a role of bromodomain-containing protein GTE4 in negatively regulating defense responses in Arabidopsis thaliana.
Results
GTE4 mainly functions as activator of gene expression upon infection with Pseudomonas syringe. Genome-wide profiling of GTE4 occupancy shows that GTE4 tends to bind to active genes, including ribosome biogenesis related genes and maintains their high expression levels during pathogen infection. However, GTE4 is also able to repress gene expression. GTE4 binds to and represses jasmonate biosynthesis gene OPR3. Disruption of GTE4 results in overaccumulation of jasmonic acid (JA) and enhanced JA-responsive gene expression. Unexpectedly, over-accumulated JA content in gte4 mutant is coupled with downregulation of JA-mediated immune defense genes and upregulation of salicylic acid (SA)-mediated immune defense genes, and enhanced resistance to Pseudomonas, likely through a noncanonical pathway.
Conclusions
Overall, we identified a new role of the chromatin factor GTE4 as negative regulator of plant immune response through inhibition of JA biosynthesis, which in turn noncanonically activates the defense system against Pseudomonas. These findings provide new knowledge of chromatic regulation of plant hormone signaling during defense responses.
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Abstract
Heat stress limits plant growth, development, and crop yield, but how plant cells precisely sense and transduce heat stress signals remains elusive. Here, we identified a conserved heat stress response mechanism to elucidate how heat stress signal is transmitted from the cytoplasm into the nucleus for epigenetic modifiers. We demonstrate that HISTONE DEACETYLASE 9 (HDA9) transduces heat signals from the cytoplasm to the nucleus to play a positive regulatory role in heat responses in Arabidopsis. Heat specifically induces HDA9 accumulation in the nucleus. Under heat stress, the phosphatase PP2AB'β directly interacts with and dephosphorylates HDA9 to protect HDA9 from 26S proteasome-mediated degradation, leading to the translocation of nonphosphorylated HDA9 to the nucleus. This heat-induced enrichment of HDA9 in the nucleus depends on the nucleoporin HOS1. In the nucleus, HDA9 binds and deacetylates the target genes related to signaling transduction and plant development to repress gene expression in a transcription factor YIN YANG 1-dependent and -independent manner, resulting in rebalance of plant development and heat response. Therefore, we uncover an HDA9-mediated positive regulatory module in the heat shock signal transduction pathway. More important, this cytoplasm-to-nucleus translocation of HDA9 in response to heat stress is conserved in wheat and rice, which confers the mechanism significant implication potential for crop breeding to cope with global climate warming.
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Wang Z, Gao M, Li Y, Zhang J, Su H, Cao M, Liu Z, Zhang X, Zhao B, Guo YD, Zhang N. The transcription factor SlWRKY37 positively regulates jasmonic acid- and dark-induced leaf senescence in tomato. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6207-6225. [PMID: 35696674 DOI: 10.1093/jxb/erac258] [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: 01/22/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
Initiation and progression of leaf senescence are triggered by various environmental stressors and phytohormones. Jasmonic acid (JA) and darkness accelerate leaf senescence in plants. However, the mechanisms that integrate these two factors to initiate and regulate leaf senescence have not been identified. Here, we report a transcriptional regulatory module centred on a novel tomato WRKY transcription factor, SlWRKY37, responsible for both JA- and dark-induced leaf senescence. The expression of SlWRKY37, together with SlMYC2, encoding a master transcription factor in JA signalling, was significantly induced by both methyl jasmonate (MeJA) and dark treatments. SlMYC2 binds directly to the promoter of SlWRKY37 to activate its expression. Knock out of SlWRKY37 inhibited JA- and dark-induced leaf senescence. Transcriptome analysis and biochemical experiments revealed SlWRKY53 and SlSGR1 (S. lycopersicum senescence-inducible chloroplast stay-green protein 1) as direct transcriptional targets of SlWRKY37 to control leaf senescence. Moreover, SlWRKY37 interacted with a VQ motif-containing protein SlVQ7, and the interaction improved the stability of SlWRKY37 and the transcriptional activation of downstream target genes. Our results reveal the physiological and molecular functions of SlWRKY37 in leaf senescence, and offer a target gene to retard leaf yellowing by reducing sensitivity to external senescence signals, such as JA and darkness.
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Affiliation(s)
- Zhirong Wang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Ming Gao
- College of Horticulture, China Agricultural University, Beijing, China
| | - Yafei Li
- College of Horticulture, China Agricultural University, Beijing, China
| | - Jialong Zhang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Hui Su
- College of Horticulture, China Agricultural University, Beijing, China
| | - Meng Cao
- College of Horticulture, China Agricultural University, Beijing, China
| | - Ziji Liu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xichun Zhang
- School of Plant Science and Technology, Beijing Agricultural University, Beijing, China
| | - Bing Zhao
- College of Horticulture, China Agricultural University, Beijing, China
| | - Yang-Dong Guo
- College of Horticulture, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Sanya, China
| | - Na Zhang
- College of Horticulture, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Sanya, China
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20
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Zhang Y, Li Y, Zhang Y, Zhang Z, Zhang D, Wang X, Lai B, Huang D, Gu L, Xie Y, Miao Y. Genome-wide H3K9 acetylation level increases with age-dependent senescence of flag leaf in rice. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4696-4715. [PMID: 35429161 DOI: 10.1093/jxb/erac155] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
Flag leaf senescence is an important biological process that drives the remobilization of nutrients to the growing organs of rice. Leaf senescence is controlled by genetic information via gene expression and histone modification, but the precise mechanism is as yet unclear. Here, we analysed genome-wide acetylated lysine residue 9 of histone H3 (H3K9ac) enrichment by chromatin immunoprecipitation-sequencing (ChIP-seq), and examined its association with transcriptomes by RNA-seq during flag leaf aging in rice (Oryza sativa). We found that genome-wide H3K9 acetylation levels increased with age-dependent senescence in rice flag leaf, and there was a positive correlation between the density and breadth of H3K9ac with gene expression and transcript elongation. During flag leaf aging, we observed 1249 up-regulated differentially expressed genes (DEGs) and 996 down-regulated DEGs, showing a strong relationship between temporal changes in gene expression and gain/loss of H3K9ac. We produced a landscape of H3K9 acetylation-modified gene expression targets that include known senescence-associated genes, metabolism-related genes, as well as miRNA biosynthesis-related genes. Our findings reveal a complex regulatory network of metabolism- and senescence-related pathways mediated by H3K9ac, and elucidate patterns of H3K9ac-mediated regulation of gene expression during flag leaf aging in rice.
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Affiliation(s)
- Yu Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanyun Li
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuanyuan Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zeyu Zhang
- Basic Forestry and Proteomics Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Deyu Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaonan Wang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Binfan Lai
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dandan Huang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yakun Xie
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ying Miao
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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21
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Vatov E, Zentgraf U, Ludewig U. Moderate DNA methylation changes associated with nitrogen remobilization and leaf senescence in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4733-4752. [PMID: 35552412 PMCID: PMC9366325 DOI: 10.1093/jxb/erac167] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
The lifespan of plants is restricted by environmental and genetic components. Following the transition to reproductive growth, leaf senescence ends cellular life in monocarpic plants to remobilize nutrients to storage organs. In Arabidopsis, we initially observed altered leaf to seed ratios, faster senescence progression, altered leaf nitrogen recovery after transient nitrogen removal, and ultimately enhanced nitrogen remobilization from the leaves in two methylation mutants (ros1 and the triple dmr1/2 cmt3 knockout). Analysis of the DNA methylome in wild type Col-0 leaves identified an initial moderate decline of cytosine methylation with progressing leaf senescence, predominantly in the CG context. Late senescence was associated with moderate de novo methylation of cytosines, primarily in the CHH context. Relatively few differentially methylated regions, including one in the ROS1 promoter linked to down-regulation of ROS1, were present, but these were unrelated to known senescence-associated genes. Differential methylation patterns were identified in transcription factor binding sites, such as the W-boxes that are targeted by WRKYs. Methylation in artificial binding sites impaired transcription factor binding in vitro. However, it remains unclear how moderate methylome changes during leaf senescence are linked with up-regulated genes during senescence.
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Affiliation(s)
- Emil Vatov
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Stuttgart, D-70593, Germany
- Center for Molecular Biology of Plants (ZMBP), University of Tübingen, Tübingen, D-72076, Germany
| | - Ulrike Zentgraf
- Center for Molecular Biology of Plants (ZMBP), University of Tübingen, Tübingen, D-72076, Germany
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22
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Sasi JM, Gupta S, Singh A, Kujur A, Agarwal M, Katiyar-Agarwal S. Know when and how to die: gaining insights into the molecular regulation of leaf senescence. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:1515-1534. [PMID: 36389097 PMCID: PMC9530073 DOI: 10.1007/s12298-022-01224-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 08/17/2022] [Accepted: 08/21/2022] [Indexed: 06/16/2023]
Abstract
Senescence is the ultimate phase in the life cycle of leaves which is crucial for recycling of nutrients to maintain plant fitness and reproductive success. The earliest visible manifestation of leaf senescence is their yellowing, which usually commences with the breakdown of chlorophyll. The degradation process involves a gradual and highly coordinated disassembly of macromolecules resulting in the accumulation of nutrients, which are subsequently mobilized from the senescing leaves to the developing organs. Leaf senescence progresses under overly tight genetic and molecular control involving a well-orchestrated and intricate network of regulators that coordinate spatio-temporally with the influence of both internal and external cues. Owing to the advancements in omics technologies, the availability of mutant resources, scalability of molecular analyses methodologies and the advanced capacity to integrate multidimensional data, our understanding of the genetic and molecular basis of leaf ageing has greatly expanded. The review provides a compilation of the multitier regulation of senescence process and the interrelation between the environment and the terminal phase of leaf development. The knowledge gained would benefit in devising the strategies for manipulation of leaf senescence process to improve crop quality and productivity.
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Affiliation(s)
- Jyothish Madambikattil Sasi
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
| | - Shitij Gupta
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
| | - Apurva Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
| | - Alice Kujur
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
- USDA-ARS Plant Genetics Research Unit, The Donald Danforth Plant Science Center, St. Louis, MO 63132 USA
- Centre of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana 502324 India
| | - Manu Agarwal
- Department of Botany, University of Delhi North Campus, Delhi, 110007 India
| | - Surekha Katiyar-Agarwal
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
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23
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Hu T, Manuela D, Hinsch V, Xu M. PICKLE associates with histone deacetylase 9 to mediate vegetative phase change in Arabidopsis. THE NEW PHYTOLOGIST 2022; 235:1070-1081. [PMID: 35460275 PMCID: PMC9324081 DOI: 10.1111/nph.18174] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/09/2022] [Indexed: 05/04/2023]
Abstract
The juvenile-to-adult vegetative phase change in flowering plants is mediated by a decrease in miR156 levels. Downregulation of MIR156A/MIR156C, the two major sources of miR156, is accompanied by a decrease in acetylation of histone 3 lysine 27 (H3K27ac) and an increase in trimethylation of H3K27 (H3K27me3) at MIR156A/MIR156C in Arabidopsis. Here, we show that histone deacetylase 9 (HDA9) is recruited to MIR156A/MIR156C during the juvenile phase and associates with the CHD3 chromatin remodeler PICKLE (PKL) to erase H3K27ac at MIR156A/MIR156C. H2Aub and H3K27me3 become enriched at MIR156A/MIR156C, and the recruitment of Polycomb Repressive Complex 2 (PRC2) to MIR156A/MIR156C is partially dependent on the activities of PKL and HDA9. Our results suggest that PKL associates with histone deacetylases to erase H3K27ac and promote PRC1 and PRC2 activities to mediate vegetative phase change and maintain plants in the adult phase after the phase transition.
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Affiliation(s)
- Tieqiang Hu
- Department of Biological SciencesUniversity of South CarolinaColumbiaSC29208USA
| | - Darren Manuela
- Department of Biological SciencesUniversity of South CarolinaColumbiaSC29208USA
| | - Valerie Hinsch
- Department of Biological SciencesUniversity of South CarolinaColumbiaSC29208USA
| | - Mingli Xu
- Department of Biological SciencesUniversity of South CarolinaColumbiaSC29208USA
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24
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Lee HG, Jeong YY, Lee H, Seo PJ. Arabidopsis HISTONE DEACETYLASE 9 Stimulates Hypocotyl Cell Elongation by Repressing GIGANTEA Expression Under Short Day Photoperiod. FRONTIERS IN PLANT SCIENCE 2022; 13:950378. [PMID: 35923878 PMCID: PMC9341324 DOI: 10.3389/fpls.2022.950378] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Developmental plasticity contributes to plant adaptation and fitness in a given condition. Hypocotyl elongation is under the tight control of complex genetic networks encompassing light, circadian, and photoperiod signaling. In this study, we demonstrate that HISTONE DEACETYLASE 9 (HDA9) mediates day length-dependent hypocotyl cell elongation. HDA9 binds to the GIGANTEA (GI) locus involved in photoperiodic hypocotyl elongation. The short day (SD)-accumulated HDA9 protein promotes histone H3 deacetylation at the GI locus during the dark period, promoting hypocotyl elongation. Consistently, HDA9-deficient mutants display reduced hypocotyl length, along with an increase in GI gene expression, only under SD conditions. Taken together, our study reveals the genetic basis of day length-dependent cell elongation in plants.
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Affiliation(s)
- Hong Gil Lee
- Department of Chemistry, Seoul National University, Seoul, South Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
| | - Yeong Yeop Jeong
- Research Institute of Basic Sciences, Seoul National University, Seoul, South Korea
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Hongwoo Lee
- Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul, South Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
- Research Institute of Basic Sciences, Seoul National University, Seoul, South Korea
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
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25
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Hou Y, Lu Q, Su J, Jin X, Jia C, An L, Tian Y, Song Y. Genome-Wide Analysis of the HDAC Gene Family and Its Functional Characterization at Low Temperatures in Tartary Buckwheat ( Fagopyrum tataricum). Int J Mol Sci 2022; 23:ijms23147622. [PMID: 35886971 PMCID: PMC9319316 DOI: 10.3390/ijms23147622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/02/2022] [Accepted: 07/05/2022] [Indexed: 02/04/2023] Open
Abstract
Histone deacetylases (HDACs), widely found in various types of eukaryotic cells, play crucial roles in biological process, including the biotic and abiotic stress responses in plants. However, no research on the HDACs of Fagopyrum tataricum has been reported. Here, 14 putative FtHDAC genes were identified and annotated in Fagopyrum tataricum. Their gene structure, motif composition, cis-acting elements, phylogenetic relationships, protein structure, alternative splicing events, subcellular localization and gene expression pattern were investigated. The gene structure showed FtHDACs were classified into three subfamilies. The promoter analysis revealed the presence of various cis-acting elements responsible for hormone, abiotic stress and developmental regulation for the specific induction of FtHDACs. Two duplication events were identified in FtHDA6-1, FtHDA6-2, and FtHDA19. The expression patterns of FtHDACs showed their correlation with the flavonoid synthesis pathway genes. In addition, alternative splicing, mRNA enrichment profiles and transgenic analysis showed the potential role of FtHDACs in cold responses. Our study characterized FtHDACs, providing a candidate gene family for agricultural breeding and crop improvement.
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Affiliation(s)
- Yukang Hou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730030, China; (Y.H.); (Q.L.); (J.S.); (X.J.); (L.A.)
| | - Qi Lu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730030, China; (Y.H.); (Q.L.); (J.S.); (X.J.); (L.A.)
| | - Jianxun Su
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730030, China; (Y.H.); (Q.L.); (J.S.); (X.J.); (L.A.)
| | - Xing Jin
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730030, China; (Y.H.); (Q.L.); (J.S.); (X.J.); (L.A.)
| | - Changfu Jia
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu 610017, China;
| | - Lizhe An
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730030, China; (Y.H.); (Q.L.); (J.S.); (X.J.); (L.A.)
| | - Yongke Tian
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730030, China; (Y.H.); (Q.L.); (J.S.); (X.J.); (L.A.)
- Correspondence: (Y.T.); (Y.S.)
| | - Yuan Song
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730030, China; (Y.H.); (Q.L.); (J.S.); (X.J.); (L.A.)
- Correspondence: (Y.T.); (Y.S.)
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26
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Huang D, Lan W, Ma W, Huang R, Lin W, Li M, Chen CY, Wu K, Miao Y. WHIRLY1 recruits the histone deacetylase HDA15 repressing leaf senescence and flowering in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1411-1429. [PMID: 35510566 DOI: 10.1111/jipb.13272] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 05/02/2022] [Indexed: 06/14/2023]
Abstract
Leaf senescence is controlled by a complex regulatory network in which robustness is ensured by the activity of transcription factors and epigenetic regulators. However, how these coordinate the process of leaf senescence remains poorly understood. We found that WHIRLY1 interacts with Histone Deacetylase (HDA)15, a Reduced Potassium Dependence3 (RPD3)/HDA1-type HDA, by using green fluorescent protein-nanotrap-mass spectrum assays. The development-dependent interaction between WHIRLY1 and HDA15 was further confirmed by bimolecular fluorescence complementation assays and co-immunoprecipitation assays in Arabidopsis. Multi-omics genome-wide transcriptome and H3K9 acetylome enrichment analysis showed that HDA15 delays leaf senescence and flowering by repressing the expression of the positive regulators of leaf senescence and flowering, such as LOX2 and LARP1C, and reducing H3K9ac levels at these loci; WHIRLY1 and HDA15 co-target to the region near the transcription start site of a subset of nutrient recycling-related genes (e.g., Glutathione S-transferases 10, non-coding RNA, and photosystem II protein D1 synthesizer attenuator PDIL1-2), as well as WRKY53 and ELF4, and co-repress their expression by removing H3K9 acetylation. Our study revealed a key transcription regulatory node of nutrient recycling and senescence-associated genes involved in leaf senescence and flowering via the recruitment of HDA15 by the single-stranded DNA/RNA-binding protein WHIRLY1.
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Affiliation(s)
- Dongmei Huang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wei Lan
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Weibo Ma
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Rulin Huang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wenfang Lin
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mengsi Li
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chia-Yang Chen
- Institute of Botany, College of Life Sciences, Taiwan University, Taibei, 106, China
| | - Keqiang Wu
- Institute of Botany, College of Life Sciences, Taiwan University, Taibei, 106, China
| | - Ying Miao
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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27
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Perrella G, Bäurle I, van Zanten M. Epigenetic regulation of thermomorphogenesis and heat stress tolerance. THE NEW PHYTOLOGIST 2022; 234:1144-1160. [PMID: 35037247 DOI: 10.1111/nph.17970] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/13/2021] [Indexed: 06/14/2023]
Abstract
Many environmental conditions fluctuate and organisms need to respond effectively. This is especially true for temperature cues that can change in minutes to seasons and often follow a diurnal rhythm. Plants cannot migrate and most cannot regulate their temperature. Therefore, a broad array of responses have evolved to deal with temperature cues from freezing to heat stress. A particular response to mildly elevated temperatures is called thermomorphogenesis, a suite of morphological adaptations that includes thermonasty, formation of thin leaves and elongation growth of petioles and hypocotyl. Thermomorphogenesis allows for optimal performance in suboptimal temperature conditions by enhancing the cooling capacity. When temperatures rise further, heat stress tolerance mechanisms can be induced that enable the plant to survive the stressful temperature, which typically comprises cellular protection mechanisms and memory thereof. Induction of thermomorphogenesis, heat stress tolerance and stress memory depend on gene expression regulation, governed by diverse epigenetic processes. In this Tansley review we update on the current knowledge of epigenetic regulation of heat stress tolerance and elevated temperature signalling and response, with a focus on thermomorphogenesis regulation and heat stress memory. In particular we highlight the emerging role of H3K4 methylation marks in diverse temperature signalling pathways.
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Affiliation(s)
- Giorgio Perrella
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Trisaia Research Centre, S.S. Ionica, km 419.5, 75026, Rotondella (Matera), Italy
| | - Isabel Bäurle
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam, Germany
| | - Martijn van Zanten
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
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28
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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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29
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Chen Q, Zhang J, Li G. Dynamic epigenetic modifications in plant sugar signal transduction. TRENDS IN PLANT SCIENCE 2022; 27:379-390. [PMID: 34865981 DOI: 10.1016/j.tplants.2021.10.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 09/28/2021] [Accepted: 10/22/2021] [Indexed: 05/21/2023]
Abstract
In eukaryotes, dynamic chromatin states are closely related to changes in gene expression. Epigenetic modifications help plants adapt to their ever-changing environment by modulating gene expression via covalent modification at specific sites on DNA or histones. Sugars provide energy, but also function as signaling molecules to control plant growth and development. Various epigenetic modifications participate in sensing and transmitting sugar signals. Here we summarize recent progress in uncovering the epigenetic mechanisms involved in sugar signal transduction, including histone acetylation and deacetylation, histone methylation and demethylation, and DNA methylation. We also highlight changes in chromatin marks when crosstalk occurs between sugar signaling and the light, temperature, and phytohormone signaling pathways, and describe potential questions and approaches for future research.
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Affiliation(s)
- Qingshuai Chen
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, Shandong, China; State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Jing Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Gang Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China.
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30
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Batalova AY, Putintseva YA, Sadovsky MG, Krutovsky KV. Comparative Genomics of Seasonal Senescence in Forest Trees. Int J Mol Sci 2022; 23:ijms23073761. [PMID: 35409113 PMCID: PMC8998842 DOI: 10.3390/ijms23073761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/27/2022] [Accepted: 03/28/2022] [Indexed: 01/13/2023] Open
Abstract
In the course of evolution, both flowering plants and some gymnosperms have developed such an adaptation to winter and unfavorable living conditions as deciduousness. Of particular interest is Siberian larch (Larix sibirica Ledeb.), which is the only species in the pine family (Pinaceae) with a seasonal deciduousness. New generation sequencing technologies make it possible to study this phenomenon at the genomic level and to reveal the genetic mechanisms of leaf and needle aging in angiosperms and gymnosperms. Using a comparative analysis of the genomes of evergreen and deciduous trees, it was found that the genes that control EXORDIUM LIKE 2 (EXL2) and DORMANCY-ASSOCIATED PROTEIN 1 (DRM1) proteins are most represented in Siberian larch, while an excess of genes that control proteins acting as immune receptors were found in evergreens. Orthologs from the family of genes that control leucine-rich repeat receptor-like kinases (LRR-RLK) contributed mostly to the distinction between evergreens and deciduous plants.
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Affiliation(s)
- Anastasia Y. Batalova
- Department of Genomics and Bioinformatics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660041 Krasnoyarsk, Russia;
| | - Yuliya A. Putintseva
- Department of Biophysics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660041 Krasnoyarsk, Russia;
| | - Michael G. Sadovsky
- Institute of Computational Modelling, Russian Academy of Sciences, Siberian Branch, 660036 Krasnoyarsk, Russia;
- V. F. Voino-Yasenetsky Krasnoyarsk State Medical University, 660022 Krasnoyarsk, Russia
- Federal Siberian Research Clinical Center, Federal Medical-Biological Agency, 660037 Krasnoyarsk, Russia
| | - Konstantin V. Krutovsky
- Department of Genomics and Bioinformatics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660041 Krasnoyarsk, Russia;
- Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, 37077 Göttingen, Germany
- Center for Integrated Breeding Research, Georg-August University of Göttingen, 37075 Göttingen, Germany
- Laboratory of Population Genetics, N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
- Scientific and Methodological Center, G. F. Morozov Voronezh State University of Forestry and Technologies, 394087 Voronezh, Russia
- Correspondence: ; Tel.: +49-551-339-3537
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31
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Hou Y, Yan Y, Cao X. Epigenetic regulation of thermomorphogenesis in Arabidopsis thaliana. ABIOTECH 2022; 3:12-24. [PMID: 36304197 PMCID: PMC9590556 DOI: 10.1007/s42994-022-00070-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 01/24/2022] [Indexed: 11/25/2022]
Abstract
Temperature is a key factor in determining plant growth and development, geographical distribution, and seasonal behavior. Plants accurately sense subtle changes in ambient temperature and alter their growth and development accordingly to improve their chances of survival and successful propagation. Thermomorphogenesis encompasses a variety of morphological changes that help plants acclimate to warm environmental temperatures. Revealing the molecular mechanism of thermomorphogenesis is important for breeding thermo-tolerant crops and ensuring food security under global climate change. Plant adaptation to elevated ambient temperature is regulated by multiple signaling pathways and epigenetic mechanisms such as histone modifications, histone variants, and non-coding RNAs. In this review, we summarize recent advances in the mechanism of epigenetic regulation during thermomorphogenesis with a focus on the model plant Arabidopsis thaliana and briefly discuss future prospects for this field.
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Affiliation(s)
- Yifeng Hou
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Yan Yan
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Beijing, 100101 China
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32
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Post-translational modification: a strategic response to high temperature in plants. ABIOTECH 2022; 3:49-64. [PMID: 36304199 PMCID: PMC9590526 DOI: 10.1007/s42994-021-00067-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 12/22/2021] [Indexed: 11/21/2022]
Abstract
With the increasing global warming, high-temperature stress is affecting plant growth and development with greater frequency. Therefore, an increasing number of studies examining the mechanism of temperature response contribute to a more optimal understanding of plant growth under environmental pressure. Post-translational modification (PTM) provides the rapid reconnection of transcriptional programs including transcription factors and signaling proteins. It is vital that plants quickly respond to changes in the environment in order to survive under stressful situations. Herein, we discuss several types of PTMs that occur in response to warm-temperature and high-temperature stress, including ubiquitination, SUMOylation, phosphorylation, histone methylation, and acetylation. This review provides a valuable resolution to this issue to enable increased crop productivity at high temperatures.
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33
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Zareen S, Ali A, Lim CJ, Khan HA, Park J, Xu ZY, Yun DJ. The Transcriptional Corepressor HOS15 Mediates Dark-Induced Leaf Senescence in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:828264. [PMID: 35283908 PMCID: PMC8914473 DOI: 10.3389/fpls.2022.828264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/14/2022] [Indexed: 05/23/2023]
Abstract
Multiple endogenous and environmental signals regulate the intricate and highly complex processes driving leaf senescence in plants. A number of genes have been identified in a variety of plant species, including Arabidopsis, which influence leaf senescence. Previously, we have shown that HOS15 is a multifunctional protein that regulates several physiological processes, including plant growth and development under adverse environmental conditions. HOS15 has also been reported to form a chromatin remodeling complex with PWR and HDA9 and to regulate the chromatin structure of numerous genes. However, unlike PWR and HDA9, the involvement of HOS15 in leaf senescence is yet to be identified. Here, we report that HOS15, together with PWR and HDA9, promotes leaf senescence via transcriptional regulation of SAG12/29, senescence marker genes, and CAB1/RCBS1A, photosynthesis-related genes. The expression of ORE1, SAG12, and SAG29 was downregulated in hos15-2 plants, whereas the expression of photosynthesis-related genes, CAB1 and RCBS1A, was upregulated. HOS15 also promoted senescence through dark stress, as its mutation led to a much greener phenotype than that of the WT. Phenotypes of double and triple mutants of HOS15 with PWR and HDA9 produced phenotypes similar to those of a single hos15-2. In line with this observation, the expression levels of NPX1, APG9, and WRKY57 were significantly elevated in hos15-2 and hos15/pwr, hos15/hda9, and hos15/pwr/hda9 mutants compared to those in the WT. Surprisingly, the total H3 acetylation level decreased in age-dependent manner and under dark stress in WT; however, it remained the same in hos15-2 plants regardless of dark stress, suggesting that dark-induced deacetylation requires functional HOS15. More interestingly, the promoters of APG9, NPX1, and WRKY57 were hyperacetylated in hos15-2 plants compared to those in WT plants. Our data reveal that HOS15 acts as a positive regulator and works in the same repressor complex with PWR and HDA9 to promote leaf senescence through aging and dark stress by repressing NPX1, APG9, and WRKY57 acetylation.
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Affiliation(s)
- Shah Zareen
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, South Korea
| | - Akhtar Ali
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, South Korea
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Chae Jin Lim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, South Korea
| | - Haris Ali Khan
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, South Korea
| | - Junghoon Park
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, South Korea
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Dae-Jin Yun
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, South Korea
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
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Wen YX, Wang JY, Zhu HH, Han GH, Huang RN, Huang L, Hong YG, Zheng SJ, Yang JL, Chen WW. Potential Role of Domains Rearranged Methyltransferase7 in Starch and Chlorophyll Metabolism to Regulate Leaf Senescence in Tomato. FRONTIERS IN PLANT SCIENCE 2022; 13:836015. [PMID: 35211145 PMCID: PMC8860812 DOI: 10.3389/fpls.2022.836015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Deoxyribonucleic acid (DNA) methylation is an important epigenetic mark involved in diverse biological processes. Here, we report the critical function of tomato (Solanum lycopersicum) Domains Rearranged Methyltransferase7 (SlDRM7) in plant growth and development, especially in leaf interveinal chlorosis and senescence. Using a hairpin RNA-mediated RNA interference (RNAi), we generated SlDRM7-RNAi lines and observed pleiotropic developmental defects including small and interveinal chlorosis leaves. Combined analyses of whole genome bisulfite sequence (WGBS) and RNA-seq revealed that silencing of SlDRM7 caused alterations in both methylation levels and transcript levels of 289 genes, which are involved in chlorophyll synthesis, photosynthesis, and starch degradation. Furthermore, the photosynthetic capacity decreased in SlDRM7-RNAi lines, consistent with the reduced chlorophyll content and repression of genes involved in chlorophyll biosynthesis, photosystem, and photosynthesis. In contrast, starch granules were highly accumulated in chloroplasts of SlDRM7-RNAi lines and associated with lowered expression of genes in the starch degradation pathway. In addition, SlDRM7 was activated by aging- and dark-induced senescence. Collectively, these results demonstrate that SlDRM7 acts as an epi-regulator to modulate the expression of genes related to starch and chlorophyll metabolism, thereby affecting leaf chlorosis and senescence in tomatoes.
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Affiliation(s)
- Yu Xin Wen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jia Yi Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Hui Hui Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Guang Hao Han
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Ru Nan Huang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Li Huang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
| | - Yi Guo Hong
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Shao Jian Zheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jian Li Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Wei Wei Chen
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
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35
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Ding X, Zhang D, Gu D, Li Z, Liang H, Zhu H, Jiang Y, Duan X. Histone H3K27 demethylase SlJMJ4 promotes dark- and ABA- induced leaf senescence in tomato. HORTICULTURE RESEARCH 2022; 9:uhab077. [PMID: 35043207 PMCID: PMC8973004 DOI: 10.1093/hr/uhab077] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/28/2021] [Accepted: 10/31/2021] [Indexed: 06/12/2023]
Abstract
Leaf senescence is a highly-programmed developmental process during the plant life cycle. ABA plays an important role in leaf senescence. However, the mechanism underlying ABA-mediated leaf senescence, particularly the upstream epigenetic regulatory network, remains largely unclear. Here, we identified that SlJMJ4, a Jumonji C (jmjC) domain-containing protein in tomato, specifically demethylates di- and tri-methylations of lysine 27 of histone H3 (H3K27) in vitro and in vivo. Overexpression of SlJMJ4 results in premature senescence phenotype and promotes dark- and ABA-induced leaf senescence in tomato. Under dark condition, SlJMJ4-promoted leaf senescence is associated with upregulated expression of transcription factors (SlORE1 and SlNAP2) and senescence-associated genes (SlSAG113, SlSAG12) via removal of H3K27me3. In responses to ABA, overexpression of SlJMJ4 increases its binding at the loci of SlORE1, SlNAP2, SlSAG113, SlSAG12, SlABI5 and SlNCED3 and decreases their H3K27me3 levels, and therefore activates their expression and mediates ABA-induced leaf senescence in tomato. Taken together, these results demonstrate that SlJMJ4 plays a positive role in leaf senescence in tomato and is implicated in ABA-induced leaf senescence by binding to many key genes related to ABA synthesis and signaling, transcription regulation and senescence and hence promoting their H3K27me3 demethylation.
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Affiliation(s)
- Xiaochun Ding
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Dandan Zhang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Dachuan Gu
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Zhiwei Li
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hanzhi Liang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong Zhu
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yueming Jiang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Xuewu Duan
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
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36
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Miryeganeh M. Epigenetic Mechanisms of Senescence in Plants. Cells 2022; 11:251. [PMID: 35053367 PMCID: PMC8773728 DOI: 10.3390/cells11020251] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 01/08/2022] [Accepted: 01/10/2022] [Indexed: 12/30/2022] Open
Abstract
Senescence is a major developmental transition in plants that requires a massive reprogramming of gene expression and includes various layers of regulations. Senescence is either an age-dependent or a stress-induced process, and is under the control of complex regulatory networks that interact with each other. It has been shown that besides genetic reprogramming, which is an important aspect of plant senescence, transcription factors and higher-level mechanisms, such as epigenetic and small RNA-mediated regulators, are also key factors of senescence-related genes. Epigenetic mechanisms are an important layer of this multilevel regulatory system that change the activity of transcription factors (TFs) and play an important role in modulating the expression of senescence-related gene. They include chromatin remodeling, DNA methylation, histone modification, and the RNA-mediated control of transcription factors and genes. This review provides an overview of the known epigenetic regulation of plant senescence, which has mostly been studied in the form of leaf senescence, and it also covers what has been reported about whole-plant senescence.
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Affiliation(s)
- Matin Miryeganeh
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0412, Japan
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37
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Cell division in the shoot apical meristem is a trigger for miR156 decline and vegetative phase transition in Arabidopsis. Proc Natl Acad Sci U S A 2021; 118:2115667118. [PMID: 34750273 DOI: 10.1073/pnas.2115667118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2021] [Indexed: 11/18/2022] Open
Abstract
What determines the rate at which a multicellular organism matures is a fundamental question in biology. In plants, the decline of miR156 with age serves as an intrinsic, evolutionarily conserved timer for the juvenile-to-adult phase transition. However, the way in which age regulates miR156 abundance is poorly understood. Here, we show that the rate of decline in miR156 is correlated with developmental age rather than chronological age. Mechanistically, we found that cell division in the apical meristem is a trigger for miR156 decline. The transcriptional activity of MIR156 genes is gradually attenuated by the deposition of the repressive histone mark H3K27me3 along with cell division. Our findings thus provide a plausible explanation of why the maturation program of a multicellular organism is unidirectional and irreversible under normal growth conditions and suggest that cell quiescence is the fountain of youth in plants.
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38
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Zioutopoulou A, Patitaki E, Xu T, Kaiserli E. The Epigenetic Mechanisms Underlying Thermomorphogenesis and Heat Stress Responses in Arabidopsis. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112439. [PMID: 34834802 PMCID: PMC8624032 DOI: 10.3390/plants10112439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/05/2021] [Accepted: 11/09/2021] [Indexed: 05/28/2023]
Abstract
Integration of temperature cues is crucial for plant survival and adaptation. Global warming is a prevalent issue, especially in modern agriculture, since the global rise in average temperature is expected to impact crop productivity worldwide. Hence, better understanding of the mechanisms by which plants respond to warmer temperatures is very important. This review focuses on the epigenetic mechanisms implicated in plant responses to high temperature and distinguishes the different epigenetic events that occur at warmer average temperatures, leading to thermomorphogenic responses, or subjected to extreme warm temperatures, leading to heat stress.
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39
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Zheng L, Li C, Ma X, Zhou H, Liu Y, Wang P, Yang H, Tamada Y, Huang J, Wang C, Hu Z, Wang X, Wang G, Li H, Hu J, Liu X, Zhou C, Zhang Y. Functional interplay of histone lysine 2-hydroxyisobutyrylation and acetylation in Arabidopsis under dark-induced starvation. Nucleic Acids Res 2021; 49:7347-7360. [PMID: 34165567 PMCID: PMC8287917 DOI: 10.1093/nar/gkab536] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 06/02/2021] [Accepted: 06/09/2021] [Indexed: 02/03/2023] Open
Abstract
Lysine 2-hydroxyisobutyrylation (Khib) is a novel type of histone acylation whose prevalence and function in plants remain unclear. Here, we identified 41 Khib sites on histones in Arabidopsis thaliana, which did not overlap with frequently modified N-tail lysines (e.g. H3K4, H3K9 and H4K8). Chromatin immunoprecipitation-sequencing (ChIP-seq) assays revealed histone Khib in 35% of protein-coding genes. Most Khib peaks were located in genic regions, and they were highly enriched at the transcription start sites. Histone Khib is highly correlated with acetylation (ac), particularly H3K23ac, which it largely resembles in its genomic and genic distribution. Notably, co-enrichment of histone Khib and H3K23ac correlates with high gene expression levels. Metabolic profiling, transcriptome analyses, and ChIP-qPCR revealed that histone Khib and H3K23ac are co-enriched on genes involved in starch and sucrose metabolism, pentose and glucuronate interconversions, and phenylpropanoid biosynthesis, and help fine-tune plant response to dark-induced starvation. These findings suggest that Khib and H3K23ac may act in concert to promote high levels of gene transcription and regulate cellular metabolism to facilitate plant adaption to stress. Finally, HDA6 and HDA9 are involved in removing histone Khib. Our findings reveal Khib as a conserved yet unique plant histone mark acting with lysine acetylation in transcription-associated epigenomic processes.
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Affiliation(s)
- Lanlan Zheng
- Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China.,Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Academy of Bio-Medicine Research, Hubei University of Medicine, Shiyan 442000, China
| | - Chen Li
- Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China.,Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Academy of Bio-Medicine Research, Hubei University of Medicine, Shiyan 442000, China
| | - Xueping Ma
- Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China.,Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Academy of Bio-Medicine Research, Hubei University of Medicine, Shiyan 442000, China
| | - Hanlin Zhou
- Key Laboratory of Three Gorges Regional Plant Genetics & Germplasm Enhancement (CTGU) /Biotechnology Research Center, China Three Gorges University, Yichang 443002, China
| | - Yuan Liu
- Key Laboratory of Three Gorges Regional Plant Genetics & Germplasm Enhancement (CTGU) /Biotechnology Research Center, China Three Gorges University, Yichang 443002, China
| | - Ping Wang
- Institute for Interdisciplinary Research, Jianghan University, Wuhan 430056, China
| | - Huilan Yang
- Institute for Interdisciplinary Research, Jianghan University, Wuhan 430056, China
| | - Yosuke Tamada
- School of Engineering, Utsunomiya University, Utsunomiya 321-8585, Japan
| | - Ji Huang
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York 10003, USA
| | - Chunfei Wang
- Center for Multi-Omics Research, Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Science, Henan University, Kaifeng 475001, China
| | - Zhubing Hu
- Center for Multi-Omics Research, Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Science, Henan University, Kaifeng 475001, China
| | - Xuening Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an Shaanxi 710119, China
| | - Guodong Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an Shaanxi 710119, China
| | - Haihong Li
- Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China
| | - Juntao Hu
- Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China
| | - Xiaoyun Liu
- Institute for Interdisciplinary Research, Jianghan University, Wuhan 430056, China
| | - Chao Zhou
- Key Laboratory of Three Gorges Regional Plant Genetics & Germplasm Enhancement (CTGU) /Biotechnology Research Center, China Three Gorges University, Yichang 443002, China
| | - Yonghong Zhang
- Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China.,Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Academy of Bio-Medicine Research, Hubei University of Medicine, Shiyan 442000, China
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40
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Singh RK, Prasad M. Delineating the epigenetic regulation of heat and drought response in plants. Crit Rev Biotechnol 2021; 42:548-561. [PMID: 34289772 DOI: 10.1080/07388551.2021.1946004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Being sessile in nature, plants cannot overlook the incursion of unfavorable environmental conditions, including heat and drought. Heat and drought severely affect plant growth, development, reproduction and therefore productivity which poses a severe threat to global food security. Plants respond to these hostile environmental circumstances by rearranging their genomic and molecular architecture. One such modification commonly known as epigenetic changes involves the perishable to inheritable changes in DNA or DNA-binding histone proteins leading to modified chromatin organization. Reversible epigenetic modifications include DNA methylation, exchange of histone variants, histone methylation, histone acetylation, ATP-dependent nucleosome remodeling, and others. These modifications are employed to regulate the spatial and temporal expression of genes in response to external stimuli or specific developmental requirements. Understanding the epigenetic regulation of stress-related gene expression in response to heat and drought would commence manifold avenues for crop improvement through molecular breeding or biotechnological approaches.
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Affiliation(s)
| | - Manoj Prasad
- National Institute of Plant Genome Research, New Delhi, India
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41
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Guo Y, Ren G, Zhang K, Li Z, Miao Y, Guo H. Leaf senescence: progression, regulation, and application. MOLECULAR HORTICULTURE 2021; 1:5. [PMID: 37789484 PMCID: PMC10509828 DOI: 10.1186/s43897-021-00006-9] [Citation(s) in RCA: 119] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/11/2021] [Indexed: 05/24/2023]
Abstract
Leaf senescence, the last stage of leaf development, is a type of postmitotic senescence and is characterized by the functional transition from nutrient assimilation to nutrient remobilization which is essential for plants' fitness. The initiation and progression of leaf senescence are regulated by a variety of internal and external factors such as age, phytohormones, and environmental stresses. Significant breakthroughs in dissecting the molecular mechanisms underpinning leaf senescence have benefited from the identification of senescence-altered mutants through forward genetic screening and functional assessment of hundreds of senescence-associated genes (SAGs) via reverse genetic research in model plant Arabidopsis thaliana as well as in crop plants. Leaf senescence involves highly complex genetic programs that are tightly tuned by multiple layers of regulation, including chromatin and transcription regulation, post-transcriptional, translational and post-translational regulation. Due to the significant impact of leaf senescence on photosynthesis, nutrient remobilization, stress responses, and productivity, much effort has been made in devising strategies based on known senescence regulatory mechanisms to manipulate the initiation and progression of leaf senescence, aiming for higher yield, better quality, or improved horticultural performance in crop plants. This review aims to provide an overview of leaf senescence and discuss recent advances in multi-dimensional regulation of leaf senescence from genetic and molecular network perspectives. We also put forward the key issues that need to be addressed, including the nature of leaf age, functional stay-green trait, coordination between different regulatory pathways, source-sink relationship and nutrient remobilization, as well as translational researches on leaf senescence.
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Affiliation(s)
- Yongfeng Guo
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101 Shandong China
| | - Guodong Ren
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Kewei Zhang
- Institute of Plant Genetics and Developmental Biology, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004 Zhejiang China
| | - Zhonghai Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083 China
| | - Ying Miao
- Fujian Provincial Key Laboratory of Plant Functional Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Hongwei Guo
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, 518055 Guangdong China
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42
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Lim CJ, Ali A, Park J, Shen M, Park KS, Baek D, Yun DJ. HOS15-PWR chromatin remodeling complex positively regulates cold stress in Arabidopsis. PLANT SIGNALING & BEHAVIOR 2021; 16:1893978. [PMID: 33641608 PMCID: PMC8078502 DOI: 10.1080/15592324.2021.1893978] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/18/2021] [Accepted: 02/18/2021] [Indexed: 06/12/2023]
Abstract
Cold stress is a major environmental constraint that restrains plant growth and productivity. To cope with cold stress, plants must be able to perceive a cold signal and regulate the expression of cold-regulated (COR) genes. In our recent study, we showed that Arabidopsis HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE 15 (HOS15) acts as a substrate receptor for CULLIN4-based ubiquitin E3 ligase complex to promote cold-induced histone deacetylase 2 C (HD2C) degradation that allows the activation of COR genes. Additionally, we found that POWERDRESS (PWR), a HOS15-interacting protein, is required for the association of HOS15 with COR gene chromatin and HD2C degradation. The HOS15/PWR complex interacts with and recruits CBF transcription factors to the promoters of COR genes. Collectively, our previous findings suggest that HOS15 and PWR function as positive regulators for the expression of COR genes, and promote cold tolerance. Accordingly, we herein discuss the role of PWR in cold tolerance.
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Affiliation(s)
- Chae Jin Lim
- Institute of Glocal Disease Control, Konkuk University, Seoul, Republic of Korea
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Akhtar Ali
- Institute of Glocal Disease Control, Konkuk University, Seoul, Republic of Korea
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Junghoon Park
- Institute of Glocal Disease Control, Konkuk University, Seoul, Republic of Korea
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Mingzhe Shen
- Division of Applied Life Science (Bk21plus), Plant Molecular Biology and Biotechnology Research Center, Research Institute of Life Sciences, Gyeongsang National University, Jinju, Republic of Korea
| | - Ki Suk Park
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Dongwon Baek
- Division of Applied Life Science (Bk21plus), Plant Molecular Biology and Biotechnology Research Center, Research Institute of Life Sciences, Gyeongsang National University, Jinju, Republic of Korea
| | - Dea-Jin Yun
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
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43
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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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44
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Wang TJ, Huang S, Zhang A, Guo P, Liu Y, Xu C, Cong W, Liu B, Xu ZY. JMJ17-WRKY40 and HY5-ABI5 modules regulate the expression of ABA-responsive genes in Arabidopsis. THE NEW PHYTOLOGIST 2021; 230:567-584. [PMID: 33423315 DOI: 10.1111/nph.17177] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 12/25/2020] [Indexed: 05/09/2023]
Abstract
Abscisic acid (ABA) plays a crucial role in the adaptation of young seedlings to environmental stresses. However, the role of epigenetic components and core transcriptional machineries in the effect of ABA on seed germination and seedling growth remain unclear. Here, we show that a histone 3 lysine 4 (H3K4) demethylase, JMJ17, regulates the expression of ABA-responsive genes during seed germination and seedling growth. Using comparative interactomics, WRKY40, a central transcriptional repressor in ABA signaling, was shown to interact with JMJ17. WRKY40 facilitates the recruitment of JMJ17 to the ABI5 chromatin, which removes gene activation marks (H3K4me3) from the ABI5 chromatin, thereby repressing its expression. Additionally, WRKY40 represses the transcriptional activation activity of HY5, which can activate ABI5 expression by directly binding to its promoter. An increase in ABA concentrations decreases the affinity of WRKY40 for the ABI5 promoter. Thus, WRKY40 and JMJ17 are released from the ABI5 chromatin, activating HY5. The accumulated ABI5 protein further shows heteromeric interaction with HY5, and thus synergistically activates its own expression. Our findings reveal a novel transcriptional switch, composed of JMJ17-WRKY40 and HY5-ABI5 modules, which regulates the ABA response during seed germination and seedling development in Arabidopsis.
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Affiliation(s)
- Tian-Jing Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Shuangzhan Huang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ai Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Peng Guo
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Yutong Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Chunming Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Weixuan Cong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
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45
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Chen J, Liu J, Jiang J, Qian S, Song J, Kabara R, Delo I, Serino G, Liu F, Hua Z, Zhong X. F-box protein CFK1 interacts with and degrades de novo DNA methyltransferase in Arabidopsis. THE NEW PHYTOLOGIST 2021; 229:3303-3317. [PMID: 33216996 PMCID: PMC7902366 DOI: 10.1111/nph.17103] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/16/2020] [Indexed: 05/07/2023]
Abstract
DNA methylation plays crucial roles in cellular development and stress responses through gene regulation and genome stability control. Precise regulation of DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2), the de novo Arabidopsis DNA methyltransferase, is crucial to maintain DNA methylation homeostasis to ensure genome integrity. Compared with the extensive studies on DRM2 targeting mechanisms, little information is known regarding the quality control of DRM2 itself. Here, we conducted yeast two-hybrid screen assay and identified an E3 ligase, COP9 INTERACTING F-BOX KELCH 1 (CFK1), as a novel DRM2-interacting partner and targets DRM2 for degradation via the ubiquitin-26S proteasome pathway in Arabidopsis thaliana. We also performed whole genome bisulfite sequencing (BS-seq) to determine the biological significance of CFK1-mediated DRM2 degradation. Loss-of-function CFK1 leads to increased DRM2 protein abundance and overexpression of CFK1 showed reduced DRM2 protein levels. Consistently, CFK1 overexpression induces genome-wide CHH hypomethylation and transcriptional de-repression at specific DRM2 target loci. This study uncovered a distinct mechanism regulating de novo DNA methyltransferase by CFK1 to control DNA methylation level.
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Affiliation(s)
- Jiani Chen
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, USA
| | - Jie Liu
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, USA
| | - Jianjun Jiang
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- 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 210014, China
| | - Shuiming Qian
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, USA
| | - Jingwen Song
- Department of Environmental and Plant Biology & Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, OH 45701, USA
| | - Rachel Kabara
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Isabel Delo
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Giovanna Serino
- Department of Biology and Biotechnology, Sapienza Università di Roma, 00185 Rome, Italy
| | - 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 210014, China
| | - Zhihua Hua
- Department of Environmental and Plant Biology & Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, OH 45701, USA
| | - Xuehua Zhong
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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46
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Jiang J, Liu J, Sanders D, Qian S, Ren W, Song J, Liu F, Zhong X. UVR8 interacts with de novo DNA methyltransferase and suppresses DNA methylation in Arabidopsis. NATURE PLANTS 2021; 7:184-197. [PMID: 33495557 PMCID: PMC7889724 DOI: 10.1038/s41477-020-00843-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 12/17/2020] [Indexed: 05/03/2023]
Abstract
DNA methylation is an important epigenetic gene regulatory mechanism conserved in eukaryotes. Emerging evidence shows DNA methylation alterations in response to environmental cues. However, the mechanism of how cells sense these signals and reprogramme the methylation landscape is poorly understood. Here, we uncovered a connection between ultraviolet B (UVB) signalling and DNA methylation involving UVB photoreceptor (UV RESISTANCE LOCUS 8 (UVR8)) and a de novo DNA methyltransferase (DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2)) in Arabidopsis. We demonstrated that UVB acts through UVR8 to inhibit DRM2-mediated DNA methylation and transcriptional de-repression. Interestingly, DNA transposons with high DNA methylation are more sensitive to UVB irradiation. Mechanistically, UVR8 interacts with and negatively regulates DRM2 by preventing its chromatin association and inhibiting the methyltransferase activity. Collectively, this study identifies UVB as a potent inhibitor of DNA methylation and provides mechanistic insights into how signalling transduction cascades intertwine with chromatin to guide genome functions.
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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
| | - Jie Liu
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - Dean Sanders
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - Shuiming Qian
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - Wendan Ren
- Department of Biochemistry, University of California, Riverside, CA, USA
| | - Jikui Song
- Department of Biochemistry, University of California, Riverside, CA, 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.
| | - Xuehua Zhong
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA.
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Favero DS, Lambolez A, Sugimoto K. Molecular pathways regulating elongation of aerial plant organs: a focus on light, the circadian clock, and temperature. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:392-420. [PMID: 32986276 DOI: 10.1111/tpj.14996] [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: 07/16/2020] [Revised: 09/11/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Abstract
Organs such as hypocotyls and petioles rapidly elongate in response to shade and temperature cues, contributing to adaptive responses that improve plant fitness. Growth plasticity in these organs is achieved through a complex network of molecular signals. Besides conveying information from the environment, this signaling network also transduces internal signals, such as those associated with the circadian clock. A number of studies performed in Arabidopsis hypocotyls, and to a lesser degree in petioles, have been informative for understanding the signaling networks that regulate elongation of aerial plant organs. In particular, substantial progress has been made towards understanding the molecular mechanisms that regulate responses to light, the circadian clock, and temperature. Signals derived from these three stimuli converge on the BAP module, a set of three different types of transcription factors that interdependently promote gene transcription and growth. Additional key positive regulators of growth that are also affected by environmental cues include the CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) and SUPPRESSOR OF PHYA-105 (SPA) E3 ubiquitin ligase proteins. In this review we summarize the key signaling pathways that regulate the growth of hypocotyls and petioles, focusing specifically on molecular mechanisms important for transducing signals derived from light, the circadian clock, and temperature. While it is clear that similarities abound between the signaling networks at play in these two organs, there are also important differences between the mechanisms regulating growth in hypocotyls and petioles.
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Affiliation(s)
- David S Favero
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Alice Lambolez
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
- Department of Biological Sciences, The University of Tokyo, Tokyo, 119-0033, Japan
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
- Department of Biological Sciences, The University of Tokyo, Tokyo, 119-0033, Japan
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48
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Qi H, Xia FN, Xiao S. Autophagy in plants: Physiological roles and post-translational regulation. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:161-179. [PMID: 32324339 DOI: 10.1111/jipb.12941] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 04/22/2020] [Indexed: 05/20/2023]
Abstract
In eukaryotes, autophagy helps maintain cellular homeostasis by degrading and recycling cytoplasmic materials via a tightly regulated pathway. Over the past few decades, significant progress has been made towards understanding the physiological functions and molecular regulation of autophagy in plant cells. Increasing evidence indicates that autophagy is essential for plant responses to several developmental and environmental cues, functioning in diverse processes such as senescence, male fertility, root meristem maintenance, responses to nutrient starvation, and biotic and abiotic stress. Recent studies have demonstrated that, similar to nonplant systems, the modulation of core proteins in the plant autophagy machinery by posttranslational modifications such as phosphorylation, ubiquitination, lipidation, S-sulfhydration, S-nitrosylation, and acetylation is widely involved in the initiation and progression of autophagy. Here, we provide an overview of the physiological roles and posttranslational regulation of autophagy in plants.
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Affiliation(s)
- Hua Qi
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Fan-Nv Xia
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Shi Xiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
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Wang J, Nan N, Li N, Liu Y, Wang TJ, Hwang I, Liu B, Xu ZY. A DNA Methylation Reader-Chaperone Regulator-Transcription Factor Complex Activates OsHKT1;5 Expression during Salinity Stress. THE PLANT CELL 2020; 32:3535-3558. [PMID: 32938753 PMCID: PMC7610284 DOI: 10.1105/tpc.20.00301] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/31/2020] [Accepted: 09/13/2020] [Indexed: 05/20/2023]
Abstract
Irrigated lands are increasingly salinized, which adversely affects agricultural productivity. To respond to high sodium (Na+) concentrations, plants harbor multiple Na+ transport systems. Rice (Oryza sativa) HIGH-AFFINITY POTASSIUM (K+) TRANSPORTER1;5 (OsHKT1;5), a Na+-selective transporter, maintains K+/Na+ homeostasis under salt stress. However, the mechanism regulating OsHKT1;5 expression remains unknown. Here, we present evidence that a protein complex consisting of rice BCL-2-ASSOCIATED ATHANOGENE4 (OsBAG4), OsMYB106, and OsSUVH7 regulates OsHKT1;5 expression in response to salt stress. We isolated a salt stress-sensitive mutant, osbag4-1, that showed significantly reduced OsHKT1;5 expression and reduced K+ and elevated Na+ levels in shoots. Using comparative interactomics, we isolated two OsBAG4-interacting proteins, OsMYB106 (a MYB transcription factor) and OsSUVH7 (a DNA methylation reader), that were crucial for OsHKT1;5 expression. OsMYB106 and OsSUVH7 bound to the MYB binding cis-element (MYBE) and the miniature inverted-repeat transposable element (MITE) upstream of the MYBE, respectively, in the OsHKT1;5 promoter. OsBAG4 functioned as a bridge between OsSUVH7 and OsMYB106 to facilitate OsMYB106 binding to the consensus MYBE in the OsHKT1;5 promoter, thereby activating the OsHKT1;5 expression. Elimination of the MITE or knockout of OsMYB106 or OsSUVH7 decreased OsHKT1;5 expression and increased salt sensitivity. Our findings reveal a transcriptional complex, consisting of a DNA methylation reader, a chaperone regulator, and a transcription factor, that collaboratively regulate OsHKT1;5 expression during salinity stress.
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Affiliation(s)
- Jie Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, People's Republic of China
| | - Nan Nan
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, People's Republic of China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, People's Republic of China
| | - Yutong Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, People's Republic of China
| | - Tian-Jing Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, People's Republic of China
| | - Inhwan Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, People's Republic of China
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, People's Republic of China
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50
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Hinckley WE, Brusslan JA. Gene expression changes occurring at bolting time are associated with leaf senescence in Arabidopsis. PLANT DIRECT 2020; 4:e00279. [PMID: 33204935 PMCID: PMC7649007 DOI: 10.1002/pld3.279] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 09/13/2020] [Accepted: 09/30/2020] [Indexed: 05/29/2023]
Abstract
In plants, the vegetative to reproductive phase transition (termed bolting in Arabidopsis) generally precedes age-dependent leaf senescence (LS). Many studies describe a temporal link between bolting time and LS, as plants that bolt early, senesce early, and plants that bolt late, senesce late. The molecular mechanisms underlying this relationship are unknown and are potentially agriculturally important, as they may allow for the development of crops that can overcome early LS caused by stress-related early-phase transition. We hypothesized that leaf gene expression changes occurring in synchrony with bolting were regulating LS. ARABIDOPSIS TRITHORAX (ATX) enzymes are general methyltransferases that regulate the adult vegetative to reproductive phase transition. We generated an atx1, atx3, and atx4 (atx1,3,4) triple T-DNA insertion mutant that displays both early bolting and early LS. This mutant was used in an RNA-seq time-series experiment to identify gene expression changes in rosette leaves that are likely associated with bolting. By comparing the early bolting mutant to vegetative WT plants of the same age, we were able to generate a list of differentially expressed genes (DEGs) that change expression with bolting as the plants age. We trimmed the list by intersection with publicly available WT datasets, which removed genes from our DEG list that were atx1,3,4 specific. The resulting 398 bolting-associated genes (BAGs) are differentially expressed in a mature rosette leaf at bolting. The BAG list contains many well-characterized LS regulators (ORE1, WRKY45, NAP, WRKY28), and GO analysis revealed enrichment for LS and LS-related processes. These bolting-associated LS regulators may contribute to the temporal coupling of bolting time to LS.
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Affiliation(s)
| | - Judy A. Brusslan
- Department of Biological SciencesCalifornia State UniversityLong Beach, Long BeachCAUSA
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