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Bente H, Köhler C. Molecular basis and evolutionary drivers of endosperm-based hybridization barriers. PLANT PHYSIOLOGY 2024; 195:155-169. [PMID: 38298124 PMCID: PMC11060687 DOI: 10.1093/plphys/kiae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 01/05/2024] [Accepted: 01/06/2024] [Indexed: 02/02/2024]
Abstract
The endosperm, a transient seed tissue, plays a pivotal role in supporting embryo growth and germination. This unique feature sets flowering plants apart from gymnosperms, marking an evolutionary innovation in the world of seed-bearing plants. Nevertheless, the importance of the endosperm extends beyond its role in providing nutrients to the developing embryo by acting as a versatile protector, preventing hybridization events between distinct species and between individuals with different ploidy. This phenomenon centers on growth and differentiation of the endosperm and the speed at which both processes unfold. Emerging studies underscore the important role played by type I MADS-box transcription factors, including the paternally expressed gene PHERES1. These factors, along with downstream signaling pathways involving auxin and abscisic acid, are instrumental in regulating endosperm development and, consequently, the establishment of hybridization barriers. Moreover, mutations in various epigenetic regulators mitigate these barriers, unveiling a complex interplay of pathways involved in their formation. In this review, we discuss the molecular underpinnings of endosperm-based hybridization barriers and their evolutionary drivers.
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Affiliation(s)
- Heinrich Bente
- Department of Plant Reproductive Biology and Epigenetics, Max Planck Institute of Molecular Plant Physiology, Potsdam 14476, Germany
| | - Claudia Köhler
- Department of Plant Reproductive Biology and Epigenetics, Max Planck Institute of Molecular Plant Physiology, Potsdam 14476, Germany
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
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2
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Xu L, Zheng S, Witzel K, Van De Slijke E, Baekelandt A, Mylle E, Van Damme D, Cheng J, De Jaeger G, Inzé D, Jiang H. Chromatin attachment to the nuclear matrix represses hypocotyl elongation in Arabidopsis thaliana. Nat Commun 2024; 15:1286. [PMID: 38346986 PMCID: PMC10861482 DOI: 10.1038/s41467-024-45577-5] [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: 07/03/2023] [Accepted: 01/26/2024] [Indexed: 02/15/2024] Open
Abstract
The nuclear matrix is a nuclear compartment that has diverse functions in chromatin regulation and transcription. However, how this structure influences epigenetic modifications and gene expression in plants is largely unknown. In this study, we show that a nuclear matrix binding protein, AHL22, together with the two transcriptional repressors FRS7 and FRS12, regulates hypocotyl elongation by suppressing the expression of a group of genes known as SMALL AUXIN UP RNAs (SAURs) in Arabidopsis thaliana. The transcriptional repression of SAURs depends on their attachment to the nuclear matrix. The AHL22 complex not only brings these SAURs, which contain matrix attachment regions (MARs), to the nuclear matrix, but it also recruits the histone deacetylase HDA15 to the SAUR loci. This leads to the removal of H3 acetylation at the SAUR loci and the suppression of hypocotyl elongation. Taken together, our results indicate that MAR-binding proteins act as a hub for chromatin and epigenetic regulators. Moreover, we present a mechanism by which nuclear matrix attachment to chromatin regulates histone modifications, transcription, and hypocotyl elongation.
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Affiliation(s)
- Linhao Xu
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466, Germany
| | - Shiwei Zheng
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466, Germany
| | - Katja Witzel
- Leibniz Institute of Vegetable and Ornamental Crops, Großbeeren, 14979, Germany
| | - Eveline Van De Slijke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Alexandra Baekelandt
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Evelien Mylle
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Daniel Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Jinping Cheng
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466, Germany
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Hua Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466, Germany.
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3
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Wong MM, Huang XJ, Bau YC, Verslues PE. AT Hook-Like 10 phosphorylation determines ribosomal RNA processing 6-like 1 (RRP6L1) chromatin association and growth suppression during water stress. PLANT, CELL & ENVIRONMENT 2024; 47:24-37. [PMID: 37727952 DOI: 10.1111/pce.14725] [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: 06/09/2023] [Revised: 09/08/2023] [Accepted: 09/10/2023] [Indexed: 09/21/2023]
Abstract
Phosphorylation of AT Hook-Like 10 (AHL10), one of the AT-hook family of plant-specific DNA binding proteins, is critical for growth suppression during moderate severity drought (low water potential, ψw ) stress. To understand how AHL10 phosphorylation determines drought response, we identified putative AHL10 interacting proteins and further characterized interaction with RRP6L1, a protein involved in epigenetic regulation. RRP6L1 and AHL10 mutants, as well as ahl10-1rrp6l1-2, had similar phenotypes of increased growth maintenance during low ψw . Chromatin precipitation demonstrated that RRP6L1 chromatin association increased during low ψw stress and was dependent upon AHL10 phosphorylation. Transcriptome analyses showed that AHL10 and RRP6L1 have concordant effects on expression of stress- and development-related genes. Together these results indicate that stress signalling can act via AHL10 phosphorylation to control the chromatin association of the key regulatory protein RRP6L1. AHL10 and RRP6L1 interaction in meristem cells is part of a mechanism to downregulate growth during low ψw stress. Interestingly, the loss of AHL13, which is homologous to AHL10 and phosphorylated at a similar C-terminal site, blocked the enhanced growth maintenance of ahl10-1. Thus, AHL10 and AHL13, despite their close homology, are not redundant but rather have distinct roles, likely related to the formation of AHL hetero-complexes.
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Affiliation(s)
- Min May Wong
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Xin-Jie Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yu-Chiuan Bau
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Paul E Verslues
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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4
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Zeng Q, Song L, Xia M, Zheng Z, Chen Z, Che X, Liu D. Overexpression of AHL proteins enhances root hair production by altering the transcription of RHD6-downstream genes. PLANT DIRECT 2023; 7:e517. [PMID: 37577137 PMCID: PMC10416611 DOI: 10.1002/pld3.517] [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: 03/16/2023] [Revised: 05/20/2023] [Accepted: 07/03/2023] [Indexed: 08/15/2023]
Abstract
AT-HOOK MOTIF NUCLEAR LOCALIZED (AHL) proteins occur in all sequenced plant species. They bind to the AT-rich DNA sequences in chromosomes and regulate gene transcription related to diverse biological processes. However, the molecular mechanism underlying how AHL proteins regulate gene transcription is poorly understood. In this research, we used root hair production as a readout to study the function of two Arabidopsis AHL proteins, AHL17, and its closest homolog AHL28. Overexpression of AHL17 or AHL28 greatly enhanced root hair production by increasing the transcription of an array of genes downstream of RHD6. RHD6 is a key transcription factor that regulates root hair development. Mutation of RHD6 completely suppressed the overproduction of root hairs by blocking the transcription of AHL17-activated genes. The overexpression of AHL17 or AHL28, however, neither affected the transcription of RHD6 nor the accumulation of RHD6 protein. These two AHL proteins also did not directly interact with RHD6. Furthermore, we found that three members of the Heat Shock Protein70 family, which have been annotated as the subunits of the plant Mediator complex, could form a complex with both AHL17 and RHD6. Our research might reveal a previously unrecognized mechanism of how AHL proteins regulate gene transcription.
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Affiliation(s)
- Qike Zeng
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life SciencesTsinghua UniversityBeijingChina
| | - Li Song
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural University at WenjiangChengduChina
| | - Mingzhe Xia
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life SciencesTsinghua UniversityBeijingChina
| | - Zai Zheng
- Hainan Yazhou Bay Seed LaboratorySanyaChina
| | - Ziang Chen
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life SciencesTsinghua UniversityBeijingChina
| | - Ximing Che
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life SciencesTsinghua UniversityBeijingChina
| | - Dong Liu
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life SciencesTsinghua UniversityBeijingChina
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5
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Zhang S, Wang T, Lima RM, Pettkó-Szandtner A, Kereszt A, Downie JA, Kondorosi E. Widely conserved AHL transcription factors are essential for NCR gene expression and nodule development in Medicago. NATURE PLANTS 2023; 9:280-288. [PMID: 36624259 PMCID: PMC9946822 DOI: 10.1038/s41477-022-01326-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 12/02/2022] [Indexed: 05/13/2023]
Abstract
Symbiotic nitrogen fixation by Rhizobium bacteria in the cells of legume root nodules alleviates the need for nitrogen fertilizers. Nitrogen fixation requires the endosymbionts to differentiate into bacteroids which can be reversible or terminal. The latter is controlled by the plant, it is more beneficial and has evolved in multiple clades of the Leguminosae family. The plant effectors of terminal differentiation in inverted repeat-lacking clade legumes (IRLC) are nodule-specific cysteine-rich (NCR) peptides, which are absent in legumes such as soybean where there is no terminal differentiation of rhizobia. It was assumed that NCRs co-evolved with specific transcription factors, but our work demonstrates that expression of NCR genes does not require NCR-specific transcription factors. Introduction of the Medicago truncatula NCR169 gene under its own promoter into soybean roots resulted in its nodule-specific expression, leading to bacteroid changes associated with terminal differentiation. We identified two AT-Hook Motif Nuclear Localized (AHL) transcription factors from both M. truncatula and soybean nodules that bound to AT-rich sequences in the NCR169 promoter inducing its expression. Whereas mutation of NCR169 arrested bacteroid development at a late stage, the absence of MtAHL1 or MtAHL2 completely blocked bacteroid differentiation indicating that they also regulate other NCR genes required for the development of nitrogen-fixing nodules. Regulation of NCRs by orthologous transcription factors in non-IRLC legumes opens up the possibility of increasing the efficiency of nitrogen fixation in legumes lacking NCRs.
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Affiliation(s)
- Senlei Zhang
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | - Ting Wang
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | - Rui M Lima
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | | | - Attila Kereszt
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | - J Allan Downie
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
- John Innes Centre, Norwich, UK
| | - Eva Kondorosi
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary.
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Dahro B, Wang Y, Khan M, Zhang Y, Fang T, Ming R, Li C, Liu JH. Two AT-Hook proteins regulate A/NINV7 expression to modulate sucrose catabolism for cold tolerance in Poncirus trifoliata. THE NEW PHYTOLOGIST 2022; 235:2331-2349. [PMID: 35695205 DOI: 10.1111/nph.18304] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/05/2022] [Indexed: 06/15/2023]
Abstract
Invertase (INV)-mediated sucrose (Suc) hydrolysis, leading to the irreversible production of glucose (Glc) and fructose (Frc), plays an essential role in abiotic stress tolerance of plants. However, the regulatory network associated with the Suc catabolism in response to cold environment remains largely elusive. Herein, the cold-induced alkaline/neutral INV gene PtrA/NINV7 of trifoliate orange (Poncirus trifoliata (L.) Raf.) was shown to function in cold tolerance via mediating the Suc hydrolysis. Meanwhile, a nuclear matrix-associated region containing A/T-rich sequences within its promoter was indispensable for the cold induction of PtrA/NINV7. Two AT-Hook Motif Containing Nuclear Localized (AHL) proteins, PtrAHL14 and PtrAHL17, were identified as upstream transcriptional activators of PtrA/NINV7 by interacting with the A/T-rich motifs. PtrAHL14 and PtrAHL17 function positively in the cold tolerance by modulating PtrA/NINV7-mediated Suc catabolism. Furthermore, both PtrAHL14 and PtrAHL17 could form homo- and heterodimers between each other, and interacted with two histone acetyltransferases (HATs), GCN5 and TAF1, leading to elevated histone3 acetylation level under the cold stress. Taken together, our findings unraveled a new cold-responsive signaling module (AHL14/17-HATs-A/NINV7) for orchestration of Suc catabolism and cold tolerance, which shed light on the molecular mechanisms underlying Suc catabolism catalyzed by A/NINVs under cold stress.
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Affiliation(s)
- Bachar Dahro
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
- Department of Horticulture, Faculty of Agriculture, Tishreen University, Lattakia, Syria
| | - Yue Wang
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Madiha Khan
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yang Zhang
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tian Fang
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ruhong Ming
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chunlong Li
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Ji-Hong Liu
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
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7
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Rahimi A, Karami O, Balazadeh S, Offringa R. miR156-independent repression of the ageing pathway by longevity-promoting AHL proteins in Arabidopsis. THE NEW PHYTOLOGIST 2022; 235:2424-2438. [PMID: 35642455 PMCID: PMC9540020 DOI: 10.1111/nph.18292] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 05/25/2022] [Indexed: 05/27/2023]
Abstract
Plants age by developmental phase changes. In Arabidopsis, the juvenile to adult vegetative phase change (VPC) is marked by clear heteroblastic changes in leaves. VPC and the subsequent vegetative to reproductive phase change are promoted by SQUAMOSA PROMOTOR BINDING PROTEIN-LIKE (SPL) transcription factors and repressed by miR156/157 targeting SPL transcripts. By genetic, phenotypic, and gene expression analyses, we studied the role of the longevity-promoting AT-HOOK MOTIF NUCLEAR LOCALIZED 15 (AHL15) and family members in SPL-driven plant ageing. Arabidopsis ahl loss-of-function mutants showed accelerated VPC and flowering, whereas AHL15 overexpression delayed these phase changes. Expression analysis and tissue-specific AHL15 overexpression revealed that AHL15 affects VPC and flowering time directly through its expression in the shoot apical meristem and young leaves, and that AHL15 represses SPL2/9/13/15 gene expression in a miR156/157-independent manner. The juvenile traits of spl loss-of-function mutants appeared to depend on enhanced expression of the AHL15 gene, whereas SPL activity prevented vegetative growth from axillary meristem by repressing AHL15 expression. Our results place AHL15 and close family members together with SPLs in a reciprocal regulatory feedback loop that modulates VPC, flowering time, and axillary meristem development in response to both internal and external signals.
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Affiliation(s)
- Arezoo Rahimi
- Plant Developmental Genetics, Institute of Biology LeidenLeiden UniversitySylviusweg 722333 BELeidenthe Netherlands
- Plant Molecular Stress Biology, Institute of Biology LeidenLeiden UniversitySylviusweg 722333 BELeidenthe Netherlands
| | - Omid Karami
- Plant Developmental Genetics, Institute of Biology LeidenLeiden UniversitySylviusweg 722333 BELeidenthe Netherlands
| | - Salma Balazadeh
- Plant Molecular Stress Biology, Institute of Biology LeidenLeiden UniversitySylviusweg 722333 BELeidenthe Netherlands
| | - Remko Offringa
- Plant Developmental Genetics, Institute of Biology LeidenLeiden UniversitySylviusweg 722333 BELeidenthe Netherlands
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Zhang WM, Cheng XZ, Fang D, Cao J. AT-HOOK MOTIF NUCLEAR LOCALIZED (AHL) proteins of ancient origin radiate new functions. Int J Biol Macromol 2022; 214:290-300. [PMID: 35716788 DOI: 10.1016/j.ijbiomac.2022.06.100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/11/2022] [Accepted: 06/12/2022] [Indexed: 11/05/2022]
Abstract
AHL (AT-HOOK MOTIF NUCLEAR LOCALIZED) protein is an important transcription factor in plants that regulates a wide range of biological process. It is considered to have evolved from an independent PPC domain in prokaryotes to a complete protein in modern plants. AT-hook motif and PPC conserved domains are the main functional domains of AHL. Since the discovery of AHL, their evolution and function have been continuously studied. The AHL gene family has been identified in multiple species and the functions of several members of the gene family have been studied. Here, we summarize the evolution and structural characteristics of AHL genes, and emphasize their biological functions. This review will provide a basis for further functional study and crop breeding.
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Affiliation(s)
- Wei-Meng Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Xiu-Zhu Cheng
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Da Fang
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Jun Cao
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, Jiangsu, China.
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Li Y, Jiang L, Mo W, Wang L, Zhang L, Cao Y. AHLs' life in plants: Especially their potential roles in responding to Fusarium wilt and repressing the seed oil accumulation. Int J Biol Macromol 2022; 208:509-519. [PMID: 35341887 DOI: 10.1016/j.ijbiomac.2022.03.130] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/27/2021] [Accepted: 03/20/2022] [Indexed: 01/04/2023]
Abstract
Members of the AT-hook motif nuclear localized (AHL) family contain diverse but poorly understood biological functions. We identified 371 AHLs in 20 land plants, varying from the early diverging lycophyte Selagineila moellendorfi to a variety of higher plants. The AHLs were divided into two clades (Clade-A and Clade-B) with three different types (Type-I, Type-II, and Type-III AHLs). The divergence between Clade-A and Clade-B likely occurred before the separation of S. moellendorfi from the vascular plant lineages. Members of the AHLs family expanded with the specific whole-genome duplication (WGD)/segmental duplication in some genomes, such as Hevea brasiliensis. The ortholog (Vf00G1914/Amo018442) exhibited opposite expression patterns between two Vernicia species (V. fordii and V. montana), indicating that it was implicated in resistance to Fusarium wilt disease. The expression of Vf09G2138 exhibited a negative correlation with lipid biosynthesis in V. fordii seeds during different stages of development, suggesting that this gene might repress the seed oil accumulation. The core AT-hook motif and PPC domain were responsible for guiding the localization of AHL in the nucleus. This study helps us to understand the evolution of AHLs in multiple plants, further highlight their functions during V. fordii seed development and response to Fusarium wilt disease.
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Affiliation(s)
- Yanli Li
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, Hunan, China; Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha 410004, Hunan, China
| | - Lan Jiang
- Central Laboratory, Yijishan Hospital of Wannan Medical College, Wuhu 241001, China
| | - Wanzhen Mo
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, Hunan, China; Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha 410004, Hunan, China
| | - Lihu Wang
- College of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, China
| | - Lin Zhang
- College of Basic Medical Sciences, Hubei University of Chinese Medicine, 430000 Wuhan, China
| | - Yunpeng Cao
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, Hunan, China; Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha 410004, Hunan, China.
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10
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Liu H, Hu D, Du P, Wang L, Liang X, Li H, Lu Q, Li S, Liu H, Chen X, Varshney RK, Hong Y. Single-cell RNA-seq describes the transcriptome landscape and identifies critical transcription factors in the leaf blade of the allotetraploid peanut (Arachis hypogaea L.). PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2261-2276. [PMID: 34174007 PMCID: PMC8541777 DOI: 10.1111/pbi.13656] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 05/26/2023]
Abstract
Single-cell RNA-seq (scRNA-seq) has been highlighted as a powerful tool for the description of human cell transcriptome, but the technology has not been broadly applied in plant cells. Herein, we describe the successful development of a robust protoplast cell isolation system in the peanut leaf. A total of 6,815 single cells were divided into eight cell clusters based on reported marker genes by applying scRNA-seq. Further, a pseudo-time analysis was used to describe the developmental trajectory and interaction network of transcription factors (TFs) of distinct cell types during leaf growth. The trajectory enabled re-investigation of the primordium-driven development processes of the mesophyll and epidermis. These results suggest that palisade cells likely differentiate into spongy cells, while the epidermal cells originated earlier than the primordium. Subsequently, the developed method integrated multiple technologies to efficiently validate the scRNA-seq result in a homogenous cell population. The expression levels of several TFs were strongly correlated with epidermal ontogeny in accordance with obtained scRNA-seq values. Additionally, peanut AHL23 (AT-HOOK MOTIF NUCLEAR LOCALIZED PROTEIN 23), which is localized in nucleus, promoted leaf growth when ectopically expressed in Arabidopsis by modulating the phytohormone pathway. Together, our study displays that application of scRNA-seq can provide new hypotheses regarding cell differentiation in the leaf blade of Arachis hypogaea. We believe that this approach will enable significant advances in the functional study of leaf blade cells in the allotetraploid peanut and other plant species.
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Affiliation(s)
- Hao Liu
- Guangdong Provincial Key Laboratory of Crop Genetic ImprovementSouth China Peanut Sub‐Center of National Center of Oilseed Crops ImprovementCrops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Dongxiu Hu
- Guangdong Provincial Key Laboratory of Crop Genetic ImprovementSouth China Peanut Sub‐Center of National Center of Oilseed Crops ImprovementCrops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Puxuan Du
- Guangdong Provincial Key Laboratory of Crop Genetic ImprovementSouth China Peanut Sub‐Center of National Center of Oilseed Crops ImprovementCrops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Liping Wang
- Guangdong Provincial Key Laboratory of Crop Genetic ImprovementSouth China Peanut Sub‐Center of National Center of Oilseed Crops ImprovementCrops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Xuanqiang Liang
- Guangdong Provincial Key Laboratory of Crop Genetic ImprovementSouth China Peanut Sub‐Center of National Center of Oilseed Crops ImprovementCrops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Haifen Li
- Guangdong Provincial Key Laboratory of Crop Genetic ImprovementSouth China Peanut Sub‐Center of National Center of Oilseed Crops ImprovementCrops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Qing Lu
- Guangdong Provincial Key Laboratory of Crop Genetic ImprovementSouth China Peanut Sub‐Center of National Center of Oilseed Crops ImprovementCrops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Shaoxiong Li
- Guangdong Provincial Key Laboratory of Crop Genetic ImprovementSouth China Peanut Sub‐Center of National Center of Oilseed Crops ImprovementCrops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Haiyan Liu
- Guangdong Provincial Key Laboratory of Crop Genetic ImprovementSouth China Peanut Sub‐Center of National Center of Oilseed Crops ImprovementCrops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Xiaoping Chen
- Guangdong Provincial Key Laboratory of Crop Genetic ImprovementSouth China Peanut Sub‐Center of National Center of Oilseed Crops ImprovementCrops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadTelanganaIndia
- State Agricultural Biotechnology CentreCentre for Crop and Food InnovationFood Futures InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Yanbin Hong
- Guangdong Provincial Key Laboratory of Crop Genetic ImprovementSouth China Peanut Sub‐Center of National Center of Oilseed Crops ImprovementCrops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
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11
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Ma X, Wu Y, Zhang G. Formation pattern and regulatory mechanisms of pollen wall in Arabidopsis. JOURNAL OF PLANT PHYSIOLOGY 2021; 260:153388. [PMID: 33706055 DOI: 10.1016/j.jplph.2021.153388] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/03/2021] [Accepted: 02/04/2021] [Indexed: 05/06/2023]
Abstract
In angiosperms, mature pollen is wrapped by a pollen wall, which is important for maintaining pollen structure and function. Pollen walls provide protection from various environmental stresses and preserve pollen germination and pollen tube growth. The pollen wall structure has been described since pollen ultrastructure investigations began in the 1960s. Pollen walls, which are the most intricate cell walls in plants, are composed of two layers: the exine layer and intine layer. Pollen wall formation is a complex process that occurs via a series of biological events that involve a large number of genes. In recent years, many reports have described the molecular mechanisms of pollen exine development. The formation process includes the development of the callose wall, the wavy morphology of primexine, the biosynthesis and transport of sporopollenin in the tapetum, and the deposition of the pollen coat. The formation mechanism of the intine layer is different from that of the exine layer. However, few studies have focused on the regulatory mechanisms of intine development. The primary component of the intine layer is pectin, which plays an essential role in the polar growth of pollen tubes. Demethylesterified pectin is mainly distributed in the shank region of the pollen tube, which can maintain the hardness of the pollen tube wall. Methylesterified pectin is mainly located in the top region, which is beneficial for improving the plasticity of the pollen tube top. In this review, we summarize the developmental process of the anther, pollen and pollen wall in Arabidopsis; furthermore, we describe the research progress on the pollen wall formation pattern and its molecular mechanisms in detail.
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Affiliation(s)
- Xiaofeng Ma
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yu Wu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Genfa Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
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12
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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: 70] [Impact Index Per Article: 23.3] [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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13
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Zhang WM, Fang D, Cheng XZ, Cao J, Tan XL. Insights Into the Molecular Evolution of AT-Hook Motif Nuclear Localization Genes in Brassica napus. FRONTIERS IN PLANT SCIENCE 2021; 12:714305. [PMID: 34567028 PMCID: PMC8458767 DOI: 10.3389/fpls.2021.714305] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/19/2021] [Indexed: 05/13/2023]
Abstract
AT-hook motif nuclear localization (AHL) proteins belong to a family of transcription factors, and play important roles in plant growth and development and response to various stresses through protein-DNA and protein-protein interactions. To better understand the Brassica napus AHL gene family, AHL genes in B. napus and related species were analyzed. Using Arabidopsis as a reference, 122 AHL gene family members were first identified in B. napus. According to the phylogenetic tree and gene organization, the BnaAHLs were classified into two clades (Clade-A and Clade-B) and three types (Type-I, Type-II, and Type-III). Gene organization and motif distribution analysis suggested that the AHL gene family is relatively conserved during evolution. These BnaAHLs are unevenly distributed on 38 chromosomes and expanded by whole-genome duplication (WGD) or segmental duplication. And large-scale loss events have also occurred in evolution. All types of BnaAHLs are subject to purification or neutral selection, while some positive selection sites are also identified in Type-II and Type-III groups. At the same time, the purification effect of Type-I members are stronger than that of the others. In addition, RNA-seq data and cis-acting element analysis also suggested that the BnaAHLs play important roles in B. napus growth and development, as well as in response to some abiotic and biotic stresses. Protein-protein interaction analysis identified some important BnaAHL-binding proteins, which also play key roles in plant growth and development. This study is helpful to fully understand the origin and evolution of the AHL gene in B. napus, and lays the foundation for their functional studies.
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14
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Tayengwa R, Sharma Koirala P, Pierce CF, Werner BE, Neff MM. Overexpression of AtAHL20 causes delayed flowering in Arabidopsis via repression of FT expression. BMC PLANT BIOLOGY 2020; 20:559. [PMID: 33308168 PMCID: PMC7731500 DOI: 10.1186/s12870-020-02733-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 11/09/2020] [Indexed: 05/30/2023]
Abstract
BACKGROUND The 29-member Arabidopsis AHL gene family is classified into three main classes based on nucleotide and protein sequence evolutionary differences. These differences include the presence or absence of introns, type and/or number of conserved AT-hook and PPC domains. AHL gene family members are divided into two phylogenetic clades, Clade-A and Clade-B. A majority of the 29 members remain functionally uncharacterized. Furthermore, the biological significance of the DNA and peptide sequence diversity, observed in the conserved motifs and domains found in the different AHL types, is a subject area that remains largely unexplored. RESULTS Transgenic plants overexpressing AtAHL20 flowered later than the wild type under both short and long days. Transcript accumulation analyses showed that 35S:AtAHL20 plants contained reduced FT, TSF, AGL8 and SPL3 mRNA levels. Similarly, overexpression of AtAHL20's orthologue in Camelina sativa, Arabidopsis' closely related Brassicaceae family member species, conferred a late-flowering phenotype via suppression of CsFT expression. However, overexpression of an aberrant AtAHL20 gene harboring a missense mutation in the AT-hook domain's highly conserved R-G-R core motif abolished the late-flowering phenotype. Data from targeted yeast-two-hybrid assays showed that AtAHL20 interacted with itself and several other Clade-A Type-I AHLs which have been previously implicated in flowering-time regulation: AtAHL19, AtAHL22 and AtAHL29. CONCLUSION We showed via gain-of-function analysis that AtAHL20 is a negative regulator of FT expression, as well as other downstream flowering time regulating genes. A similar outcome in Camelina sativa transgenic plants overexpressing CsAHL20 suggest that this is a conserved function. Our results demonstrate that AtAHL20 acts as a photoperiod-independent negative regulator of transition to flowering.
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Affiliation(s)
- Reuben Tayengwa
- Program in Molecular Plant Sciences, Washington State University, Pullman, WA, 99164, USA.
- Department Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA.
- Present address: Plant Sciences and Horticultural Landscape Department, University of Maryland, College Park, MD, 20742, USA.
| | - Pushpa Sharma Koirala
- Department Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
- Present address: Washington State Department of Fish and Wildlife, Olympia, WA, 987501, USA
| | - Courtney F Pierce
- Department Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
- Present address: United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, CO, 80521, USA
| | - Breanna E Werner
- Department Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
- Present address: Washington State University College of Nursing, Spokane, WA, 99202, USA
| | - Michael M Neff
- Program in Molecular Plant Sciences, Washington State University, Pullman, WA, 99164, USA
- Department Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
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15
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Desvoyes B, Gutierrez C. Roles of plant retinoblastoma protein: cell cycle and beyond. EMBO J 2020; 39:e105802. [PMID: 32865261 PMCID: PMC7527812 DOI: 10.15252/embj.2020105802] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/16/2020] [Accepted: 08/06/2020] [Indexed: 12/16/2022] Open
Abstract
The human retinoblastoma (RB1) protein is a tumor suppressor that negatively regulates cell cycle progression through its interaction with members of the E2F/DP family of transcription factors. However, RB-related (RBR) proteins are an early acquisition during eukaryote evolution present in plant lineages, including unicellular algae, ancient plants (ferns, lycophytes, liverworts, mosses), gymnosperms, and angiosperms. The main RBR protein domains and interactions with E2Fs are conserved in all eukaryotes and not only regulate the G1/S transition but also the G2/M transition, as part of DREAM complexes. RBR proteins are also important for asymmetric cell division, stem cell maintenance, and the DNA damage response (DDR). RBR proteins play crucial roles at every developmental phase transition, in association with chromatin factors, as well as during the reproductive phase during female and male gametes production and embryo development. Here, we review the processes where plant RBR proteins play a role and discuss possible avenues of research to obtain a full picture of the multifunctional roles of RBR for plant life.
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16
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Xiong SX, Zeng QY, Hou JQ, Hou LL, Zhu J, Yang M, Yang ZN, Lou Y. The temporal regulation of TEK contributes to pollen wall exine patterning. PLoS Genet 2020; 16:e1008807. [PMID: 32407354 PMCID: PMC7252695 DOI: 10.1371/journal.pgen.1008807] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 05/27/2020] [Accepted: 04/28/2020] [Indexed: 11/18/2022] Open
Abstract
Pollen wall consists of several complex layers which form elaborate species-specific patterns. In Arabidopsis, the transcription factor ABORTED MICROSPORE (AMS) is a master regulator of exine formation, and another transcription factor, TRANSPOSABLE ELEMENT SILENCING VIA AT-HOOK (TEK), specifies formation of the nexine layer. However, knowledge regarding the temporal regulatory roles of TEK in pollen wall development is limited. Here, TEK-GFP driven by the AMS promoter was prematurely expressed in the tapetal nuclei, leading to complete male sterility in the pAMS:TEK-GFP (pat) transgenic lines with the wild-type background. Cytological observations in the pat anthers showed impaired callose synthesis and aberrant exine patterning. CALLOSE SYNTHASE5 (CalS5) is required for callose synthesis, and expression of CalS5 in pat plants was significantly reduced. We demonstrated that TEK negatively regulates CalS5 expression after the tetrad stage in wild-type anthers and further discovered that premature TEK-GFP in pat directly represses CalS5 expression through histone modification. Our findings show that TEK flexibly mediates its different functions via different temporal regulation, revealing that the temporal regulation of TEK is essential for exine patterning. Moreover, the result that the repression of CalS5 by TEK after the tetrad stage coincides with the timing of callose wall dissolution suggests that tapetum utilizes temporal regulation of genes to stop callose wall synthesis, which, together with the activation of callase activity, achieves microspore release and pollen wall patterning. To develop into mature pollen grains, microspores require formation of the pollen wall. To date, pollen wall developmental events, including production and transportation of pollen wall components, synthesis and degradation of the callose wall, and deposition and demixing of primexine, have been studied in Arabidopsis, and a number of anther- or tapetum-specific genes involved in pollen wall formation have been uncovered. However, whether the specific expression patterns of these genes contribute to pollen wall development or patterning remains unclear. Here, we show that TEK, a transcription factor that specifies formation of nexine (the inner layer of the pollen wall exine), represses the expression of the callose synthase CalS5 after the tetrad stage, which accurately fits with the timing of callose wall dissolution causing microspore release. Moreover, we show that premature expression of TEK in the wild-type anthers disturbs callose wall synthesis and pollen wall patterning. This work reveals that a pollen wall regulator must be kept under a strict temporal control to perform its functions, and that these temporal controls are coordinated with other pollen wall developmental events to determine pollen wall formation and patterning.
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Affiliation(s)
- Shuang-Xi Xiong
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai, China
| | - Qiu-Ye Zeng
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jian-Qiao Hou
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Ling-Li Hou
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jun Zhu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Min Yang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Zhong-Nan Yang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yue Lou
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
- * E-mail:
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17
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Xu L, Jiang H. Writing and Reading Histone H3 Lysine 9 Methylation in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2020; 11:452. [PMID: 32435252 PMCID: PMC7218100 DOI: 10.3389/fpls.2020.00452] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/27/2020] [Indexed: 05/05/2023]
Abstract
In eukaryotes, histone H3 lysine 9 methylation (H3K9me) mediates the silencing of invasive and repetitive sequences by preventing the expression of aberrant gene products and the activation of transposition. In Arabidopsis, while it is well known that dimethylation of histone H3 at lysine 9 (H3K9me2) is maintained through a feedback loop between H3K9me2 and DNA methylation, the details of the H3K9me2-dependent silencing pathway have not been fully elucidated. Recently, the regulation and the function of H3K9 methylation have been extensively characterized. In this review, we summarize work from the recent studies regarding the regulation of H3K9me2, emphasizing the process of deposition and reading and the biological significance of H3K9me2 in Arabidopsis.
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Affiliation(s)
| | - Hua Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
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18
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AT-Hook Transcription Factors Restrict Petiole Growth by Antagonizing PIFs. Curr Biol 2020; 30:1454-1466.e6. [DOI: 10.1016/j.cub.2020.02.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 10/26/2019] [Accepted: 02/06/2020] [Indexed: 12/20/2022]
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19
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Zhao L, Lü Y, Chen W, Yao J, Li Y, Li Q, Pan J, Fang S, Sun J, Zhang Y. Genome-wide identification and analyses of the AHL gene family in cotton (Gossypium). BMC Genomics 2020; 21:69. [PMID: 31969111 PMCID: PMC6977275 DOI: 10.1186/s12864-019-6406-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 12/16/2019] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Members of the AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) family are involved in various plant biological processes via protein-DNA and protein-protein interaction. However, no the systematic identification and analysis of AHL gene family have been reported in cotton. RESULTS To investigate the potential functions of AHLs in cotton, genome-wide identification, expressions and structure analysis of the AHL gene family were performed in this study. 48, 51 and 99 AHL genes were identified from the G.raimondii, G.arboreum and G.hirsutum genome, respectively. Phylogenetic analysis revealed that the AHLs in cotton evolved into 2 clades, Clade-A with 4-5 introns and Clade-B with intronless (excluding AHL20-2). Based on the composition of the AT-hook motif(s) and PPC/DUF 296 domain, AHL proteins were classified into three types (Type-I/-II/-III), with Type-I AHLs forming Clade-B, and the other two types together diversifying in Clade-A. The detection of synteny and collinearity showed that the AHLs expanded with the specific WGD in cotton, and the sequence structure of AHL20-2 showed the tendency of increasing intron in three different Gossypium spp. The ratios of non-synonymous (Ka) and synonymous (Ks) substitution rates of orthologous gene pairs revealed that the AHL genes of G.hirsutum had undergone through various selection pressures, purifying selection mainly in A-subgenome and positive selection mainly in D-subgenome. Examination of their expression patterns showed most of AHLs of Clade-B expressed predominantly in stem, while those of Clade-A in ovules, suggesting that the AHLs within each clade shared similar expression patterns with each other. qRT-PCR analysis further confirmed that some GhAHLs higher expression in stems and ovules. CONCLUSION In this study, 48, 51 and 99 AHL genes were identified from three cotton genomes respectively. AHLs in cotton were classified into two clades by phylogenetic relationship and three types based on the composition of motif and domain. The AHLs expanded with segmental duplication, not tandem duplication. The expression profiles of GhAHLs revealed abundant differences in expression levels in various tissues and at different stages of ovules development. Our study provided significant insights into the potential functions of AHLs in regulating the growth and development in cotton.
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Affiliation(s)
- Lanjie Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, China
| | - Youjun Lü
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, China.,Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China.,Shihezi University, Shihezi, 832003, Xinjiang, China
| | - Wei Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, China
| | - Jinbo Yao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, China
| | - Yan Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, China
| | - Qiulin Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, China
| | - Jingwen Pan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, China
| | - Shengtao Fang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, China
| | - Jie Sun
- Shihezi University, Shihezi, 832003, Xinjiang, China.
| | - Yongshan Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, Henan, China.
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20
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Genome-wide identification, expression profiling, and network analysis of AT-hook gene family in maize. Genomics 2019; 112:1233-1244. [PMID: 31323298 DOI: 10.1016/j.ygeno.2019.07.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 06/26/2019] [Accepted: 07/15/2019] [Indexed: 11/23/2022]
Abstract
AT-hook motif nuclear localized (AHL) genes have diverse but poorly understood biological functions. We identified and analyzed 37 AHL genes in maize. We also discovered four and one additional AHLs in rice and sorghum, respectively, besides those reported earlier. The maize AHLs were classified into two clades (A and B) and three distinct types (I, II, and III) as also reported in Arabidopsis. Phylogenetic and ortholog analyses showed that, while the evolutionary classification was conserved in plants, expansion of the AHL gene family in maize was accompanied with new biological functions. Gene structure analysis showed that, while all but one Type-I AHLs lacked an intron, origin of Type-II and Type-III AHLs was associated with the gain of introns suggesting evolutionarily distinct temporal and spatial expression patterns and, likely, neofunctionalization. Gene duplication analysis revealed that AHLs in maize expanded via dispersive duplication further supporting their functional diversity. To discern these functions, we analyzed 71 transcriptomes from diverse tissues and developmental stages of maize and classified AHLs into eight groups with distinct temporal/spatial expression profiles. Coexpression analysis implicated 5 AHLs and 33 novel genes in networks specific to endosperm, seed, root, leaf, and reproductive tissues indicating their role in the development of these organs. Major processes coregulated by AHLs include pollen development, drought response, senescence, and wound response. We also identified interactions of AHL proteins in coregulating important processes including stress response. These novel insights into the role of AHLs in plant development provide a platform for functional analyses in maize and related grasses.
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21
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Xu Y, Prunet N, Gan ES, Wang Y, Stewart D, Wellmer F, Huang J, Yamaguchi N, Tatsumi Y, Kojima M, Kiba T, Sakakibara H, Jack TP, Meyerowitz EM, Ito T. SUPERMAN regulates floral whorl boundaries through control of auxin biosynthesis. EMBO J 2018; 37:embj.201797499. [PMID: 29764982 DOI: 10.15252/embj.201797499] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 03/25/2018] [Accepted: 04/04/2018] [Indexed: 01/23/2023] Open
Abstract
Proper floral patterning, including the number and position of floral organs in most plant species, is tightly controlled by the precise regulation of the persistence and size of floral meristems (FMs). In Arabidopsis, two known feedback pathways, one composed of WUSCHEL (WUS) and CLAVATA3 (CLV3) and the other composed of AGAMOUS (AG) and WUS, spatially and temporally control floral stem cells, respectively. However, mounting evidence suggests that other factors, including phytohormones, are also involved in floral meristem regulation. Here, we show that the boundary gene SUPERMAN (SUP) bridges floral organogenesis and floral meristem determinacy in another pathway that involves auxin signaling. SUP interacts with components of polycomb repressive complex 2 (PRC2) and fine-tunes local auxin signaling by negatively regulating the expression of the auxin biosynthesis genes YUCCA1/4 (YUC1/4). In sup mutants, derepressed local YUC1/4 activity elevates auxin levels at the boundary between whorls 3 and 4, which leads to an increase in the number and the prolonged maintenance of floral stem cells, and consequently an increase in the number of reproductive organs. Our work presents a new floral meristem regulatory mechanism, in which SUP, a boundary gene, coordinates floral organogenesis and floral meristem size through fine-tuning auxin biosynthesis.
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Affiliation(s)
- Yifeng Xu
- Temasek Life Sciences Laboratory (TLL), National University of Singapore, Singapore, Singapore.,Plant Stem Cell Regulation and Floral Patterning Laboratory, Biological Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Nathanaël Prunet
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA.,Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Eng-Seng Gan
- Temasek Life Sciences Laboratory (TLL), National University of Singapore, Singapore, Singapore
| | - Yanbin Wang
- Temasek Life Sciences Laboratory (TLL), National University of Singapore, Singapore, Singapore
| | - Darragh Stewart
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Frank Wellmer
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.,Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Jiangbo Huang
- Temasek Life Sciences Laboratory (TLL), National University of Singapore, Singapore, Singapore.,Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Nobutoshi Yamaguchi
- Plant Stem Cell Regulation and Floral Patterning Laboratory, Biological Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan.,Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Kawaguchi-shi, Saitama, Japan
| | - Yoshitaka Tatsumi
- Plant Stem Cell Regulation and Floral Patterning Laboratory, Biological Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Mikiko Kojima
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Kawaguchi-shi, Saitama, Japan.,RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Takatoshi Kiba
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Kawaguchi-shi, Saitama, Japan.,RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Hitoshi Sakakibara
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Kawaguchi-shi, Saitama, Japan.,RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Thomas P Jack
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Elliot M Meyerowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
| | - Toshiro Ito
- Temasek Life Sciences Laboratory (TLL), National University of Singapore, Singapore, Singapore .,Plant Stem Cell Regulation and Floral Patterning Laboratory, Biological Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan.,Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.,Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
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22
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Lee K, Seo PJ. Coordination of matrix attachment and ATP-dependent chromatin remodeling regulate auxin biosynthesis and Arabidopsis hypocotyl elongation. PLoS One 2017; 12:e0181804. [PMID: 28746399 PMCID: PMC5529009 DOI: 10.1371/journal.pone.0181804] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/09/2017] [Indexed: 01/08/2023] Open
Abstract
Hypocotyl elongation is extensively controlled by hormone signaling networks. In particular, auxin metabolism and signaling play key roles in light-dependent hypocotyl growth. The nuclear matrix facilitates organization of DNA within the nucleus, and dynamic interactions between nuclear matrix and DNA are related to gene regulation. Conserved scaffold/matrix attachment regions (S/MARs) are anchored to the nuclear matrix by the AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) proteins in Arabidopsis. Here, we found that ESCAROLA (ESC)/AHL27 and SUPPRESSOR OF PHYTOCHROME B-4 #3 (SOB3)/AHL29 redundantly regulate auxin biosynthesis in the control of hypocotyl elongation. The light-inducible AHL proteins bind directly to an S/MAR region of the YUCCA 9 (YUC9) promoter and suppress its expression to inhibit hypocotyl growth in light-grown seedlings. In addition, they recruit the SWI2/SNF2-RELATED 1 (SWR1) complex and promote exchange of H2A with the histone variant H2A.Z at the YUC9 locus to further elaborately control auxin biosynthesis. Consistent with these results, the long hypocotyl phenotypes of light-grown genetic mutants of the AHLs and H2A.Z-exchanging components were suppressed by potent chemical inhibitors of auxin transport and YUC enzymes. These results suggest that the coordination of matrix attachment and chromatin modification underlies auxin biosynthesis in light-dependent hypocotyl growth.
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Affiliation(s)
- Kyounghee Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Republic of Korea
| | - Pil Joon Seo
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Republic of Korea
- * E-mail:
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Jiang H, Moreno-Romero J, Santos-González J, De Jaeger G, Gevaert K, Van De Slijke E, Köhler C. Ectopic application of the repressive histone modification H3K9me2 establishes post-zygotic reproductive isolation in Arabidopsis thaliana. Genes Dev 2017; 31:1272-1287. [PMID: 28743695 PMCID: PMC5558928 DOI: 10.1101/gad.299347.117] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 06/27/2017] [Indexed: 11/24/2022]
Abstract
Hybrid seed lethality as a consequence of interspecies or interploidy hybridizations is a major mechanism of reproductive isolation in plants. This mechanism is manifested in the endosperm, a dosage-sensitive tissue supporting embryo growth. Deregulated expression of imprinted genes such as ADMETOS (ADM) underpin the interploidy hybridization barrier in Arabidopsis thaliana; however, the mechanisms of their action remained unknown. In this study, we show that ADM interacts with the AT hook domain protein AHL10 and the SET domain-containing SU(VAR)3-9 homolog SUVH9 and ectopically recruits the heterochromatic mark H3K9me2 to AT-rich transposable elements (TEs), causing deregulated expression of neighboring genes. Several hybrid incompatibility genes identified in Drosophila encode for dosage-sensitive heterochromatin-interacting proteins, which has led to the suggestion that hybrid incompatibilities evolve as a consequence of interspecies divergence of selfish DNA elements and their regulation. Our data show that imbalance of dosage-sensitive chromatin regulators underpins the barrier to interploidy hybridization in Arabidopsis, suggesting that reproductive isolation as a consequence of epigenetic regulation of TEs is a conserved feature in animals and plants.
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Affiliation(s)
- Hua Jiang
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Linnean Center of Plant Biology, Uppsala 75007, Sweden
| | - Jordi Moreno-Romero
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Linnean Center of Plant Biology, Uppsala 75007, Sweden
| | - Juan Santos-González
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Linnean Center of Plant Biology, Uppsala 75007, Sweden
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Kris Gevaert
- Department of Biochemistry, Ghent University, Ghent 9052, Belgium
- VIB Center for Medical Biotechnology, Ghent 9052, Belgium
| | - Eveline Van De Slijke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Linnean Center of Plant Biology, Uppsala 75007, Sweden
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24
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Cis-acting determinants of paramutation. Semin Cell Dev Biol 2015; 44:22-32. [DOI: 10.1016/j.semcdb.2015.08.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 08/20/2015] [Indexed: 11/23/2022]
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Guo S, Sun B, Looi LS, Xu Y, Gan ES, Huang J, Ito T. Co-ordination of Flower Development Through Epigenetic Regulation in Two Model Species: Rice and Arabidopsis. PLANT & CELL PHYSIOLOGY 2015; 56:830-42. [PMID: 25746984 DOI: 10.1093/pcp/pcv037] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 02/24/2015] [Indexed: 05/21/2023]
Abstract
Angiosperms produce flowers for reproduction. Flower development is a multistep developmental process, beginning with the initiation of the floral meristems, followed by floral meristem identity specification and maintenance, organ primordia initiation, floral organ identity specification, floral stem cell termination and finally floral organ maturation. During flower development, each of a large number of genes is expressed in a spatiotemporally regulated manner. Underlying these molecular and phenotypic events are various genetic and epigenetic pathways, consisting of diverse transcription factors, chromatin-remodeling factors and signaling molecules. Over the past 30 years, genetic, biochemical and genomic assays have revealed the underlying genetic frameworks that control flower development. Here, we will review the transcriptional regulation of flower development in two model species: Arabidopsis thaliana and rice (Oryza sativa). We focus on epigenetic regulation that functions to co-ordinate transcription pathways in flower development.
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Affiliation(s)
- Siyi Guo
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Republic of Singapore These authors contributed equally to this work
| | - Bo Sun
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Republic of Singapore These authors contributed equally to this work
| | - Liang-Sheng Looi
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Republic of Singapore Department of Biological Sciences, National University of Singapore, 117604, Republic of Singapore
| | - Yifeng Xu
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Republic of Singapore
| | - Eng-Seng Gan
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Republic of Singapore Department of Biological Sciences, National University of Singapore, 117604, Republic of Singapore
| | - Jiangbo Huang
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Republic of Singapore Department of Biological Sciences, National University of Singapore, 117604, Republic of Singapore
| | - Toshiro Ito
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Republic of Singapore Department of Biological Sciences, National University of Singapore, 117604, Republic of Singapore
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Kumari A, Kumar J, Kumar A, Chaudhury A, Singh SP. Grafting triggers differential responses between scion and rootstock. PLoS One 2015; 10:e0124438. [PMID: 25874958 PMCID: PMC4395316 DOI: 10.1371/journal.pone.0124438] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Accepted: 03/13/2015] [Indexed: 02/06/2023] Open
Abstract
Grafting is a well-established practice to facilitate asexual propagation in horticultural and agricultural crops. It has become a method for studying molecular aspects of root-to-shoot and/or shoot-to-root signaling events. The objective of this study was to investigate differences in gene expression between the organs of the scion and rootstock of a homograft (Arabidopsis thaliana). MapMan and Gene Ontology enrichment analysis revealed differentially expressed genes from numerous functional categories related to stress responses in the developing flower buds and leaves of scion and rootstock. Meta-analysis suggested induction of drought-type responses in flower buds and leaves of the scion. The flower buds of scion showed over-representation of the transcription factor genes, such as Homeobox, NAC, MYB, bHLH, B3, C3HC4, PLATZ etc. The scion leaves exhibited higher accumulation of the regulatory genes for flower development, such as SEPALLATA 1-4, Jumonji C and AHL16. Differential transcription of genes related to ethylene, gibberellic acid and other stimuli was observed between scion and rootstock. The study is useful in understanding the molecular basis of grafting and acclimation of scion on rootstock.
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Affiliation(s)
- Anita Kumari
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
- Guru Jambheshwar University of Science and Technology, Hisar, Haryana, India
| | - Jitendra Kumar
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Anil Kumar
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Ashok Chaudhury
- Guru Jambheshwar University of Science and Technology, Hisar, Haryana, India
| | - Sudhir P. Singh
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
- * E-mail:
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27
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Clavel M, Pélissier T, Descombin J, Jean V, Picart C, Charbonel C, Saez-Vásquez J, Bousquet-Antonelli C, Deragon JM. Parallel action of AtDRB2 and RdDM in the control of transposable element expression. BMC PLANT BIOLOGY 2015; 15:70. [PMID: 25849103 PMCID: PMC4351826 DOI: 10.1186/s12870-015-0455-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 02/13/2015] [Indexed: 05/03/2023]
Abstract
BACKGROUND In plants and animals, a large number of double-stranded RNA binding proteins (DRBs) have been shown to act as non-catalytic cofactors of DICERs and to participate in the biogenesis of small RNAs involved in RNA silencing. We have previously shown that the loss of Arabidopsis thaliana's DRB2 protein results in a significant increase in the population of RNA polymerase IV (p4) dependent siRNAs, which are involved in the RNA-directed DNA methylation (RdDM) process. RESULTS Surprisingly, despite this observation, we show in this work that DRB2 is part of a high molecular weight complex that does not involve RdDM actors but several chromatin regulator proteins, such as MSI4, PRMT4B and HDA19. We show that DRB2 can bind transposable element (TE) transcripts in vivo but that drb2 mutants do not have a significant variation in TE DNA methylation. CONCLUSION We propose that DRB2 is part of a repressive epigenetic regulator complex involved in a negative feedback loop, adjusting epigenetic state to transcription level at TE loci, in parallel of the RdDM pathway. Loss of DRB2 would mainly result in an increased production of TE transcripts, readily converted in p4-siRNAs by the RdDM machinery.
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Affiliation(s)
- Marion Clavel
- />Université de Perpignan Via Domitia, LGDP UMR CNRS-UPVD 5096, 58 Av. Paul Alduy, 66860 Perpignan Cedex, France
- />CNRS UMR5096 LGDP, Perpignan Cedex, France
- />Present address: IBMP, UPR 2357, 12, rue du général Zimmer, 67084 Strasbourg cedex, France
| | - Thierry Pélissier
- />Université de Perpignan Via Domitia, LGDP UMR CNRS-UPVD 5096, 58 Av. Paul Alduy, 66860 Perpignan Cedex, France
- />CNRS UMR5096 LGDP, Perpignan Cedex, France
- />Present address: UMR6293 CNRS - INSERM U1103 – GreD, Clermont Université, 24 avenue des Landais, B.P. 80026, 63171 Aubière Cedex, France
| | - Julie Descombin
- />Université de Perpignan Via Domitia, LGDP UMR CNRS-UPVD 5096, 58 Av. Paul Alduy, 66860 Perpignan Cedex, France
- />CNRS UMR5096 LGDP, Perpignan Cedex, France
| | - Viviane Jean
- />Université de Perpignan Via Domitia, LGDP UMR CNRS-UPVD 5096, 58 Av. Paul Alduy, 66860 Perpignan Cedex, France
- />CNRS UMR5096 LGDP, Perpignan Cedex, France
| | - Claire Picart
- />Université de Perpignan Via Domitia, LGDP UMR CNRS-UPVD 5096, 58 Av. Paul Alduy, 66860 Perpignan Cedex, France
- />CNRS UMR5096 LGDP, Perpignan Cedex, France
| | - Cyril Charbonel
- />Université de Perpignan Via Domitia, LGDP UMR CNRS-UPVD 5096, 58 Av. Paul Alduy, 66860 Perpignan Cedex, France
- />CNRS UMR5096 LGDP, Perpignan Cedex, France
| | - Julio Saez-Vásquez
- />Université de Perpignan Via Domitia, LGDP UMR CNRS-UPVD 5096, 58 Av. Paul Alduy, 66860 Perpignan Cedex, France
- />CNRS UMR5096 LGDP, Perpignan Cedex, France
| | - Cécile Bousquet-Antonelli
- />Université de Perpignan Via Domitia, LGDP UMR CNRS-UPVD 5096, 58 Av. Paul Alduy, 66860 Perpignan Cedex, France
- />CNRS UMR5096 LGDP, Perpignan Cedex, France
| | - Jean-Marc Deragon
- />Université de Perpignan Via Domitia, LGDP UMR CNRS-UPVD 5096, 58 Av. Paul Alduy, 66860 Perpignan Cedex, France
- />CNRS UMR5096 LGDP, Perpignan Cedex, France
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28
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Kenzior A, Folk WR. Arabidopsis thaliana MSI4/FVE associates with members of a novel family of plant specific PWWP/RRM domain proteins. PLANT MOLECULAR BIOLOGY 2015; 87:329-339. [PMID: 25600937 DOI: 10.1007/s11103-014-0280-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 12/30/2014] [Indexed: 06/04/2023]
Abstract
AtMSI4/FVE/ACG1, one of five Arabidopsis thaliana genes encoding MSI1-like proteins, helps determine plant growth and development (including control of flowering), as well as responses to certain biotic and abiotic stresses. We reasoned that the product of this gene, AtMSI4, acts through protein partners, which we have co-immunopurified with AtMSI4 from A. thaliana suspension culture cells and identified by liquid chromatography-mass spectrometry (LC-MS). Many of the proteins associated with AtMSI4 have distinct RNA recognition motif (RRM) domains, which we determined to be responsible for association with AtMSI4; and most of the associated RRM domain proteins also contain PWWP domains that are specific to plants. We propose these novel ATMSI4-associated proteins help form nucleoprotein complexes that determine pleiotropic functional properties of AtMSI4/FVE/ACG1 involving plant development and responses to stress.
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Affiliation(s)
- Alexander Kenzior
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, MO, 65211, USA,
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29
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Jia QS, Zhu J, Xu XF, Lou Y, Zhang ZL, Zhang ZP, Yang ZN. Arabidopsis AT-hook protein TEK positively regulates the expression of arabinogalactan proteins for Nexine formation. MOLECULAR PLANT 2015; 8:251-60. [PMID: 25616387 DOI: 10.1016/j.molp.2014.10.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 08/19/2014] [Accepted: 10/03/2014] [Indexed: 05/08/2023]
Abstract
Nexine is a conserved layer of the pollen wall. We previously reported that the nexine layer is absent in the knockout mutant of Arabidopsis TRANSPOSABLE ELEMENT SILENCING VIA AT-HOOK (TEK) gene. In this study, we investigated the molecular regulatory functions of TEK in pollen development and identified the genes encoding Arabinogalactan proteins (AGPs) as direct targets of TEK, which are essential for nexine formation. Phenotypic similarity between tek and the TEK-SRDX transgenic lines suggest that TEK plays a role in transcriptional activation in anther development. Microarray analysis identified a total of 661 genes downregulated in tek, including four genes encoding AGPs, AGP6, AGP11, AGP23, and AGP40. Electrophoretic mobility shift assays showed that TEK could directly bind the nuclear matrix attachment region (MAR) and the promoter of AGP6. Chromatin immunoprecipitation followed by PCR analysis demonstrated that TEK is enriched in the promoters of the four AGP genes. Expression of AGP6 driven by the TEK promoter in tek partially rescued both nexine formation and plant fertility. These results indicate that TEK directly regulates AGP expression in the anther to control nexine layer formation. We also proposed that glycoproteins might be essential components of the nexine layer in the pollen wall.
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Affiliation(s)
- Qi-Shi Jia
- College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China; College of Agriculture, Henan University of Science and Technology, Luoyang 471003, China
| | - Jun Zhu
- College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xiao-Feng Xu
- College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Yue Lou
- College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Zhan-Lin Zhang
- College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Zhi-Ping Zhang
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhong-Nan Yang
- College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China.
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30
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da Costa-Nunes JA, Capitão C, Kozak J, Costa-Nunes P, Ducasa GM, Pontes O, Angelis KJ. The AtRAD21.1 and AtRAD21.3 Arabidopsis cohesins play a synergistic role in somatic DNA double strand break damage repair. BMC PLANT BIOLOGY 2014; 14:353. [PMID: 25511710 PMCID: PMC4273318 DOI: 10.1186/s12870-014-0353-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 11/26/2014] [Indexed: 05/19/2023]
Abstract
BACKGROUND The RAD21 cohesin plays, besides its well-recognised role in chromatid cohesion, a role in DNA double strand break (dsb) repair. In Arabidopsis there are three RAD21 paralog genes (AtRAD21.1, AtRAD21.2 and AtRAD21.3), yet only AtRAD21.1 has been shown to be required for DNA dsb damage repair. Further investigation of the role of cohesins in DNA dsb repair was carried out and is here reported. RESULTS We show for the first time that not only AtRAD21.1 but also AtRAD21.3 play a role in somatic DNA dsb repair. Comet data shows that the lack of either cohesins induces a similar high basal level of DNA dsb in the nuclei and a slower DNA dsb repair kinetics in both cohesin mutants. The observed AtRAD21.3 transcriptional response to DNA dsb induction reinforces further the role of this cohesin in DNA dsb repair. The importance of AtRAD21.3 in DNA dsb damage repair, after exposure to DNA dsb damage inducing agents, is notorious and recognisably evident at the phenotypical level, particularly when the AtRAD21.1 gene is also disrupted. CONCLUSIONS Our data demonstrates that both Arabidopsis cohesin (AtRAD21.1 and AtRAD21.3) play a role in somatic DNA dsb repair. Furthermore, the phenotypical data from the atrad21.1 atrad21.3 double mutant indicates that these two cohesins function synergistically in DNA dsb repair. The implications of this data are discussed.
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Affiliation(s)
- José A da Costa-Nunes
- />Instituto de Tecnologia Química e Biológica (ITQB), Universidade Nova de Lisboa (UNL), Av. República, Apartado 127, 2781-901 Oeiras, Portugal
| | - Cláudio Capitão
- />Laboratório de Biotecnologia de Células Vegetais, ITQB, UNL, Av. República, Apartado 127, 2781-901 Oeiras, Portugal
- />Current address: Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - Jaroslav Kozak
- />Molecular Farming Lab., Institute of Experimental Botany AS CR, Na Karlovce 1, 160 00 Praha 6, Czech Republic
| | - Pedro Costa-Nunes
- />Department of Biology, University of New Mexico, 235 Castetter Hall, MSC03 2020, 1 University of New Mexico, Albuquerque, NM 87131-0001 New Mexico USA
- />Current address: Nuclear Organization and Epigenetics Lab., Shanghai Center for Plant Stress Biology (PSC), No. 3888 Chenhua Road, Shanghai, 201602 P. R. China
| | - Gloria M Ducasa
- />Department of Biology, University of New Mexico, 235 Castetter Hall, MSC03 2020, 1 University of New Mexico, Albuquerque, NM 87131-0001 New Mexico USA
| | - Olga Pontes
- />Department of Biology, University of New Mexico, 235 Castetter Hall, MSC03 2020, 1 University of New Mexico, Albuquerque, NM 87131-0001 New Mexico USA
- />Current address: Nuclear Organization and Epigenetics Lab., Shanghai Center for Plant Stress Biology (PSC), No. 3888 Chenhua Road, Shanghai, 201602 P. R. China
| | - Karel J Angelis
- />Molecular Farming Lab., Institute of Experimental Botany AS CR, Na Karlovce 1, 160 00 Praha 6, Czech Republic
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31
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Jumonji demethylases moderate precocious flowering at elevated temperature via regulation of FLC in Arabidopsis. Nat Commun 2014; 5:5098. [DOI: 10.1038/ncomms6098] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 08/27/2014] [Indexed: 01/27/2023] Open
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32
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Xu Y, Gan ES, Zhou J, Wee WY, Zhang X, Ito T. Arabidopsis MRG domain proteins bridge two histone modifications to elevate expression of flowering genes. Nucleic Acids Res 2014; 42:10960-74. [PMID: 25183522 PMCID: PMC4176166 DOI: 10.1093/nar/gku781] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Trimethylation of lysine 36 of histone H3 (H3K36me3) is found to be associated with various transcription events. In Arabidopsis, the H3K36me3 level peaks in the first half of coding regions, which is in contrast to the 3'-end enrichment in animals. The MRG15 family proteins function as 'reader' proteins by binding to H3K36me3 to control alternative splicing or prevent spurious intragenic transcription in animals. Here, we demonstrate that two closely related Arabidopsis homologues (MRG1 and MRG2) are localised to the euchromatin and redundantly ensure the increased transcriptional levels of two flowering time genes with opposing functions, FLOWERING LOCUS C and FLOWERING LOCUS T (FT). MRG2 directly binds to the FT locus and elevates the expression in an H3K36me3-dependent manner. MRG1/2 binds to H3K36me3 with their chromodomain and interact with the histone H4-specific acetyltransferases (HAM1 and HAM2) to achieve a high expression level through active histone acetylation at the promoter and 5' regions of target loci. Together, this study presents a mechanistic link between H3K36me3 and histone H4 acetylation. Our data also indicate that the biological functions of MRG1/2 have diversified from their animal homologues during evolution, yet they still maintain their conserved H3K36me3-binding molecular function.
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Affiliation(s)
- Yifeng Xu
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Eng-Seng Gan
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Republic of Singapore Department of Biological Sciences, National University of Singapore, Singapore 117543, Republic of Singapore
| | - Jie Zhou
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Wan-Yi Wee
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Xiaoyu Zhang
- Department of Plant Biology, University of Georgia, Athens, GA 30602-7271, USA
| | - Toshiro Ito
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Republic of Singapore Department of Biological Sciences, National University of Singapore, Singapore 117543, Republic of Singapore
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Jung JH, Lee HJ, Park MJ, Park CM. Beyond ubiquitination: proteolytic and nonproteolytic roles of HOS1. TRENDS IN PLANT SCIENCE 2014; 19:538-45. [PMID: 24768209 DOI: 10.1016/j.tplants.2014.03.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 03/18/2014] [Accepted: 03/28/2014] [Indexed: 05/09/2023]
Abstract
The E3 ubiquitin ligase HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES 1 (HOS1) functions as a cold signaling attenuator by degrading the INDUCER OF CBF EXPRESSION 1 transcription factor, which is a key regulator of the cold-induced transcriptome and freezing tolerance in plants. Recent studies demonstrate that HOS1 also plays nonproteolytic roles in gene expression regulation. HOS1 acts as a chromatin remodeling factor that modulates FLOWERING LOCUS C chromatin in cold regulation of flowering time. It associates with the nuclear pore complex to facilitate nucleocytoplasmic mRNA export to maintain circadian periodicity over a range of light and temperature conditions. In this review, we summarize recent advances in molecular mechanisms underlying HOS1 function during plant development in response to fluctuating environmental conditions.
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Affiliation(s)
- Jae-Hoon Jung
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK
| | - Hyo-Jun Lee
- Department of Chemistry, Seoul National University, Seoul 151-742, Korea
| | - Mi-Jeong Park
- Department of Chemistry, Seoul National University, Seoul 151-742, Korea
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, Seoul 151-742, Korea; Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-742, Korea.
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34
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The tapetal AHL family protein TEK determines nexine formation in the pollen wall. Nat Commun 2014; 5:3855. [PMID: 24804694 PMCID: PMC4024750 DOI: 10.1038/ncomms4855] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 04/10/2014] [Indexed: 12/03/2022] Open
Abstract
The pollen wall, an essential structure for pollen function, consists of two layers, an inner intine and an outer exine. The latter is further divided into sexine and nexine. Many genes involved in sexine development have been reported, in which the MYB transcription factor Male Sterile 188 (MS188) specifies sexine in Arabidopsis. However, nexine formation remains poorly understood. Here we report the knockout of TRANSPOSABLE ELEMENT SILENCING VIA AT-HOOK (TEK) leads to nexine absence in Arabidopsis. TEK encodes an AT-hook nuclear localized family protein highly expressed in tapetum during the tetrad stage. Absence of nexine in tek disrupts the deposition of intine without affecting sexine formation. We find that ABORTED MICROSPORES directly regulates the expression of TEK and MS188 in tapetum for the nexine and sexine formation, respectively. Our data show that a transcriptional cascade in the tapetum specifies the development of pollen wall. The nexine is a conserved layer of the pollen wall in land plants. The authors show that the AHL family protein TRANSPOSABLE ELEMENT SILENCING VIA AT-HOOK (TEK) is necessary for nexine formation in Arabidopsis, acting downstream of the transcription factor ABORTED MICROSPORES (AMS).
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35
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Liu X, Yang S, Zhao M, Luo M, Yu CW, Chen CY, Tai R, Wu K. Transcriptional repression by histone deacetylases in plants. MOLECULAR PLANT 2014; 7:764-72. [PMID: 24658416 DOI: 10.1093/mp/ssu033] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Reversible histone acetylation and deacetylation at the N-terminus of histone tails play crucial roles in regulation of eukaryotic gene activity. Acetylation of core histones usually induces an 'open' chromatin structure and is associated with gene activation, whereas deacetylation of histone is often correlated with 'closed' chromatin and gene repression. Histone deacetylation is catalyzed by histone deacetylases (HDACs). A growing number of studies have demonstrated the importance of histone deacetylation/acetylation on genome stability, transcriptional regulation, and development in plants. Furthermore, HDACs were shown to interact with various chromatin remolding factors and transcription factors involved in transcriptional repression in multiple developmental processes. In this review, we summarized recent findings on the transcriptional repression mediated by HDACs in plants.
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Affiliation(s)
- Xuncheng Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
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36
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Xu Y, Gan ES, Ito T. The AT-hook/PPC domain protein TEK negatively regulates floral repressors including MAF4 and MAF5. PLANT SIGNALING & BEHAVIOR 2013; 8:25006. [PMID: 23733063 PMCID: PMC3999084 DOI: 10.4161/psb.25006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Epigenetic regulations of transposable elements (TEs) and TE-like repeat sequences help to protect genomic integrity and control various developmental processes, including flowering time. This complex action of gene silencing requires the coordination of many key players including DNA methylases, histone deacetylases and histone methyltranferases. We have recently reported that an AT-hook DNA binding protein, TRANSPOSABLE ELEMENT SILENCING VIA AT-HOOK (TEK), participates in silencing TEs and TE-like sequence containing genes, such as Ler FLOWERING LOCUS C (FLC) and FWA. TEK knockdown in amiTEK plants causes increased histone acetylation, reduced H3K9me2 and DNA hypomethylation in the target loci, which ultimately leads to the upregulation of FLC and FWA as well as TE reactivation. In this report, we show that, besides FLC, other FLC-like genes MADS AFFECTING FLOWERING 4 (MAF4) and MAF5 are also upregulated in amiTEK. Here we discuss the role of the nuclear matrix protein TEK in the maintenance of genome integrity and in the control of flowering.
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Affiliation(s)
- Yifeng Xu
- Temasek Life Sciences Laboratory (TLL); 1 Research Link; National University of Singapore; Singapore
| | - Eng-Seng Gan
- Temasek Life Sciences Laboratory (TLL); 1 Research Link; National University of Singapore; Singapore
- Department of Biological Sciences; Faculty of Science; National University of Singapore; Singapore
| | - Toshiro Ito
- Temasek Life Sciences Laboratory (TLL); 1 Research Link; National University of Singapore; Singapore
- Department of Biological Sciences; Faculty of Science; National University of Singapore; Singapore
- Correspondence to: Toshiro Ito,
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Xu Y, Gan ES, He Y, Ito T. Flowering and genome integrity control by a nuclear matrix protein in Arabidopsis. Nucleus 2013; 4:274-6. [PMID: 23836195 DOI: 10.4161/nucl.25612] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The matrix attachment regions (MARs) binding proteins could finely orchestrate temporal and spatial gene expression during development. In Arabidopsis, transposable elements (TEs) and TE-like repeat sequences are transcriptionally repressed or attenuated by the coordination of many key players including DNA methyltransferases, histone deacetylases, histone methyltransferases and the siRNA pathway, which help to protect genomic integrity and control multiple developmental processes such as flowering. We have recently reported that an AT-hook nuclear matrix binding protein, TRANSPOSABLE ELEMENT SILENCING VIA AT-HOOK (TEK), participates in a histone deacetylation (HDAC) complex to silence TEs and genes containing a TE-like sequence, including AtMu1, FWA and FLOWERING LOCUS C (FLC) in Ler background. We have shown that TEK knockdown causes increased histone acetylation, reduced H3K9me2 and moderate reduction of DNA methylation in the target loci, leading to the de-repression of FLC and FWA, as well as TE reactivation. Here we discuss the role of TEK as a putative MAR binding protein which functions in the maintenance of genome integrity and in flowering control by silencing TEs and repeat-containing genes.
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Affiliation(s)
- Yifeng Xu
- Temasek Life Sciences Laboratory (TLL); 1 Research Link; National University of Singapore; Singapore, Singapore; Department of Biological Sciences; Faculty of Science; National University of Singapore; Singapore, Singapore
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Gan ES, Huang J, Ito T. Functional Roles of Histone Modification, Chromatin Remodeling and MicroRNAs in Arabidopsis Flower Development. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2013; 305:115-61. [DOI: 10.1016/b978-0-12-407695-2.00003-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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