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Kumar K, Kumari A, Durgesh K, Sevanthi AM, Sharma S, Singh NK, Gaikwad K. Identification of superior haplotypes for flowering time in pigeonpea through candidate gene-based association study of a diverse minicore collection. PLANT CELL REPORTS 2024; 43:156. [PMID: 38819495 DOI: 10.1007/s00299-024-03230-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 05/05/2024] [Indexed: 06/01/2024]
Abstract
KEY MESSAGE In current study candidate gene (261 genes) based association mapping on 144 pigeonpea accessions for flowering time and related traits and 29 MTAs producing eight superior haplotypes were identified. In the current study, we have conducted an association analysis for flowering-associated traits in a diverse pigeonpea mini-core collection comprising 144 accessions using the SNP data of 261 flowering-related genes. In total, 13,449 SNPs were detected in the current study, which ranged from 743 (ICP10228) to 1469 (ICP6668) among the individuals. The nucleotide diversity (0.28) and Watterson estimates (0.34) reflected substantial diversity, while Tajima's D (-0.70) indicated the abundance of rare alleles in the collection. A total of 29 marker trait associations (MTAs) were identified, among which 19 were unique to days to first flowering (DOF) and/or days to fifty percent flowering (DFF), 9 to plant height (PH), and 1 to determinate (Det) growth habit using 3 years of phenotypic data. Among these MTAs, six were common to DOF and/or DFF, and four were common to DOF/DFF along with the PH, reflecting their pleiotropic action. These 29 MTAs spanned 25 genes, among which 10 genes clustered in the protein-protein network analysis, indicating their concerted involvement in floral induction. Furthermore, we identified eight haplotypes, four of which regulate late flowering, while the remaining four regulate early flowering using the MTAs. Interestingly, haplotypes conferring late flowering (H001, H002, and H008) were found to be taller, while those involved in early flowering (H003) were shorter in height. The expression pattern of these genes, as inferred from the transcriptome data, also underpinned their involvement in floral induction. The haplotypes identified will be highly useful to the pigeonpea breeding community for haplotype-based breeding.
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Affiliation(s)
- Kuldeep Kumar
- ICAR-National Institute for Plant Biotechnology, Pusa, New Delhi, India
- ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India
- The Graduate School, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India
| | - Anita Kumari
- Department of Botany, North Campus, University of Delhi, Delhi, New Delhi, India
| | - Kumar Durgesh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India
| | | | - Sandhya Sharma
- ICAR-National Institute for Plant Biotechnology, Pusa, New Delhi, India
| | | | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, Pusa, New Delhi, India.
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Jun SE, Shim JS, Park HJ. Beyond NPK: Mineral Nutrient-Mediated Modulation in Orchestrating Flowering Time. PLANTS (BASEL, SWITZERLAND) 2023; 12:3299. [PMID: 37765463 PMCID: PMC10535918 DOI: 10.3390/plants12183299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023]
Abstract
Flowering time in plants is a complex process regulated by environmental conditions such as photoperiod and temperature, as well as nutrient conditions. While the impact of major nutrients like nitrogen, phosphorus, and potassium on flowering time has been well recognized, the significance of micronutrient imbalances and their deficiencies should not be neglected because they affect the floral transition from the vegetative stage to the reproductive stage. The secondary major nutrients such as calcium, magnesium, and sulfur participate in various aspects of flowering. Micronutrients such as boron, zinc, iron, and copper play crucial roles in enzymatic reactions and hormone biosynthesis, affecting flower development and reproduction as well. The current review comprehensively explores the interplay between microelements and flowering time, and summarizes the underlying mechanism in plants. Consequently, a better understanding of the interplay between microelements and flowering time will provide clues to reveal the roles of microelements in regulating flowering time and to improve crop reproduction in plant industries.
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Affiliation(s)
- Sang Eun Jun
- Department of Molecular Genetics, Dong-A University, Busan 49315, Republic of Korea;
| | - Jae Sun Shim
- School of Biological Science and Technology, College of Natural Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Hee Jin Park
- Department of Biological Sciences and Research Center of Ecomimetics, College of Natural Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
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Zhang C, Jian M, Li W, Yao X, Tan C, Qian Q, Hu Y, Liu X, Hou X. Gibberellin signaling modulates flowering via the DELLA-BRAHMA-NF-YC module in Arabidopsis. THE PLANT CELL 2023; 35:3470-3484. [PMID: 37294919 PMCID: PMC10473208 DOI: 10.1093/plcell/koad166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 05/19/2023] [Accepted: 05/25/2023] [Indexed: 06/11/2023]
Abstract
Gibberellin (GA) plays a key role in floral induction by activating the expression of floral integrator genes in plants, but the epigenetic regulatory mechanisms underlying this process remain unclear. Here, we show that BRAHMA (BRM), a core subunit of the chromatin-remodeling SWItch/sucrose nonfermentable (SWI/SNF) complex that functions in various biological processes by regulating gene expression, is involved in GA-signaling-mediated flowering via the formation of the DELLA-BRM-NF-YC module in Arabidopsis (Arabidopsis thaliana). DELLA, BRM, and NF-YC transcription factors interact with one another, and DELLA proteins promote the physical interaction between BRM and NF-YC proteins. This impairs the binding of NF-YCs to SOC1, a major floral integrator gene, to inhibit flowering. On the other hand, DELLA proteins also facilitate the binding of BRM to SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1). The GA-induced degradation of DELLA proteins disturbs the DELLA-BRM-NF-YC module, prevents BRM from inhibiting NF-YCs, and decreases the DNA-binding ability of BRM, which promote the deposition of H3K4me3 on SOC1 chromatin, leading to early flowering. Collectively, our findings show that BRM is a key epigenetic partner of DELLA proteins during the floral transition. Moreover, they provide molecular insights into how GA signaling coordinates an epigenetic factor with a transcription factor to regulate the expression of a flowering gene and flowering in plants.
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Affiliation(s)
- Chunyu Zhang
- Guangdong Provincial Key Laboratory of Applied Botany and State Key Laboratory of Plant Diversity and Prominent Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Mingyang Jian
- Guangdong Provincial Key Laboratory of Applied Botany and State Key Laboratory of Plant Diversity and Prominent Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Weijun Li
- Guangdong Provincial Key Laboratory of Applied Botany and State Key Laboratory of Plant Diversity and Prominent Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xiani Yao
- Guangdong Provincial Key Laboratory of Applied Botany and State Key Laboratory of Plant Diversity and Prominent Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Cuirong Tan
- Guangdong Provincial Key Laboratory of Applied Botany and State Key Laboratory of Plant Diversity and Prominent Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Qian Qian
- Guangdong Provincial Key Laboratory of Applied Botany and State Key Laboratory of Plant Diversity and Prominent Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yilong Hu
- Guangdong Provincial Key Laboratory of Applied Botany and State Key Laboratory of Plant Diversity and Prominent Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xu Liu
- Guangdong Provincial Key Laboratory of Applied Botany and State Key Laboratory of Plant Diversity and Prominent Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xingliang Hou
- Guangdong Provincial Key Laboratory of Applied Botany and State Key Laboratory of Plant Diversity and Prominent Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
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Bardani E, Kallemi P, Tselika M, Katsarou K, Kalantidis K. Spotlight on Plant Bromodomain Proteins. BIOLOGY 2023; 12:1076. [PMID: 37626962 PMCID: PMC10451976 DOI: 10.3390/biology12081076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 07/28/2023] [Accepted: 07/30/2023] [Indexed: 08/27/2023]
Abstract
Bromodomain-containing proteins (BRD-proteins) are the "readers" of histone lysine acetylation, translating chromatin state into gene expression. They act alone or as components of larger complexes and exhibit diverse functions to regulate gene expression; they participate in chromatin remodeling complexes, mediate histone modifications, serve as scaffolds to recruit transcriptional regulators or act themselves as transcriptional co-activators or repressors. Human BRD-proteins have been extensively studied and have gained interest as potential drug targets for various diseases, whereas in plants, this group of proteins is still not well investigated. In this review, we aimed to concentrate scientific knowledge on these chromatin "readers" with a focus on Arabidopsis. We organized plant BRD-proteins into groups based on their functions and domain architecture and summarized the published work regarding their interactions, activity and diverse functions. Overall, it seems that plant BRD-proteins are indispensable components and fine-tuners of the complex network plants have built to regulate development, flowering, hormone signaling and response to various biotic or abiotic stresses. This work will facilitate the understanding of their roles in plants and highlight BRD-proteins with yet undiscovered functions.
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Affiliation(s)
- Eirini Bardani
- Department of Biology, University of Crete, Voutes University Campus, 71500 Heraklion, Greece; (E.B.); (P.K.); (M.T.)
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013 Heraklion, Greece
| | - Paraskevi Kallemi
- Department of Biology, University of Crete, Voutes University Campus, 71500 Heraklion, Greece; (E.B.); (P.K.); (M.T.)
| | - Martha Tselika
- Department of Biology, University of Crete, Voutes University Campus, 71500 Heraklion, Greece; (E.B.); (P.K.); (M.T.)
| | - Konstantina Katsarou
- Department of Biology, University of Crete, Voutes University Campus, 71500 Heraklion, Greece; (E.B.); (P.K.); (M.T.)
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013 Heraklion, Greece
| | - Kriton Kalantidis
- Department of Biology, University of Crete, Voutes University Campus, 71500 Heraklion, Greece; (E.B.); (P.K.); (M.T.)
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013 Heraklion, Greece
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Chen G, Mishina K, Zhu H, Kikuchi S, Sassa H, Oono Y, Komatsuda T. Genome-Wide Analysis of Snf2 Gene Family Reveals Potential Role in Regulation of Spike Development in Barley. Int J Mol Sci 2022; 24:ijms24010457. [PMID: 36613901 PMCID: PMC9820626 DOI: 10.3390/ijms24010457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/16/2022] [Accepted: 12/20/2022] [Indexed: 12/29/2022] Open
Abstract
Sucrose nonfermenting 2 (Snf2) family proteins, as the catalytic core of ATP-dependent chromatin remodeling complexes, play important roles in nuclear processes as diverse as DNA replication, transcriptional regulation, and DNA repair and recombination. The Snf2 gene family has been characterized in several plant species; some of its members regulate flower development in Arabidopsis. However, little is known about the members of the family in barley (Hordeum vulgare). Here, 38 Snf2 genes unevenly distributed among seven chromosomes were identified from the barley (cv. Morex) genome. Phylogenetic analysis categorized them into 18 subfamilies. They contained combinations of 21 domains and consisted of 3 to 34 exons. Evolution analysis revealed that segmental duplication contributed predominantly to the expansion of the family in barley, and the duplicated gene pairs have undergone purifying selection. About eight hundred Snf2 family genes were identified from 20 barley accessions, ranging from 38 to 41 genes in each. Most of these genes were subjected to purification selection during barley domestication. Most were expressed abundantly during spike development. This study provides a comprehensive characterization of barley Snf2 family members, which should help to improve our understanding of their potential regulatory roles in barley spike development.
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Affiliation(s)
- Gang Chen
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba 305-8602, Japan
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo 271-8510, Japan
| | - Kohei Mishina
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba 305-8602, Japan
| | - Hongjing Zhu
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba 305-8602, Japan
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo 271-8510, Japan
| | - Shinji Kikuchi
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo 271-8510, Japan
| | - Hidenori Sassa
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo 271-8510, Japan
| | - Youko Oono
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba 305-8602, Japan
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo 271-8510, Japan
- Correspondence: (Y.O.); (T.K.); Tel.: +81-29-838-7443 (Y.O.); +86-531-6665-8143 (T.K.)
| | - Takao Komatsuda
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba 305-8602, Japan
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo 271-8510, Japan
- Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Jinan 252100, China
- Correspondence: (Y.O.); (T.K.); Tel.: +81-29-838-7443 (Y.O.); +86-531-6665-8143 (T.K.)
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6
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Ornelas-Ayala D, Cortés-Quiñones C, Olvera-Herrera J, García-Ponce B, Garay-Arroyo A, Álvarez-Buylla ER, Sanchez MDLP. A Green Light to Switch on Genes: Revisiting Trithorax on Plants. PLANTS (BASEL, SWITZERLAND) 2022; 12:75. [PMID: 36616203 PMCID: PMC9824250 DOI: 10.3390/plants12010075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/18/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
The Trithorax Group (TrxG) is a highly conserved multiprotein activation complex, initially defined by its antagonistic activity with the PcG repressor complex. TrxG regulates transcriptional activation by the deposition of H3K4me3 and H3K36me3 marks. According to the function and evolutionary origin, several proteins have been defined as TrxG in plants; nevertheless, little is known about their interactions and if they can form TrxG complexes. Recent evidence suggests the existence of new TrxG components as well as new interactions of some TrxG complexes that may be acting in specific tissues in plants. In this review, we bring together the latest research on the topic, exploring the interactions and roles of TrxG proteins at different developmental stages, required for the fine-tuned transcriptional activation of genes at the right time and place. Shedding light on the molecular mechanism by which TrxG is recruited and regulates transcription.
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7
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Guo J, Cai G, Li YQ, Zhang YX, Su YN, Yuan DY, Zhang ZC, Liu ZZ, Cai XW, Guo J, Li L, Chen S, He XJ. Comprehensive characterization of three classes of Arabidopsis SWI/SNF chromatin remodelling complexes. NATURE PLANTS 2022; 8:1423-1439. [PMID: 36471048 DOI: 10.1038/s41477-022-01282-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 10/19/2022] [Indexed: 05/12/2023]
Abstract
Although SWI/SNF chromatin remodelling complexes are known to regulate diverse biological functions in plants, the classification, compositions and functional mechanisms of the complexes remain to be determined. Here we comprehensively characterized SWI/SNF complexes by affinity purification and mass spectrometry in Arabidopsis thaliana, and found three classes of SWI/SNF complexes, which we termed BAS, SAS and MAS (BRM-, SYD- and MINU1/2-associated SWI/SNF complexes). By investigating multiple developmental phenotypes of SWI/SNF mutants, we found that three classes of SWI/SNF complexes have both overlapping and specific functions in regulating development. To investigate how the three classes of SWI/SNF complexes differentially regulate development, we mapped different SWI/SNF components on chromatin at the whole-genome level and determined their effects on chromatin accessibility. While all three classes of SWI/SNF complexes regulate chromatin accessibility at proximal promoter regions, SAS is a major SWI/SNF complex that is responsible for mediating chromatin accessibility at distal promoter regions and intergenic regions. Histone modifications are related to both the association of SWI/SNF complexes with chromatin and the SWI/SNF-dependent chromatin accessibility. Three classes of SWI/SNF-dependent accessibility may enable different sets of transcription factors to access chromatin. These findings lay a foundation for further investigation of the function of three classes of SWI/SNF complexes in plants.
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Affiliation(s)
- Jing Guo
- College of Life Sciences, Beijing Normal University, Beijing, China
- National Institute of Biological Sciences, Beijing, China
| | - Guang Cai
- National Institute of Biological Sciences, Beijing, China
| | - Yong-Qiang Li
- National Institute of Biological Sciences, Beijing, China
| | - Yi-Xuan Zhang
- National Institute of Biological Sciences, Beijing, China
| | - Yin-Na Su
- National Institute of Biological Sciences, Beijing, China
| | - Dan-Yang Yuan
- National Institute of Biological Sciences, Beijing, China
| | | | - Zhen-Zhen Liu
- National Institute of Biological Sciences, Beijing, China
| | - Xue-Wei Cai
- National Institute of Biological Sciences, Beijing, China
| | - Jing Guo
- National Institute of Biological Sciences, Beijing, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing, China
| | - She Chen
- National Institute of Biological Sciences, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China.
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Guo M, Zhao H, He Z, Zhang W, She Z, Mohammadi MA, Shi C, Yan M, Tian D, Qin Y. Comparative Expression Profiling of Snf2 Family Genes During Reproductive Development and Stress Responses in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:910663. [PMID: 35712583 PMCID: PMC9194907 DOI: 10.3389/fpls.2022.910663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
Sucrose non-fermenting 2 (Snf2) protein family, as chromatin remodeling factors, is an enormous and the most diverse protein family, which contributes to biological processes of replication, transcription, and DNA repair using the energy of adenosine triphosphate (ATP) hydrolysis. The members of Snf2 family proteins have been well characterized in Arabidopsis, rice, and tomato. Although this family received significant attention, few genes were identified uniquely for their roles in mediating reproductive development and stress tolerance in rice. In the present study, we comprehensively analyzed the expression profiling of Snf2 genes during reproductive development and biotic/abiotic stresses. Our results showed that five proteins (OsCHR712/715/720/726/739) were mainly localized in the nucleus, while OsCHR715/739 were also slightly expressed in the cell membrane. There were abundant cis-acting elements in the putative promoter of Snf2 genes, including dehydration, MeJA, MYB binding site for drought, ABA-responsive, and stress-responsive element. Most of the genes were induced immediately after Magnaporthe oryzae infection at 12 h post-infection (hpi). About 55% of the total genes were upregulated under salt and drought stresses during the entire time, and 22-35% of the total genes were upregulated at 3 h. It was noteworthy that the seven genes (OsCHR705, OsCHR706, OsCHR710, OsCHR714, OsCHR721, OsCHR726, and OsCHR737) were upregulated, and one gene (OsCHR712) was downregulated under salt and drought stresses, respectively. The deficiency of OsCHR726 mutations displayed a hypersensitive phenotype under salt stress. These results will be significantly useful features for the validation of the rice Snf2 genes and facilitate understanding of the genetic engineering of crops with improved biotic and abiotic stresses.
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Affiliation(s)
- Mingliang Guo
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Heming Zhao
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Zhimei He
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenchao Zhang
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zeyuan She
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
| | - Mohammad Aqa Mohammadi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chao Shi
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Maokai Yan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
| | - Dagang Tian
- Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Yuan Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Pingtan Science and Technology Research Institute, Fujian Agriculture and Forestry University, Fuzhou, China
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Guo M, Zhang W, Mohammadi MA, He Z, She Z, Yan M, Shi C, Lin L, Wang A, Liu J, Tian D, Zhao H, Qin Y. OsDDM1b Controls Grain Size by Influencing Cell Cycling and Regulating Homeostasis and Signaling of Brassinosteroid in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:873993. [PMID: 35463416 PMCID: PMC9024357 DOI: 10.3389/fpls.2022.873993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Snf2 family proteins are the crucial subunits of chromatin-remodeling complexes (CRCs), which contributes to the biological processes of transcription, replication, and DNA repair using ATP as energy. Some CRC subunits have been confirmed to be the critical regulators in various aspects of plant growth and development and in epigenetic mechanisms such as histone modification, DNA methylation, and histone variants. However, the functions of Snf2 family genes in rice were poorly investigated. In this study, the relative expression profile of 40 members of Snf2 family in rice was studied at certain developmental stages of seed. Our results revealed that OsCHR741/OsDDM1b (Decrease in DNA methylation 1) was accumulated highly in the early developmental stage of seeds. We further analyzed the OsDDM1b T-DNA insertion loss-of-function of mutant, which exhibited dwarfism, smaller organ size, and shorter and wider grain size than the wild type (Hwayoung, HY), yet no difference in 1,000-grain weight. Consistent with the grain size, the outer parenchyma cell layers of lemma in osddm1b developed more cells with decreased size. OsDDM1b encoded a nucleus, membrane-localized protein and was distributed predominately in young spikelets and seeds, asserting its role in grain size. Meanwhile, the osddm1b was less sensitive to brassinosteroids (BRs) while the endogenous BR levels increased. We detected changes in the expression levels of the BR signaling pathway and feedback-inhibited genes with and without exogenous BR application, and the alterations of expression were also observed in grain size-related genes in the osddm1b. Altogether, our results suggest that OsDDM1b plays a crucial role in grain size via influencing cell proliferation and regulating BR signaling and homeostasis.
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Affiliation(s)
- Mingliang Guo
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenchao Zhang
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mohammad Aqa Mohammadi
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
| | - Zhimei He
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zeyuan She
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
| | - Maokai Yan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
| | - Chao Shi
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lingwei Lin
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Aqiong Wang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jindian Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dagang Tian
- Biotechnology Research Institute, Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Heming Zhao
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Yuan Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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10
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Yang J, Xu Y, Wang J, Gao S, Huang Y, Hung FY, Li T, Li Q, Yue L, Wu K, Yang S. The chromatin remodelling ATPase BRAHMA interacts with GATA-family transcription factor GNC to regulate flowering time in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:835-847. [PMID: 34545936 DOI: 10.1093/jxb/erab430] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 09/20/2021] [Indexed: 05/13/2023]
Abstract
BRAHMA (BRM) is the ATPase of the SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodelling complex, which is indispensable for transcriptional inhibition and activation, associated with vegetative and reproductive development in Arabidopsis thaliana. Here, we show that BRM directly binds to the chromatin of SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1), which integrates multiple flowering signals to regulate floral transition, leading to flowering. In addition, genetic and molecular analysis showed that BRM interacts with GNC (GATA, NITRATE-INDUCIBLE, CARBON METABOLISM INVOLVED), a GATA transcription factor that represses flowering by directly repressing SOC1 expression. Furthermore, BRM is recruited by GNC to directly bind to the chromatin of SOC1. The transcript level of SOC1 is elevated in brm-3, gnc, and brm-3/gnc mutants, which is associated with increased histone H3 lysine 4 tri-methylation (H3K4Me3) but decreased DNA methylation. Taken together, our results indicate that BRM associates with GNC to regulate SOC1 expression and flowering time.
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Affiliation(s)
- Jie Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yingchao Xu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Jianhao Wang
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Sujuan Gao
- College of Light Industry and Food Science, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Academy of Contemporary Agricultural Engineering Innovations, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Yisui Huang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Fu-Yu Hung
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Tao Li
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Qing Li
- Guangdong Provincial Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agrobiological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Lin Yue
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Keqiang Wu
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Songguang Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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11
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Gao S, Zeng X, Wang J, Xu Y, Yu C, Huang Y, Wang F, Wu K, Yang S. Arabidopsis SUMO E3 Ligase SIZ1 Interacts with HDA6 and Negatively Regulates HDA6 Function during Flowering. Cells 2021; 10:cells10113001. [PMID: 34831226 PMCID: PMC8616286 DOI: 10.3390/cells10113001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/13/2021] [Accepted: 10/31/2021] [Indexed: 01/12/2023] Open
Abstract
The changes in histone acetylation mediated by histone deacetylases (HDAC) play a crucial role in plant development and response to environmental changes. Mammalian HDACs are regulated by post-translational modifications (PTM), such as phosphorylation, acetylation, ubiquitination and small ubiquitin-like modifier (SUMO) modification (SUMOylation), which affect enzymatic activity and transcriptional repression. Whether PTMs of plant HDACs alter their functions are largely unknown. In this study, we demonstrated that the Arabidopsis SUMO E3 ligase SAP AND MIZ1 DOMAIN-CONTAINING LIGASE1 (SIZ1) interacts with HISTONE DEACETYLASE 6 (HDA6) both in vitro and in vivo. Biochemical analyses indicated that HDA6 is not modified by SUMO1. Overexpression of HDA6 in siz1-3 background results in a decreased level of histone H3 acetylation, indicating that the activity of HDA6 is increased in siz1-3 plants. Chromatin immunoprecipitation (ChIP) assays showed that SIZ1 represses HDA6 binding to its target genes FLOWERING LOCUS C (FLC) and MADS AFFECTING FLOWERING 4 (MAF4), resulting in the upregulation of FLC and MAF4 by increasing the level of histone H3 acetylation. Together, these findings indicate that the Arabidopsis SUMO E3 ligase SIZ1 interacts with HDA6 and negatively regulates HDA6 function.
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Affiliation(s)
- Sujuan Gao
- Key Laboratory of Green Processing and Intelligent Manufacturing of Lingnan Specialty Food, College of Light Industry and Food Science, Zhongkai University of Agriculture and Engineering, Ministry of Agriculture, Guangzhou 510225, China;
| | - Xueqin Zeng
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (X.Z.); (F.W.)
| | - Jianhao Wang
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510000, China;
| | - Yingchao Xu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (Y.X.); (Y.H.)
| | - Chunwei Yu
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan;
| | - Yishui Huang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (Y.X.); (Y.H.)
| | - Feng Wang
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (X.Z.); (F.W.)
| | - Keqiang Wu
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan;
- Correspondence: (K.W.); (S.Y.)
| | - Songguang Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (Y.X.); (Y.H.)
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Correspondence: (K.W.); (S.Y.)
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12
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Jarończyk K, Sosnowska K, Zaborowski A, Pupel P, Bucholc M, Małecka E, Siwirykow N, Stachula P, Iwanicka-Nowicka R, Koblowska M, Jerzmanowski A, Archacki R. Bromodomain-containing subunits BRD1, BRD2, and BRD13 are required for proper functioning of SWI/SNF complexes in Arabidopsis. PLANT COMMUNICATIONS 2021; 2:100174. [PMID: 34327319 PMCID: PMC8299063 DOI: 10.1016/j.xplc.2021.100174] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 01/12/2021] [Accepted: 03/02/2021] [Indexed: 05/26/2023]
Abstract
SWI/SNF chromatin remodelers are evolutionarily conserved multiprotein complexes that use the energy of ATP hydrolysis to change chromatin structure. A characteristic feature of SWI/SNF remodelers is the occurrence in both the catalytic ATPase subunit and some auxiliary subunits, of bromodomains, the protein motifs capable of binding acetylated histones. Here, we report that the Arabidopsis bromodomain-containing proteins BRD1, BRD2, and BRD13 are likely true SWI/SNF subunits that interact with the core SWI/SNF components SWI3C and SWP73B. Loss of function of each single BRD protein caused early flowering but had a negligible effect on other developmental pathways. By contrast, a brd triple mutation (brdx3) led to more pronounced developmental abnormalities, indicating functional redundancy among the BRD proteins. The brdx3 phenotypes, including hypersensitivity to abscisic acid and the gibberellin biosynthesis inhibitor paclobutrazol, resembled those of swi/snf mutants. Furthermore, the BRM protein level and occupancy at the direct target loci SCL3, ABI5, and SVP were reduced in the brdx3 mutant background. Finally, a brdx3 brm-3 quadruple mutant, in which SWI/SNF complexes were devoid of all constituent bromodomains, phenocopied a loss-of-function mutation in BRM. Taken together, our results demonstrate the relevance of BRDs as SWI/SNF subunits and suggest their cooperation with the bromodomain of BRM ATPase.
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Affiliation(s)
- Kamila Jarończyk
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | | | - Adam Zaborowski
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Piotr Pupel
- Department of Plant Physiology, Genetics and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland
| | - Maria Bucholc
- Institute of Biochemistry and Biophysics PAS, 02-106 Warsaw, Poland
| | - Ewelina Małecka
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Nina Siwirykow
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Paulina Stachula
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Roksana Iwanicka-Nowicka
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
- Institute of Biochemistry and Biophysics PAS, 02-106 Warsaw, Poland
| | - Marta Koblowska
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
- Institute of Biochemistry and Biophysics PAS, 02-106 Warsaw, Poland
| | - Andrzej Jerzmanowski
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
- Institute of Biochemistry and Biophysics PAS, 02-106 Warsaw, Poland
| | - Rafał Archacki
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
- Institute of Biochemistry and Biophysics PAS, 02-106 Warsaw, Poland
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13
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Nishioka S, Sakamoto T, Matsunaga S. Roles of BRAHMA and Its Interacting Partners in Plant Chromatin Remodeling. CYTOLOGIA 2020. [DOI: 10.1508/cytologia.85.263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Sakiko Nishioka
- Department of Applied Biological Science, Faculty of Science and Technology Tokyo University of Science
| | - Takuya Sakamoto
- Department of Applied Biological Science, Faculty of Science and Technology Tokyo University of Science
| | - Sachihiro Matsunaga
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo
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14
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Kinoshita A, Richter R. Genetic and molecular basis of floral induction in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2490-2504. [PMID: 32067033 PMCID: PMC7210760 DOI: 10.1093/jxb/eraa057] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 02/03/2020] [Indexed: 05/18/2023]
Abstract
Many plants synchronize their life cycles in response to changing seasons and initiate flowering under favourable environmental conditions to ensure reproductive success. To confer a robust seasonal response, plants use diverse genetic programmes that integrate environmental and endogenous cues and converge on central floral regulatory hubs. Technological advances have allowed us to understand these complex processes more completely. Here, we review recent progress in our understanding of genetic and molecular mechanisms that control flowering in Arabidopsis thaliana.
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Affiliation(s)
- Atsuko Kinoshita
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
- Correspondence: or
| | - René Richter
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Australia
- Correspondence: or
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15
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Yang J, Yuan L, Yen MR, Zheng F, Ji R, Peng T, Gu D, Yang S, Cui Y, Chen PY, Wu K, Liu X. SWI3B and HDA6 interact and are required for transposon silencing in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:809-822. [PMID: 31883159 DOI: 10.1111/tpj.14666] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 10/23/2019] [Accepted: 11/20/2019] [Indexed: 05/14/2023]
Abstract
Although the interplay of covalent histone acetylation/deacetylation and ATP-dependent chromatin remodelling is crucial for the regulation of chromatin structure and gene expression in eukaryotes, the underlying molecular mechanism in plants remains largely unclear. Here we show a direct interaction between Arabidopsis SWI3B, an essential subunit of the SWI/SNF chromatin-remodelling complex, and the RPD3/HDA1-type histone deacetylase HDA6 both in vitro and in vivo. Furthermore, SWI3B and HDA6 co-repress the transcription of a subset of transposons. Both SWI3B and HDA6 maintain transposon silencing by decreasing histone H3 lysine 9 acetylation, but increasing histone H3 lysine 9 di-methylation, DNA methylation and nucleosome occupancy. Our findings reveal that SWI3B and HDA6 may act in the same co-repressor complex to maintain transposon silencing in Arabidopsis.
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Affiliation(s)
- Jie Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049, China
| | - Lianyu Yuan
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- College of Food Science, Southwest University, Chongqing, 400715, China
| | - Ming-Ren Yen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 106, Taiwan
| | - Feng Zheng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Rujun Ji
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049, China
| | - Tao Peng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049, China
| | - Dachuan Gu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Songguang Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Yuhai Cui
- London Research and Development Center, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, Western University, London, ON, Canada
| | - Pao-Yang Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 106, Taiwan
| | - Keqiang Wu
- Institute of Plant Biology, National Taiwan University, Taipei, 106, Taiwan
| | - Xuncheng Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China
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16
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Thouly C, Le Masson M, Lai X, Carles CC, Vachon G. Unwinding BRAHMA Functions in Plants. Genes (Basel) 2020; 11:genes11010090. [PMID: 31941094 PMCID: PMC7017052 DOI: 10.3390/genes11010090] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/02/2020] [Accepted: 01/07/2020] [Indexed: 02/07/2023] Open
Abstract
The ATP-dependent Switch/Sucrose non-fermenting (SWI/SNF) chromatin remodeling complex (CRC) regulates the transcription of many genes by destabilizing interactions between DNA and histones. In plants, BRAHMA (BRM), one of the two catalytic ATPase subunits of the complex, is the closest homolog of the yeast and animal SWI2/SNF2 ATPases. We summarize here the advances describing the roles of BRM in plant development as well as its recently reported chromatin-independent role in pri-miRNA processing in vitro and in vivo. We also enlighten the roles of plant-specific partners that physically interact with BRM. Three main types of partners can be distinguished: (i) DNA-binding proteins such as transcription factors which mostly cooperate with BRM in developmental processes, (ii) enzymes such as kinases or proteasome-related proteins that use BRM as substrate and are often involved in response to abiotic stress, and (iii) an RNA-binding protein which is involved with BRM in chromatin-independent pri-miRNA processing. This overview contributes to the understanding of the central position occupied by BRM within regulatory networks controlling fundamental biological processes in plants.
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17
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Jing Y, Guo Q, Lin R. The Chromatin-Remodeling Factor PICKLE Antagonizes Polycomb Repression of FT to Promote Flowering. PLANT PHYSIOLOGY 2019; 181:656-668. [PMID: 31377725 PMCID: PMC6776858 DOI: 10.1104/pp.19.00596] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/16/2019] [Indexed: 05/19/2023]
Abstract
Changing daylength (or photoperiod) is a seasonal cue used by many plants to adjust the timing of their floral transition to ensure reproductive success. An inductive long-day photoperiod triggers the expression of FLOWERING LOCUS T (FT), which promotes flowering. FT, encoding a major component of florigen, is induced in leaf veins specifically at dusk through the photoperiod pathway; however, the modulation of FT expression in response to photoperiod cues remains poorly understood. Here, we report that the balance between Polycomb group (PcG) and Trithorax group (TrxG) proteins sets appropriate FT expression in long days in Arabidopsis (Arabidopsis thaliana). In PcG mutant lines, FT was highly derepressed, but FT expression was decreased to an almost wild-type level and pattern upon the additional disruption of chromatin-remodeling factors PICKLE (PKL) and ARABIDOPSIS HOMOLOG OF TRITHORAX1 (ATX1), but not by disruption of photoperiod pathway components. PKL interacts with ATX1 to mediate trimethylation of histone H3 on lysine-4 at the FT locus, leading to antagonistic effects of PKL and ATX1 on PcG proteins in the regulation of FT expression. Therefore, the TrxG-like protein PKL prevents PcG-mediated silencing to ensure specific and appropriate expression of FT, thereby determining the proper flowering response.
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Affiliation(s)
- Yanjun Jing
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Qiang Guo
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rongcheng Lin
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Beijing 100093, China
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18
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Lee ZH, Hirakawa T, Yamaguchi N, Ito T. The Roles of Plant Hormones and Their Interactions with Regulatory Genes in Determining Meristem Activity. Int J Mol Sci 2019; 20:ijms20164065. [PMID: 31434317 PMCID: PMC6720427 DOI: 10.3390/ijms20164065] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/08/2019] [Accepted: 08/16/2019] [Indexed: 12/11/2022] Open
Abstract
Plants, unlike animals, have developed a unique system in which they continue to form organs throughout their entire life cycle, even after embryonic development. This is possible because plants possess a small group of pluripotent stem cells in their meristems. The shoot apical meristem (SAM) plays a key role in forming all of the aerial structures of plants, including floral meristems (FMs). The FMs subsequently give rise to the floral organs containing reproductive structures. Studies in the past few decades have revealed the importance of transcription factors and secreted peptides in meristem activity using the model plant Arabidopsis thaliana. Recent advances in genomic, transcriptomic, imaging, and modeling technologies have allowed us to explore the interplay between transcription factors, secreted peptides, and plant hormones. Two different classes of plant hormones, cytokinins and auxins, and their interaction are particularly important for controlling SAM and FM development. This review focuses on the current issues surrounding the crosstalk between the hormonal and genetic regulatory network during meristem self-renewal and organogenesis.
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Affiliation(s)
- Ze Hong Lee
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
| | - Takeshi Hirakawa
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
| | - Nobutoshi Yamaguchi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, 4-1-8, Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Toshiro Ito
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0192, Japan.
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19
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Torres ES, Deal RB. The histone variant H2A.Z and chromatin remodeler BRAHMA act coordinately and antagonistically to regulate transcription and nucleosome dynamics in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:144-162. [PMID: 30742338 PMCID: PMC7259472 DOI: 10.1111/tpj.14281] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 11/28/2018] [Accepted: 12/18/2018] [Indexed: 05/17/2023]
Abstract
Plants adapt to environmental changes by regulating transcription and chromatin organization. The histone H2A variant H2A.Z and the SWI2/SNF2 ATPase BRAHMA (BRM) have overlapping roles in positively and negatively regulating environmentally responsive genes in Arabidopsis, but the extent of this overlap was uncharacterized. Both factors have been associated with various changes in nucleosome positioning and stability in different contexts, but their specific roles in transcriptional regulation and chromatin organization need further characterization. We show that H2A.Z and BRM co-localize at thousands of sites, where they interact both cooperatively and antagonistically in transcriptional repression and activation of genes involved in development and responses to environmental stimuli. We identified eight classes of genes that show distinct relationships between H2A.Z and BRM with respect to their roles in transcription. These include activating and silencing transcription both redundantly and antagonistically. We found that H2A.Z contributes to a range of different nucleosome properties, while BRM stabilizes nucleosomes where it binds and destabilizes or repositions flanking nucleosomes. We also found that, at many genes regulated by both BRM and H2A.Z, both factors overlap with binding sites of the light-regulated transcription factor FAR1-Related Sequence 9 (FRS9) and that a subset of these FRS9 binding sites are dependent on H2A.Z and BRM for accessibility. Collectively, we comprehensively characterized the antagonistic and cooperative contributions of H2A.Z and BRM to transcriptional regulation, and illuminated several interrelated roles in chromatin organization. The variability observed in their individual functions implies that both BRM and H2A.Z have more context-dependent roles than previously assumed.
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Affiliation(s)
- E. Shannon Torres
- Department of Biology, Emory University, Atlanta, GA 30322
- Graduate Program in Genetics and Molecular Biology of the Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA 30322
| | - Roger B. Deal
- Department of Biology, Emory University, Atlanta, GA 30322
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20
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Identification and Expression Analysis of Snf2 Family Proteins in Tomato ( Solanum lycopersicum). Int J Genomics 2019; 2019:5080935. [PMID: 31049349 PMCID: PMC6458923 DOI: 10.1155/2019/5080935] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 12/18/2018] [Indexed: 02/03/2023] Open
Abstract
As part of chromatin-remodeling complexes (CRCs), sucrose nonfermenting 2 (Snf2) family proteins alter chromatin structure and nucleosome position by utilizing the energy of ATP, which allows other regulatory proteins to access DNA. Plant genomes encode a large number of Snf2 proteins, and some of them have been shown to be the key regulators at different developmental stages in Arabidopsis. Yet, little is known about the functions of Snf2 proteins in tomato (Solanum lycopersicum). In this study, 45 Snf2s were identified by the homologous search using representative sequences from yeast (S. cerevisiae), fruit fly (D. melanogaster), and Arabidopsis (A. thaliana) against the tomato genome annotation dataset. Tomato Snf2 proteins (also named SlCHRs) could be clustered into 6 groups and distributed on 11 chromosomes. All SlCHRs contained a helicase-C domain with about 80 amino acid residues and a SNF2-N domain with more variable amino acid residues. In addition, other conserved motifs were also identified in SlCHRs by using the MEME program. Expression profile analysis indicated that tomato Snf2 family genes displayed a wide range of expressions in different tissues and some of them were regulated by the environmental stimuli such as salicylic acid, abscisic acid, salt, and cold. Taken together, these results provide insights into the functions of SlCHRs in tomato.
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21
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Gaillochet C, Jamge S, van der Wal F, Angenent G, Immink R, Lohmann JU. A molecular network for functional versatility of HECATE transcription factors. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:57-70. [PMID: 29667268 DOI: 10.1111/tpj.13930] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 03/15/2018] [Accepted: 03/27/2018] [Indexed: 05/16/2023]
Abstract
During the plant life cycle, diverse signaling inputs are continuously integrated and engage specific genetic programs depending on the cellular or developmental context. Consistent with an important role in this process, HECATE (HEC) basic helix-loop-helix transcription factors display diverse functions, from photomorphogenesis to the control of shoot meristem dynamics and gynoecium patterning. However, the molecular mechanisms underlying their functional versatility and the deployment of specific HEC subprograms remain elusive. To address this issue, we systematically identified proteins with the capacity to interact with HEC1, the best-characterized member of the family, and integrated this information with our data set of direct HEC1 target genes. The resulting core genetic modules were consistent with specific developmental functions of HEC1, including its described activities in light signaling, gynoecium development and auxin homeostasis. Importantly, we found that HEC genes also play a role in the modulation of flowering time, and uncovered that their role in gynoecium development may involve the direct transcriptional regulation of NGATHA1 (NGA1) and NGA2 genes. NGA factors were previously shown to contribute to fruit development, but our data now show that they also modulate stem cell homeostasis in the shoot apical meristem. Taken together, our results delineate a molecular network underlying the functional versatility of HEC transcription factors. Our analyses have not only allowed us to identify relevant target genes controlling shoot stem cell activity and a so far undescribed biological function of HEC1, but also provide a rich resource for the mechanistic elucidation of further context-dependent HEC activities.
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Affiliation(s)
- Christophe Gaillochet
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 230, Heidelberg, D-69120, Germany
| | - Suraj Jamge
- Wageningen Plant Research, Wageningen University, PO Box 16, Wageningen, 6700AA, The Netherlands
| | - Froukje van der Wal
- Wageningen Plant Research, Wageningen University, PO Box 16, Wageningen, 6700AA, The Netherlands
| | - Gerco Angenent
- Wageningen Plant Research, Wageningen University, PO Box 16, Wageningen, 6700AA, The Netherlands
| | - Richard Immink
- Wageningen Plant Research, Wageningen University, PO Box 16, Wageningen, 6700AA, The Netherlands
| | - Jan U Lohmann
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 230, Heidelberg, D-69120, Germany
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22
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Archacki R, Yatusevich R, Buszewicz D, Krzyczmonik K, Patryn J, Iwanicka-Nowicka R, Biecek P, Wilczynski B, Koblowska M, Jerzmanowski A, Swiezewski S. Arabidopsis SWI/SNF chromatin remodeling complex binds both promoters and terminators to regulate gene expression. Nucleic Acids Res 2017; 45:3116-3129. [PMID: 27994035 PMCID: PMC5389626 DOI: 10.1093/nar/gkw1273] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 12/08/2016] [Indexed: 12/23/2022] Open
Abstract
ATP-dependent chromatin remodeling complexes are important regulators of gene expression in Eukaryotes. In plants, SWI/SNF-type complexes have been shown critical for transcriptional control of key developmental processes, growth and stress responses. To gain insight into mechanisms underlying these roles, we performed whole genome mapping of the SWI/SNF catalytic subunit BRM in Arabidopsis thaliana, combined with transcript profiling experiments. Our data show that BRM occupies thousands of sites in Arabidopsis genome, most of which located within or close to genes. Among identified direct BRM transcriptional targets almost equal numbers were up- and downregulated upon BRM depletion, suggesting that BRM can act as both activator and repressor of gene expression. Interestingly, in addition to genes showing canonical pattern of BRM enrichment near transcription start site, many other genes showed a transcription termination site-centred BRM occupancy profile. We found that BRM-bound 3΄ gene regions have promoter-like features, including presence of TATA boxes and high H3K4me3 levels, and possess high antisense transcriptional activity which is subjected to both activation and repression by SWI/SNF complex. Our data suggest that binding to gene terminators and controlling transcription of non-coding RNAs is another way through which SWI/SNF complex regulates expression of its targets.
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Affiliation(s)
- Rafal Archacki
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, Warsaw 02-096, Poland.,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Ruslan Yatusevich
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Daniel Buszewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Katarzyna Krzyczmonik
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Jacek Patryn
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, Warsaw 02-096, Poland.,College of Inter-FacultyIndividual Studies in Mathematics and Natural Sciences, Warsaw 02-089, Poland
| | - Roksana Iwanicka-Nowicka
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, Warsaw 02-096, Poland.,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Przemyslaw Biecek
- Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics,University of Warsaw, Warsaw 02-097, Poland.,Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw 00-662, Poland
| | - Bartek Wilczynski
- Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics,University of Warsaw, Warsaw 02-097, Poland
| | - Marta Koblowska
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, Warsaw 02-096, Poland.,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Andrzej Jerzmanowski
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, Warsaw 02-096, Poland.,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Szymon Swiezewski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
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23
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Zhang J, Lai J, Wang F, Yang S, He Z, Jiang J, Li Q, Wu Q, Liu Y, Yu M, Du J, Xie Q, Wu K, Yang C. A SUMO Ligase AtMMS21 Regulates the Stability of the Chromatin Remodeler BRAHMA in Root Development. PLANT PHYSIOLOGY 2017; 173:1574-1582. [PMID: 28115583 PMCID: PMC5338659 DOI: 10.1104/pp.17.00014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 01/20/2017] [Indexed: 05/08/2023]
Abstract
Chromatin remodeling is essential for gene expression regulation in plant development and response to stresses. Brahma (BRM) is a conserved ATPase in the SWI/SNF chromatin remodeling complex and is involved in various biological processes in plant cells, but the regulation mechanism on BRM protein remains unclear. Here, we report that BRM interacts with AtMMS21, a SUMO ligase in Arabidopsis (Arabidopsis thaliana). The interaction was confirmed in different approaches in vivo and in vitro. The mutants of BRM and AtMMS21 displayed a similar defect in root development. In the mms21-1 mutant, the protein level of BRM-GFP was significantly lower than that in wild type, but the RNA level of BRM did not change. Biochemical evidence indicated that BRM was modified by SUMO3, and the reaction was enhanced by AtMMS21. Furthermore, overexpression of wild-type AtMMS21 but not the mutated AtMMS21 without SUMO ligase activity was able to recover the stability of BRM in mms21-1 Overexpression of BRM in mms21-1 partially rescued the developmental defect of roots. Taken together, these results supported that AtMMS21 regulates the protein stability of BRM in root development.
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Affiliation(s)
- Juanjuan Zhang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China (J.Z., J.L., F.W., Z.H., J.J., Q.W., Y.L., M.Y., J.D., C.Y.)
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China (S.Y.)
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., Q.X.)
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China (Q.L., Q.X.); and
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan (K.W.)
| | - Jianbin Lai
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China (J.Z., J.L., F.W., Z.H., J.J., Q.W., Y.L., M.Y., J.D., C.Y.)
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China (S.Y.)
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., Q.X.)
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China (Q.L., Q.X.); and
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan (K.W.)
| | - Feige Wang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China (J.Z., J.L., F.W., Z.H., J.J., Q.W., Y.L., M.Y., J.D., C.Y.)
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China (S.Y.)
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., Q.X.)
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China (Q.L., Q.X.); and
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan (K.W.)
| | - Songguang Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China (J.Z., J.L., F.W., Z.H., J.J., Q.W., Y.L., M.Y., J.D., C.Y.)
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China (S.Y.)
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., Q.X.)
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China (Q.L., Q.X.); and
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan (K.W.)
| | - Zhipeng He
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China (J.Z., J.L., F.W., Z.H., J.J., Q.W., Y.L., M.Y., J.D., C.Y.)
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China (S.Y.)
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., Q.X.)
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China (Q.L., Q.X.); and
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan (K.W.)
| | - Jieming Jiang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China (J.Z., J.L., F.W., Z.H., J.J., Q.W., Y.L., M.Y., J.D., C.Y.)
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China (S.Y.)
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., Q.X.)
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China (Q.L., Q.X.); and
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan (K.W.)
| | - Qingliang Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China (J.Z., J.L., F.W., Z.H., J.J., Q.W., Y.L., M.Y., J.D., C.Y.)
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China (S.Y.)
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., Q.X.)
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China (Q.L., Q.X.); and
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan (K.W.)
| | - Qian Wu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China (J.Z., J.L., F.W., Z.H., J.J., Q.W., Y.L., M.Y., J.D., C.Y.)
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China (S.Y.)
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., Q.X.)
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China (Q.L., Q.X.); and
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan (K.W.)
| | - Yiyang Liu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China (J.Z., J.L., F.W., Z.H., J.J., Q.W., Y.L., M.Y., J.D., C.Y.)
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China (S.Y.)
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., Q.X.)
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China (Q.L., Q.X.); and
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan (K.W.)
| | - Mengyuan Yu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China (J.Z., J.L., F.W., Z.H., J.J., Q.W., Y.L., M.Y., J.D., C.Y.)
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China (S.Y.)
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., Q.X.)
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China (Q.L., Q.X.); and
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan (K.W.)
| | - Jinju Du
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China (J.Z., J.L., F.W., Z.H., J.J., Q.W., Y.L., M.Y., J.D., C.Y.)
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China (S.Y.)
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., Q.X.)
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China (Q.L., Q.X.); and
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan (K.W.)
| | - Qi Xie
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China (J.Z., J.L., F.W., Z.H., J.J., Q.W., Y.L., M.Y., J.D., C.Y.)
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China (S.Y.)
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., Q.X.)
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China (Q.L., Q.X.); and
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan (K.W.)
| | - Keqiang Wu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China (J.Z., J.L., F.W., Z.H., J.J., Q.W., Y.L., M.Y., J.D., C.Y.)
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China (S.Y.)
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., Q.X.)
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China (Q.L., Q.X.); and
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan (K.W.)
| | - Chengwei Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China (J.Z., J.L., F.W., Z.H., J.J., Q.W., Y.L., M.Y., J.D., C.Y.);
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China (S.Y.);
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., Q.X.);
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China (Q.L., Q.X.); and
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan (K.W.)
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24
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Zhang D, Li Y, Zhang X, Zha P, Lin R. The SWI2/SNF2 Chromatin-Remodeling ATPase BRAHMA Regulates Chlorophyll Biosynthesis in Arabidopsis. MOLECULAR PLANT 2017; 10:155-167. [PMID: 27865928 DOI: 10.1016/j.molp.2016.11.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 11/02/2016] [Accepted: 11/08/2016] [Indexed: 05/20/2023]
Abstract
Chlorophyll biosynthesis is critical for chloroplast development and photosynthesis in plants. Although reactions in the chlorophyll biosynthetic pathway have been largely known, little is known about the regulatory mechanisms of this pathway. In this study, we found that the dark-grown knockout and knockdown mutants as well as RNA-interference transgenic seedlings of BRAHMA (BRM), which encodes an SWI2/SNF2 chromatin-remodeling ATPase, had higher greening rates, accumulated less protochlorophyllide, and produced less reactive oxygen species than Arabidopsis wild-type plants did upon light exposure. The expression of NADPH:protochlorophyllide oxidoreductase A (PORA), PORB, and PORC, which catalyze a key step in chlorophyll biosynthesis, was increased in the brm mutants. We found that BRM physically interacted with the bHLH transcription factor PHYTOCHROME-INTERACTING FACTOR 1 (PIF1) through its N-terminal domains. Furthermore, we demonstrated that BRM was directly recruited to the cis-regulatory regions of PORC, but not of PORA and PORB, at least partially in a PIF1-dependent manner and the level of histone H3 lysine 4 tri-methylation (H3K4me3) at PORC loci was increased in the brm mutant. Taken together, our data indicate that the chromatin-remodeling enzyme BRM modulates PORC expression through interacting with PIF1, providing a novel regulatory mechanism by which plants fine-tune chlorophyll biosynthesis during the transition from heterotrophic to autotrophic growth.
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Affiliation(s)
- Dong Zhang
- Key Laboratory of Photobiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China; College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yuhong Li
- Key Laboratory of Photobiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China; College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xinyu Zhang
- Key Laboratory of Photobiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China; College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Ping Zha
- Key Laboratory of Photobiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China; College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Rongcheng Lin
- Key Laboratory of Photobiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China; College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China.
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25
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Fletcher JC. State of the Art: trxG Factor Regulation of Post-embryonic Plant Development. FRONTIERS IN PLANT SCIENCE 2017; 8:1925. [PMID: 29184559 PMCID: PMC5694493 DOI: 10.3389/fpls.2017.01925] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 10/24/2017] [Indexed: 05/07/2023]
Abstract
Multicellular organisms rely on the precise and consistent regulation of gene expression to direct their development in tissue- and cell-type specific patterns. This regulatory activity involves arrays of DNA-binding transcription factors and epigenetic factors that modify chromatin structure. Among the chromatin modifiers, trithorax (trxG) and Polycomb (PcG) group proteins play important roles in orchestrating the stable activation and repression of gene expression, respectively. These proteins have generally antagonistic functions in maintaining cell and tissue homeostasis as well as in mediating widespread transcriptional reprogramming during developmental transitions. Plants utilize multiple trxG factors to regulate gene transcription as they modulate their development in response to both endogenous and environmental cues. Here, I will discuss the roles of trxG factors and their associated proteins in post-embryonic plant development.
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Affiliation(s)
- Jennifer C. Fletcher
- Plant Gene Expression Center, United States Department of Agriculture – Agricultural Research Service, Albany, CA, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- *Correspondence: Jennifer C. Fletcher,
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26
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Xu Y, Guo C, Zhou B, Li C, Wang H, Zheng B, Ding H, Zhu Z, Peragine A, Cui Y, Poethig S, Wu G. Regulation of Vegetative Phase Change by SWI2/SNF2 Chromatin Remodeling ATPase BRAHMA. PLANT PHYSIOLOGY 2016; 172:2416-2428. [PMID: 27803189 PMCID: PMC5129735 DOI: 10.1104/pp.16.01588] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 10/30/2016] [Indexed: 05/05/2023]
Abstract
Plants progress from a juvenile vegetative phase of development to an adult vegetative phase of development before they enter the reproductive phase. miR156 has been shown to be the master regulator of the juvenile-to-adult transition in plants. However, the mechanism of how miR156 is transcriptionally regulated still remains elusive. In a forward genetic screen, we identified that a mutation in the SWI2/SNF2 chromatin remodeling ATPase BRAHMA (BRM) exhibited an accelerated vegetative phase change phenotype by reducing the expression of miR156, which in turn caused a corresponding increase in the levels of SQUAMOSA PROMOTER BINDING PROTEIN LIKE genes. BRM regulates miR156 expression by directly binding to the MIR156A promoter. Mutations in BRM not only increased occupancy of the -2 and +1 nucleosomes proximal to the transcription start site at the MIR156A locus but also the levels of trimethylated histone H3 at Lys 27. The precocious phenotype of brm mutant was partially suppressed by a second mutation in SWINGER (SWN), but not by a mutation in CURLEY LEAF, both of which are key components of the Polycomb Group Repressive Complex 2 in plants. Our results indicate that BRM and SWN act antagonistically at the nucleosome level to fine-tune the temporal expression of miR156 to regulate vegetative phase change in Arabidopsis.
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Affiliation(s)
- Yunmin Xu
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China (Y.X., C.G., B. Zhou., H.W., B. Zheng, H.D., Z.Z., G.W.)
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada (C.L., Y.C.); and
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (A.P., S.P.)
| | - Changkui Guo
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China (Y.X., C.G., B. Zhou., H.W., B. Zheng, H.D., Z.Z., G.W.)
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada (C.L., Y.C.); and
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (A.P., S.P.)
| | - Bingying Zhou
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China (Y.X., C.G., B. Zhou., H.W., B. Zheng, H.D., Z.Z., G.W.)
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada (C.L., Y.C.); and
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (A.P., S.P.)
| | - Chenlong Li
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China (Y.X., C.G., B. Zhou., H.W., B. Zheng, H.D., Z.Z., G.W.)
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada (C.L., Y.C.); and
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (A.P., S.P.)
| | - Huasen Wang
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China (Y.X., C.G., B. Zhou., H.W., B. Zheng, H.D., Z.Z., G.W.)
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada (C.L., Y.C.); and
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (A.P., S.P.)
| | - Ben Zheng
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China (Y.X., C.G., B. Zhou., H.W., B. Zheng, H.D., Z.Z., G.W.)
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada (C.L., Y.C.); and
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (A.P., S.P.)
| | - Han Ding
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China (Y.X., C.G., B. Zhou., H.W., B. Zheng, H.D., Z.Z., G.W.)
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada (C.L., Y.C.); and
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (A.P., S.P.)
| | - Zhujun Zhu
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China (Y.X., C.G., B. Zhou., H.W., B. Zheng, H.D., Z.Z., G.W.)
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada (C.L., Y.C.); and
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (A.P., S.P.)
| | - Angela Peragine
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China (Y.X., C.G., B. Zhou., H.W., B. Zheng, H.D., Z.Z., G.W.)
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada (C.L., Y.C.); and
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (A.P., S.P.)
| | - Yuhai Cui
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China (Y.X., C.G., B. Zhou., H.W., B. Zheng, H.D., Z.Z., G.W.)
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada (C.L., Y.C.); and
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (A.P., S.P.)
| | - Scott Poethig
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China (Y.X., C.G., B. Zhou., H.W., B. Zheng, H.D., Z.Z., G.W.)
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada (C.L., Y.C.); and
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (A.P., S.P.)
| | - Gang Wu
- Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China (Y.X., C.G., B. Zhou., H.W., B. Zheng, H.D., Z.Z., G.W.);
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada (C.L., Y.C.); and
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (A.P., S.P.)
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27
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Pons C, Martí C, Forment J, Crisosto CH, Dandekar AM, Granell A. A genetic genomics-expression approach reveals components of the molecular mechanisms beyond the cell wall that underlie peach fruit woolliness due to cold storage. PLANT MOLECULAR BIOLOGY 2016; 92:483-503. [PMID: 27714490 DOI: 10.1007/s11103-016-0526-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 08/06/2016] [Indexed: 05/14/2023]
Abstract
Peach fruits subjected to prolonged cold storage (CS) to delay decay and over-ripening often develop a form of chilling injury (CI) called mealiness/woolliness (WLT), a flesh textural disorder characterized by lack of juiciness. Transcript profiles were analyzed after different lengths of CS and subsequent shelf life ripening (SLR) in pools of fruits from siblings of the Pop-DG population with contrasting sensitivity to develop WLT. This was followed by quantitative PCR on pools and individual lines of the Pop-DG population to validate and extend the microarray results. Relative tolerance to WLT development during SLR was related to the fruit's ability to recover from cold and the reactivation of normal ripening, processes that are probably regulated by transcription factors involved in stress protection, stress recovery and induction of ripening. Furthermore, our results showed that altered ripening in WLT fruits during shelf life is probably due, in part, to cold-induced desynchronization of the ripening program involving ethylene and auxin hormonal regulation of metabolism and cell wall. In addition, we found strong correlation between expression of RNA translation and protein assembly genes and the visual injury symptoms.
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Affiliation(s)
- Clara Pons
- Instituto de Biología Molecular y Celular de Plantas. Consejo Superior de Investigaciones Científicas (CSIC) -Universidad Politécnica de Valencia (UPV), 46022, Valencia, Spain.
| | - Cristina Martí
- Instituto de Biología Molecular y Celular de Plantas. Consejo Superior de Investigaciones Científicas (CSIC) -Universidad Politécnica de Valencia (UPV), 46022, Valencia, Spain
| | - Javier Forment
- Instituto de Biología Molecular y Celular de Plantas. Consejo Superior de Investigaciones Científicas (CSIC) -Universidad Politécnica de Valencia (UPV), 46022, Valencia, Spain
| | - Carlos H Crisosto
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Abhaya M Dandekar
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas. Consejo Superior de Investigaciones Científicas (CSIC) -Universidad Politécnica de Valencia (UPV), 46022, Valencia, Spain
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28
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Zhou Y, Hartwig B, James GV, Schneeberger K, Turck F. Complementary Activities of TELOMERE REPEAT BINDING Proteins and Polycomb Group Complexes in Transcriptional Regulation of Target Genes. THE PLANT CELL 2016; 28:87-101. [PMID: 26721861 PMCID: PMC4746681 DOI: 10.1105/tpc.15.00787] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 11/11/2015] [Accepted: 12/25/2015] [Indexed: 05/19/2023]
Abstract
In multicellular organisms, Polycomb Repressive Complex 1 (PRC1) and PRC2 repress target genes through histone modification and chromatin compaction. Arabidopsis thaliana mutants strongly compromised in the pathway cannot develop differentiated organs. LIKE HETEROCHROMATIN PROTEIN1 (LHP1) is so far the only known plant PRC1 component that directly binds to H3K27me3, the histone modification set by PRC2, and also associates genome-wide with trimethylation of lysine 27 of histone H3 (H3K27me3). Surprisingly, lhp1 mutants show relatively mild phenotypic alterations. To explain this paradox, we screened for genetic enhancers of lhp1 mutants to identify novel components repressing target genes together with, or in parallel to, LHP1. Two enhancing mutations were mapped to TELOMERE REPEAT BINDING PROTEIN1 (TRB1) and its paralog TRB3. We show that TRB1 binds to thousands of genomic sites containing telobox or related cis-elements with a significant increase of sites and strength of binding in the lhp1 background. Furthermore, in combination with lhp1, but not alone, trb1 mutants show increased transcription of LHP1 targets, such as floral meristem identity genes, which are more likely to be bound by TRB1 in the lhp1 background. By contrast, expression of a subset of LHP1-independent TRB1 target genes, many involved in primary metabolism, is decreased in the absence of TRB1 alone. Thus, TRB1 is a bivalent transcriptional modulator that maintains downregulation of Polycomb Group (PcG) target genes in lhp1 mutants, while it sustains high expression of targets that are regulated independently of PcG.
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Affiliation(s)
- Yue Zhou
- Department Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
| | - Benjamin Hartwig
- Department Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
| | - Geo Velikkakam James
- Department Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
| | - Korbinian Schneeberger
- Department Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
| | - Franziska Turck
- Department Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
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29
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Han SK, Wu MF, Cui S, Wagner D. Roles and activities of chromatin remodeling ATPases in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:62-77. [PMID: 25977075 DOI: 10.1111/tpj.12877] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 05/04/2015] [Accepted: 05/06/2015] [Indexed: 05/18/2023]
Abstract
Chromatin remodeling ATPases and their associated complexes can alter the accessibility of the genome in the context of chromatin by using energy derived from the hydrolysis of ATP to change the positioning, occupancy and composition of nucleosomes. In animals and plants, these remodelers have been implicated in diverse processes ranging from stem cell maintenance and differentiation to developmental phase transitions and stress responses. Detailed investigation of their roles in individual processes has suggested a higher level of selectivity of chromatin remodeling ATPase activity than previously anticipated, and diverse mechanisms have been uncovered that can contribute to the selectivity. This review summarizes recent advances in understanding the roles and activities of chromatin remodeling ATPases in plants.
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Affiliation(s)
- Soon-Ki Han
- Howard Hughes Medical Institute and Department of Biology, University of Washington, Seattle, WA, 98195, USA
| | - Miin-Feng Wu
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sujuan Cui
- Hebei Key Laboratory of Molecular Cell Biology, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
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30
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Sacharowski SP, Gratkowska DM, Sarnowska EA, Kondrak P, Jancewicz I, Porri A, Bucior E, Rolicka AT, Franzen R, Kowalczyk J, Pawlikowska K, Huettel B, Torti S, Schmelzer E, Coupland G, Jerzmanowski A, Koncz C, Sarnowski TJ. SWP73 Subunits of Arabidopsis SWI/SNF Chromatin Remodeling Complexes Play Distinct Roles in Leaf and Flower Development. THE PLANT CELL 2015; 27:1889-906. [PMID: 26106148 PMCID: PMC4531355 DOI: 10.1105/tpc.15.00233] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 06/03/2015] [Indexed: 05/03/2023]
Abstract
Arabidopsis thaliana SWP73A and SWP73B are homologs of mammalian BRAHMA-associated factors (BAF60s) that tether SWITCH/SUCROSE NONFERMENTING chromatin remodeling complexes to transcription factors of genes regulating various cell differentiation pathways. Here, we show that Arabidopsis thaliana SWP73s modulate several important developmental pathways. While undergoing normal vegetative development, swp73a mutants display reduced expression of FLOWERING LOCUS C and early flowering in short days. By contrast, swp73b mutants are characterized by retarded growth, severe defects in leaf and flower development, delayed flowering, and male sterility. MNase-Seq, transcript profiling, and ChIP-Seq studies demonstrate that SWP73B binds the promoters of ASYMMETRIC LEAVES1 and 2, KANADI1 and 3, and YABBY2, 3, and 5 genes, which regulate leaf development and show coordinately altered transcription in swp73b plants. Lack of SWP73B alters the expression patterns of APETALA1, APETALA3, and the MADS box gene AGL24, whereas other floral organ identity genes show reduced expression correlating with defects in flower development. Consistently, SWP73B binds to the promoter regions of APETALA1 and 3, SEPALLATA3, LEAFY, UNUSUAL FLORAL ORGANS, TERMINAL FLOWER1, AGAMOUS-LIKE24, and SUPPRESSOR OF CONSTANS OVEREXPRESSION1 genes, and the swp73b mutation alters nucleosome occupancy on most of these loci. In conclusion, SWP73B acts as important modulator of major developmental pathways, while SWP73A functions in flowering time control.
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Affiliation(s)
- Sebastian P Sacharowski
- Institute of Biochemistry and Biophysics PAS, Department of Protein Biosynthesis, 02-106 Warsaw, Poland
| | - Dominika M Gratkowska
- Institute of Biochemistry and Biophysics PAS, Department of Protein Biosynthesis, 02-106 Warsaw, Poland
| | | | - Paulina Kondrak
- Institute of Biochemistry and Biophysics PAS, Department of Protein Biosynthesis, 02-106 Warsaw, Poland Warsaw University of Life Sciences, 02-787 Warsaw, Poland
| | - Iga Jancewicz
- Institute of Biochemistry and Biophysics PAS, Department of Protein Biosynthesis, 02-106 Warsaw, Poland Warsaw University of Life Sciences, 02-787 Warsaw, Poland
| | - Aimone Porri
- Max-Planck Institut für Pflanzenzüchtungsforschung, D-50829 Köln, Germany
| | - Ernest Bucior
- Institute of Biochemistry and Biophysics PAS, Department of Protein Biosynthesis, 02-106 Warsaw, Poland Universtity of Warsaw, Faculty of Biology, Institute of Experimental Plant Biology, Department of Plant Molecular Biology, 02-106 Warsaw, Poland
| | - Anna T Rolicka
- Institute of Biochemistry and Biophysics PAS, Department of Protein Biosynthesis, 02-106 Warsaw, Poland Universtity of Warsaw, Faculty of Biology, Institute of Experimental Plant Biology, Department of Plant Molecular Biology, 02-106 Warsaw, Poland
| | - Rainer Franzen
- Max-Planck Institut für Pflanzenzüchtungsforschung, D-50829 Köln, Germany
| | - Justyna Kowalczyk
- Institute of Biochemistry and Biophysics PAS, Department of Protein Biosynthesis, 02-106 Warsaw, Poland
| | - Katarzyna Pawlikowska
- Institute of Biochemistry and Biophysics PAS, Department of Protein Biosynthesis, 02-106 Warsaw, Poland
| | - Bruno Huettel
- Max Planck Genome Centre Cologne, D-50820 Köln, Germany
| | - Stefano Torti
- Max-Planck Institut für Pflanzenzüchtungsforschung, D-50829 Köln, Germany
| | - Elmon Schmelzer
- Max-Planck Institut für Pflanzenzüchtungsforschung, D-50829 Köln, Germany
| | - George Coupland
- Max-Planck Institut für Pflanzenzüchtungsforschung, D-50829 Köln, Germany
| | - Andrzej Jerzmanowski
- Institute of Biochemistry and Biophysics PAS, Department of Protein Biosynthesis, 02-106 Warsaw, Poland Universtity of Warsaw, Faculty of Biology, Institute of Experimental Plant Biology, Department of Plant Molecular Biology, 02-106 Warsaw, Poland
| | - Csaba Koncz
- Max-Planck Institut für Pflanzenzüchtungsforschung, D-50829 Köln, Germany Institute of Plant Biology, Biological Research Center of Hungarian Academy, H-6724 Szeged, Hungary
| | - Tomasz J Sarnowski
- Institute of Biochemistry and Biophysics PAS, Department of Protein Biosynthesis, 02-106 Warsaw, Poland
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31
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Jarillo JA, Piñeiro M. H2A.Z mediates different aspects of chromatin function and modulates flowering responses in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:96-109. [PMID: 25943140 DOI: 10.1111/tpj.12873] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 04/17/2015] [Accepted: 04/22/2015] [Indexed: 05/23/2023]
Abstract
Eukaryotic organisms have canonical histones and a number of histone variants that perform specialized functions and confer particular structural properties to the nucleosomes that contain them. The histone H2A family comprises several variants, with H2A.Z being the most evolutionarily conserved. This variant is essential in eukaryotes and has emerged as a key player in chromatin function, performing an essential role in gene transcription and genome stability. During recent years, biochemical, genetic and genomic studies have begun to uncover the role of several ATP-dependent chromatin-remodeling complexes in H2A.Z deposition and removal. These ATPase complexes are widely conserved from yeast to mammals. In Arabidopsis there are homologs for most of the subunits of these complexes, and their functions are just beginning to be unveiled. In this review, we discuss the major contributions made in relation to the biology of the H2A.Z in plants, and more specifically concerning the function of this histone variant in the transition from vegetative to reproductive development. Recent advances in the understanding of the molecular mechanisms underlying the H2A.Z-mediated modulation of the floral transition, and thermosensory flowering responses in particular, are discussed. The emerging picture shows that plants contain chromatin-remodeling complexes related to those involved in modulating the dynamics of H2A.Z in other eukaryotes, but their precise biochemical nature remains elusive.
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Affiliation(s)
- José A Jarillo
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigaciones Agrarias-Universidad Politécnica de Madrid, 28223, Madrid, Spain
| | - Manuel Piñeiro
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigaciones Agrarias-Universidad Politécnica de Madrid, 28223, Madrid, Spain
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32
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Yang S, Li C, Zhao L, Gao S, Lu J, Zhao M, Chen CY, Liu X, Luo M, Cui Y, Yang C, Wu K. The Arabidopsis SWI2/SNF2 Chromatin Remodeling ATPase BRAHMA Targets Directly to PINs and Is Required for Root Stem Cell Niche Maintenance. THE PLANT CELL 2015; 27:1670-80. [PMID: 25991732 PMCID: PMC4498203 DOI: 10.1105/tpc.15.00091] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 05/05/2015] [Indexed: 05/02/2023]
Abstract
BRAHMA (BRM), a SWI/SNF chromatin remodeling ATPase, is essential for the transcriptional reprogramming associated with development and cell differentiation in Arabidopsis thaliana. In this study, we show that loss-of-function mutations in BRM led to defective maintenance of the root stem cell niche, decreased meristematic activity, and stunted root growth. Mutations of BRM affected auxin distribution by reducing local expression of several PIN-FORMED (PIN) genes in the stem cells and impaired the expression of the stem cell transcription factor genes PLETHORA (PLT1) and PLT2. Chromatin immunoprecipitation assays showed that BRM could directly target to the chromatin of PIN1, PIN2, PIN3, PIN4, and PIN7. In addition, genetic interaction assays indicate that PLTs acted downstream of BRM, and overexpression of PLT2 partially rescued the stem cell niche defect of brm mutants. Taken together, these results support the idea that BRM acts in the PLT pathway to maintain the root stem cell niche by altering the expression of PINs.
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Affiliation(s)
- Songguang Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Chenlong Li
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3, Canada Department of Biology, Western University, London, Ontario N6A 5B7, Canada
| | - Linmao Zhao
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Sujuan Gao
- College of Light Industry and Food Science, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Jingxia Lu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Minglei Zhao
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Chia-Yang Chen
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Xuncheng Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Ming Luo
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yuhai Cui
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3, Canada
| | - Chengwei Yang
- Guangdong Key Lab of Biotechnology for Plant Development, College of Life Science, South China Normal University, Guangzhou 510631, China
| | - Keqiang Wu
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
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33
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Zhang C, Cao L, Rong L, An Z, Zhou W, Ma J, Shen WH, Zhu Y, Dong A. The chromatin-remodeling factor AtINO80 plays crucial roles in genome stability maintenance and in plant development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:655-68. [PMID: 25832737 DOI: 10.1111/tpj.12840] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Revised: 03/25/2015] [Accepted: 03/25/2015] [Indexed: 05/10/2023]
Abstract
INO80 is a conserved chromatin-remodeling factor in eukaryotes. While a previous study reported that the Arabidopsis thaliana INO80 (AtINO80) is required for somatic homologous recombination (HR), the role of AtINO80 in plant growth and development remains obscure. Here, we identified and characterized two independent atino80 mutant alleles, atino80-5 and atino80-6, which display similar and pleiotropic phenotypes, including smaller plant and organ size, and late flowering. Under standard growth conditions, atino80-5 showed decreased HR; however, after genotoxic treatment, HR in the mutant increased, accompanied by more DNA double-strand breaks and stronger cellular responses. Transcription analysis showed that many developmental and environmental responsive genes are overrepresented in the perturbed genes in atino80-5. These genes significantly overlapped with the category of H2A.Z body-enriched genes. AtINO80 also interacts with H2A.Z, and facilitates the enrichment of H2A.Z at the ends of the key flowering repressor genes FLC and MAF4/5. Our characterization of the atino80-5 and atino80-6 mutants confirms and extends the previous AtINO80 study, and provides perspectives for linking studies of epigenetic mechanisms involved in plant chromatin stability with plant response to developmental and environmental cues.
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Affiliation(s)
- Chi Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 20043, China
| | - Lin Cao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 20043, China
| | - Liang Rong
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 20043, China
| | - Zengxuan An
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 20043, China
| | - Wangbin Zhou
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 20043, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 20043, China
| | - Wen-Hui Shen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 20043, China
- Institut de Biologie Moléculaire des Plantes, UPR2357 CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084, Strasbourg Cédex, France
| | - Yan Zhu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 20043, China
| | - Aiwu Dong
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 20043, China
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34
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PcG and trxG in plants - friends or foes. Trends Genet 2015; 31:252-62. [PMID: 25858128 DOI: 10.1016/j.tig.2015.03.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 03/07/2015] [Accepted: 03/09/2015] [Indexed: 01/07/2023]
Abstract
The highly-conserved Polycomb group (PcG) and trithorax group (trxG) proteins play major roles in regulating gene expression and maintaining developmental states in many organisms. However, neither the recruitment of Polycomb repressive complexes (PRC) nor the mechanisms of PcG and trxG-mediated gene silencing and activation are well understood. Recent progress in Arabidopsis research challenges the dominant model of PRC2-dependent recruitment of PRC1 to target genes. Moreover, evidence indicates that diverse forms of PRC1, with shared components, are a common theme in plants and mammals. Although trxG is known to antagonize PcG, emerging data reveal that trxG can also repress gene expression, acting cooperatively with PcG. We discuss these recent findings and highlight the employment of diverse epigenetic mechanisms during development in plants and animals.
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35
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Zhao M, Yang S, Chen CY, Li C, Shan W, Lu W, Cui Y, Liu X, Wu K. Arabidopsis BREVIPEDICELLUS interacts with the SWI2/SNF2 chromatin remodeling ATPase BRAHMA to regulate KNAT2 and KNAT6 expression in control of inflorescence architecture. PLoS Genet 2015; 11:e1005125. [PMID: 25822547 PMCID: PMC4379049 DOI: 10.1371/journal.pgen.1005125] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 03/04/2015] [Indexed: 01/08/2023] Open
Abstract
BREVIPEDICELLUS (BP or KNAT1), a class-I KNOTTED1-like homeobox (KNOX) transcription factor in Arabidopsis thaliana, contributes to shaping the normal inflorescence architecture through negatively regulating other two class-I KNOX genes, KNAT2 and KNAT6. However, the molecular mechanism of BP-mediated transcription regulation remains unclear. In this study, we showed that BP directly interacts with the SWI2/SNF2 chromatin remodeling ATPase BRAHMA (BRM) both in vitro and in vivo. Loss-of-function BRM mutants displayed inflorescence architecture defects, with clustered inflorescences, horizontally orientated pedicels, and short pedicels and internodes, a phenotype similar to the bp mutants. Furthermore, the transcript levels of KNAT2 and KNAT6 were elevated in brm-3, bp-9 and brm-3 bp-9 double mutants. Increased histone H3 lysine 4 tri-methylation (H3K4me3) levels were detected in brm-3, bp-9 and brm-3 bp-9 double mutants. Moreover, BRM and BP co-target to KNAT2 and KNAT6 genes, and BP is required for the binding of BRM to KNAT2 and KNAT6. Taken together, our results indicate that BP interacts with the chromatin remodeling factor BRM to regulate the expression of KNAT2 and KNAT6 in control of inflorescence architecture. BP is a class-I KNOX transcription factor that controls normal inflorescence architecture development by repressing the expression of two KNOX genes, KNAT2 and KNAT6. In this study, we showed that Arabidopsis BP directly interacts with the SWI2/SNF2 chromatin remodeling ATPase BRM. brm and bp mutants displayed similar inflorescence architecture defects, with clustered inflorescences, horizontally orientated pedicels, and short pedicels and internodes. Furthermore, BP and BRM co-target to KNAT2 and KNAT6 genes and repress their expression. This work reveals a new regulatory mechanism that BP associates with BRM in control of inflorescence architecture development.
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Affiliation(s)
- Minglei Zhao
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Songguang Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Chia-Yang Chen
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
| | - Chenlong Li
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, Ontario, Canada
- Department of Biology, Western University, London, Ontario, Canada
| | - Wei Shan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/ Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou, China
| | - Wangjin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/ Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou, China
| | - Yuhai Cui
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, Ontario, Canada
- Department of Biology, Western University, London, Ontario, Canada
| | - Xuncheng Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- * E-mail: (XL); (KW)
| | - Keqiang Wu
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
- * E-mail: (XL); (KW)
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The Arabidopsis SWI2/SNF2 chromatin Remodeler BRAHMA regulates polycomb function during vegetative development and directly activates the flowering repressor gene SVP. PLoS Genet 2015; 11:e1004944. [PMID: 25615622 PMCID: PMC4304717 DOI: 10.1371/journal.pgen.1004944] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 12/10/2014] [Indexed: 11/19/2022] Open
Abstract
The chromatin remodeler BRAHMA (BRM) is a Trithorax Group (TrxG) protein that antagonizes the functions of Polycomb Group (PcG) proteins in fly and mammals. Recent studies also implicate such a role for Arabidopsis (Arabidopsis thaliana) BRM but the molecular mechanisms underlying the antagonism are unclear. To understand the interplay between BRM and PcG during plant development, we performed a genome-wide analysis of trimethylated histone H3 lysine 27 (H3K27me3) in brm mutant seedlings by chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq). Increased H3K27me3 deposition at several hundred genes was observed in brm mutants and this increase was partially supressed by removal of the H3K27 methyltransferase CURLY LEAF (CLF) or SWINGER (SWN). ChIP experiments demonstrated that BRM directly binds to a subset of the genes and prevents the inappropriate association and/or activity of PcG proteins at these loci. Together, these results indicate a crucial role of BRM in restricting the inappropriate activity of PcG during plant development. The key flowering repressor gene SHORT VEGETATIVE PHASE (SVP) is such a BRM target. In brm mutants, elevated PcG occupancy at SVP accompanies a dramatic increase in H3K27me3 levels at this locus and a concomitant reduction of SVP expression. Further, our gain- and loss-of-function genetic evidence establishes that BRM controls flowering time by directly activating SVP expression. This work reveals a genome-wide functional interplay between BRM and PcG and provides new insights into the impacts of these proteins in plant growth and development.
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Affiliation(s)
- Jose C Reyes
- Molecular Biology Department, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas (CSIC), Av. Americo Vespucio, 41092 Seville, Spain
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Jégu T, Latrasse D, Delarue M, Hirt H, Domenichini S, Ariel F, Crespi M, Bergounioux C, Raynaud C, Benhamed M. The BAF60 subunit of the SWI/SNF chromatin-remodeling complex directly controls the formation of a gene loop at FLOWERING LOCUS C in Arabidopsis. THE PLANT CELL 2014; 26:538-51. [PMID: 24510722 PMCID: PMC3967024 DOI: 10.1105/tpc.113.114454] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
SWI/SNF complexes mediate ATP-dependent chromatin remodeling to regulate gene expression. Many components of these complexes are evolutionarily conserved, and several subunits of Arabidopsis thaliana SWI/SNF complexes are involved in the control of flowering, a process that depends on the floral repressor FLOWERING LOCUS C (FLC). BAF60 is a SWI/SNF subunit, and in this work, we show that BAF60, via a direct targeting of the floral repressor FLC, induces a change at the high-order chromatin level and represses the photoperiod flowering pathway in Arabidopsis. BAF60 accumulates in the nucleus and controls the formation of the FLC gene loop by modulation of histone density, composition, and posttranslational modification. Physiological analysis of BAF60 RNA interference mutant lines allowed us to propose that this chromatin-remodeling protein creates a repressive chromatin configuration at the FLC locus.
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Affiliation(s)
- Teddy Jégu
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Université Paris-Sud XI, 91405 Orsay, France
| | - David Latrasse
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Université Paris-Sud XI, 91405 Orsay, France
| | - Marianne Delarue
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Université Paris-Sud XI, 91405 Orsay, France
| | - Heribert Hirt
- Institut des Sciences du Végétal, UPR CNRS, F-91190 Gif-sur-Yvette, France
| | - Séverine Domenichini
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Université Paris-Sud XI, 91405 Orsay, France
| | - Federico Ariel
- Unité de Recherche en Génomique Végétale Plant Genomics, INRA/CNRS/University of Evry, F-91057 Evry, France
| | - Martin Crespi
- Unité de Recherche en Génomique Végétale Plant Genomics, INRA/CNRS/University of Evry, F-91057 Evry, France
| | - Catherine Bergounioux
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Université Paris-Sud XI, 91405 Orsay, France
| | - Cécile Raynaud
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Université Paris-Sud XI, 91405 Orsay, France
| | - Moussa Benhamed
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Université Paris-Sud XI, 91405 Orsay, France
- Address correspondence to
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Vercruyssen L, Verkest A, Gonzalez N, Heyndrickx KS, Eeckhout D, Han SK, Jégu T, Archacki R, Van Leene J, Andriankaja M, De Bodt S, Abeel T, Coppens F, Dhondt S, De Milde L, Vermeersch M, Maleux K, Gevaert K, Jerzmanowski A, Benhamed M, Wagner D, Vandepoele K, De Jaeger G, Inzé D. ANGUSTIFOLIA3 binds to SWI/SNF chromatin remodeling complexes to regulate transcription during Arabidopsis leaf development. THE PLANT CELL 2014; 26:210-29. [PMID: 24443518 PMCID: PMC3963571 DOI: 10.1105/tpc.113.115907] [Citation(s) in RCA: 163] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 12/16/2013] [Accepted: 12/24/2013] [Indexed: 05/18/2023]
Abstract
The transcriptional coactivator ANGUSTIFOLIA3 (AN3) stimulates cell proliferation during Arabidopsis thaliana leaf development, but the molecular mechanism is largely unknown. Here, we show that inducible nuclear localization of AN3 during initial leaf growth results in differential expression of important transcriptional regulators, including GROWTH REGULATING FACTORs (GRFs). Chromatin purification further revealed the presence of AN3 at the loci of GRF5, GRF6, CYTOKININ RESPONSE FACTOR2, CONSTANS-LIKE5 (COL5), HECATE1 (HEC1), and ARABIDOPSIS RESPONSE REGULATOR4 (ARR4). Tandem affinity purification of protein complexes using AN3 as bait identified plant SWITCH/SUCROSE NONFERMENTING (SWI/SNF) chromatin remodeling complexes formed around the ATPases BRAHMA (BRM) or SPLAYED. Moreover, SWI/SNF ASSOCIATED PROTEIN 73B (SWP73B) is recruited by AN3 to the promoters of GRF5, GRF3, COL5, and ARR4, and both SWP73B and BRM occupy the HEC1 promoter. Furthermore, we show that AN3 and BRM genetically interact. The data indicate that AN3 associates with chromatin remodelers to regulate transcription. In addition, modification of SWI3C expression levels increases leaf size, underlining the importance of chromatin dynamics for growth regulation. Our results place the SWI/SNF-AN3 module as a major player at the transition from cell proliferation to cell differentiation in a developing leaf.
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Affiliation(s)
- Liesbeth Vercruyssen
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Aurine Verkest
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Nathalie Gonzalez
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Ken S. Heyndrickx
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Soon-Ki Han
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Teddy Jégu
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618, Université Paris-Sud XI, 91405 Orsay, France
| | - Rafal Archacki
- Laboratory of Plant Molecular Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Jelle Van Leene
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Megan Andriankaja
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Stefanie De Bodt
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Thomas Abeel
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Frederik Coppens
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Stijn Dhondt
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Liesbeth De Milde
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Mattias Vermeersch
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Katrien Maleux
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Kris Gevaert
- Department of Medical Protein Research and Biochemistry, VIB, 90 00 Ghent, Belgium
- Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Andrzej Jerzmanowski
- Laboratory of Plant Molecular Biology, University of Warsaw, 02-106 Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Moussa Benhamed
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618, Université Paris-Sud XI, 91405 Orsay, France
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Klaas Vandepoele
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Address correspondence to
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Archacki R, Buszewicz D, Sarnowski TJ, Sarnowska E, Rolicka AT, Tohge T, Fernie AR, Jikumaru Y, Kotlinski M, Iwanicka-Nowicka R, Kalisiak K, Patryn J, Halibart-Puzio J, Kamiya Y, Davis SJ, Koblowska MK, Jerzmanowski A. BRAHMA ATPase of the SWI/SNF chromatin remodeling complex acts as a positive regulator of gibberellin-mediated responses in arabidopsis. PLoS One 2013; 8:e58588. [PMID: 23536800 PMCID: PMC3594165 DOI: 10.1371/journal.pone.0058588] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2012] [Accepted: 02/05/2013] [Indexed: 11/19/2022] Open
Abstract
SWI/SNF chromatin remodeling complexes perform a pivotal function in the regulation of eukaryotic gene expression. Arabidopsis (Arabidopsis thaliana) mutants in major SWI/SNF subunits display embryo-lethal or dwarf phenotypes, indicating their critical role in molecular pathways controlling development and growth. As gibberellins (GA) are major positive regulators of plant growth, we wanted to establish whether there is a link between SWI/SNF and GA signaling in Arabidopsis. This study revealed that in brm-1 plants, depleted in SWI/SNF BRAHMA (BRM) ATPase, a number of GA-related phenotypic traits are GA-sensitive and that the loss of BRM results in markedly decreased level of endogenous bioactive GA. Transcriptional profiling of brm-1 and the GA biosynthesis mutant ga1-3, as well as the ga1-3/brm-1 double mutant demonstrated that BRM affects the expression of a large set of GA-responsive genes including genes responsible for GA biosynthesis and signaling. Furthermore, we found that BRM acts as an activator and directly associates with promoters of GA3ox1, a GA biosynthetic gene, and SCL3, implicated in positive regulation of the GA pathway. Many GA-responsive gene expression alterations in the brm-1 mutant are likely due to depleted levels of active GAs. However, the analysis of genetic interactions between BRM and the DELLA GA pathway repressors, revealed that BRM also acts on GA-responsive genes independently of its effect on GA level. Given the central position occupied by SWI/SNF complexes within regulatory networks controlling fundamental biological processes, the identification of diverse functional intersections of BRM with GA-dependent processes in this study suggests a role for SWI/SNF in facilitating crosstalk between GA-mediated regulation and other cellular pathways.
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Affiliation(s)
- Rafal Archacki
- Department of Plant Molecular Biology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Daniel Buszewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Tomasz J. Sarnowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | | | - Anna T. Rolicka
- Department of Plant Molecular Biology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Takayuki Tohge
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Alisdair R. Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Yusuke Jikumaru
- RIKEN Plant Science Center, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Maciej Kotlinski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Roksana Iwanicka-Nowicka
- Department of Plant Molecular Biology, Faculty of Biology, University of Warsaw, Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Katarzyna Kalisiak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Jacek Patryn
- Department of Plant Molecular Biology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Joanna Halibart-Puzio
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Yuji Kamiya
- RIKEN Plant Science Center, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Seth J. Davis
- Max-Planck Institute for Plant Breeding, Cologne, Germany
| | - Marta K. Koblowska
- Department of Plant Molecular Biology, Faculty of Biology, University of Warsaw, Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Andrzej Jerzmanowski
- Department of Plant Molecular Biology, Faculty of Biology, University of Warsaw, Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- * E-mail:
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41
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Jing Y, Zhang D, Wang X, Tang W, Wang W, Huai J, Xu G, Chen D, Li Y, Lin R. Arabidopsis chromatin remodeling factor PICKLE interacts with transcription factor HY5 to regulate hypocotyl cell elongation. THE PLANT CELL 2013; 25:242-56. [PMID: 23314848 PMCID: PMC3584539 DOI: 10.1105/tpc.112.105742] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Revised: 12/13/2012] [Accepted: 12/27/2012] [Indexed: 05/18/2023]
Abstract
Photomorphogenesis is a critical plant developmental process that involves light-mediated transcriptome changes, histone modifications, and inhibition of hypocotyl growth. However, the chromatin-based regulatory mechanism underlying this process remains largely unknown. Here, we identify ENHANCED PHOTOMORPHOGENIC1 (EPP1), previously known as PICKLE (PKL), an ATP-dependent chromatin remodeling factor of the chromodomain/helicase/DNA binding family, as a repressor of photomorphogenesis in Arabidopsis thaliana. We show that PKL/EPP1 expression is repressed by light in the hypocotyls in a photoreceptor-dependent manner. Furthermore, we reveal that the transcription factor ELONGATED HYPOCOTYL5 (HY5) binds to the promoters of cell elongation-related genes and recruits PKL/EPP1 through their physical interaction. PKL/EPP1 in turn negatively regulates HY5 by repressing trimethylation of histone H3 Lys 27 at the target loci, thereby regulating the expression of these genes and, thus, hypocotyl elongation. We also show that HY5 possesses transcriptional repression activity. Our study reveals a crucial role for a chromatin remodeling factor in repressing photomorphogenesis and demonstrates that transcription factor-mediated recruitment of chromatin-remodeling machinery is important for plant development in response to changing light environments.
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Affiliation(s)
- Yanjun Jing
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Dong Zhang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Wang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weijiang Tang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Wanqing Wang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junling Huai
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Gang Xu
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongqin Chen
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunliang Li
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rongcheng Lin
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- Address correspondence to
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A SWI/SNF chromatin-remodeling complex acts in noncoding RNA-mediated transcriptional silencing. Mol Cell 2012; 49:298-309. [PMID: 23246435 PMCID: PMC3560041 DOI: 10.1016/j.molcel.2012.11.011] [Citation(s) in RCA: 156] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 09/24/2012] [Accepted: 11/06/2012] [Indexed: 12/21/2022]
Abstract
RNA-mediated transcriptional silencing prevents deleterious effects of transposon activity and controls the expression of protein-coding genes. It involves long noncoding RNAs (lncRNAs). In Arabidopsis thaliana, some of those lncRNAs are produced by a specialized RNA Polymerase V (Pol V). The mechanism by which lncRNAs affect chromatin structure and mRNA production remains mostly unknown. Here we identify the SWI/SNF ATP-dependent nucleosome-remodeling complex as a component of the RNA-mediated transcriptional silencing pathway. We found that SWI3B, an essential subunit of the SWI/SNF complex, physically interacts with a lncRNA-binding protein, IDN2. SWI/SNF subunits contribute to lncRNA-mediated transcriptional silencing. Moreover, Pol V mediates stabilization of nucleosomes on silenced regions. We propose that Pol V-produced lncRNAs mediate transcriptional silencing by guiding the SWI/SNF complex and establishing positioned nucleosomes on specific genomic loci. We further propose that guiding ATP-dependent chromatin-remodeling complexes may be a more general function of lncRNAs.
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43
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Sang Y, Silva-Ortega CO, Wu S, Yamaguchi N, Wu MF, Pfluger J, Gillmor CS, Gallagher KL, Wagner D. Mutations in two non-canonical Arabidopsis SWI2/SNF2 chromatin remodeling ATPases cause embryogenesis and stem cell maintenance defects. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 72:1000-14. [PMID: 23062007 PMCID: PMC3561502 DOI: 10.1111/tpj.12009] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
SWI2/SNF2 chromatin remodeling ATPases play important roles in plant and metazoan development. Whereas metazoans generally encode one or two SWI2/SNF2 ATPase genes, Arabidopsis encodes four such chromatin regulators: the well-studied BRAHMA and SPLAYED ATPases, as well as two closely related non-canonical SWI2/SNF2 ATPases, CHR12 and CHR23. No developmental role has as yet been described for CHR12 and CHR23. Here, we show that although strong single chr12 or chr23 mutants are morphologically indistinguishable from the wild type, chr12 chr23 double mutants cause embryonic lethality. The double mutant embryos fail to initiate root and shoot meristems, and display few and aberrant cell divisions. Weak double mutant embryos give rise to viable seedlings with dramatic defects in the maintenance of both the shoot and the root stem cell populations. Paradoxically, the stem cell defects are correlated with increased expression of the stem cell markers WUSCHEL and WOX5. During subsequent development, the meristem defects are partially overcome to allow for the formation of very small, bushy adult plants. Based on the observed morphological defects, we named the two chromatin remodelers MINUSCULE 1 and 2. Possible links between minu1 minu2 defects and defects in hormone signaling and replication-coupled chromatin assembly are discussed.
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Affiliation(s)
- Yi Sang
- Department of Biology, University of Pennsylvania, 415 S. University Ave, Philadelphia, PA, 19104
| | - Claudia O. Silva-Ortega
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), CINVESTAV-IPN, Irapuato, Guanajuato, C.P 36821, MEXICO
| | - Shuang Wu
- Department of Biology, University of Pennsylvania, 415 S. University Ave, Philadelphia, PA, 19104
| | - Nobutoshi Yamaguchi
- Department of Biology, University of Pennsylvania, 415 S. University Ave, Philadelphia, PA, 19104
| | - Miin-Feng Wu
- Department of Biology, University of Pennsylvania, 415 S. University Ave, Philadelphia, PA, 19104
| | - Jennifer Pfluger
- Department of Biology, University of Pennsylvania, 415 S. University Ave, Philadelphia, PA, 19104
| | - C. Stewart Gillmor
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), CINVESTAV-IPN, Irapuato, Guanajuato, C.P 36821, MEXICO
| | - Kimberly L. Gallagher
- Department of Biology, University of Pennsylvania, 415 S. University Ave, Philadelphia, PA, 19104
- authors for correspondence: Doris Wagner, tel: 215-898-0483, fax: 215 898-8780, ; Kimberly L. Gallagher, tel: 215 746-3605, fax: 215 898-8780,
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, 415 S. University Ave, Philadelphia, PA, 19104
- authors for correspondence: Doris Wagner, tel: 215-898-0483, fax: 215 898-8780, ; Kimberly L. Gallagher, tel: 215 746-3605, fax: 215 898-8780,
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Li G, Zhang J, Li J, Yang Z, Huang H, Xu L. Imitation Switch chromatin remodeling factors and their interacting RINGLET proteins act together in controlling the plant vegetative phase in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 72:261-70. [PMID: 22694359 DOI: 10.1111/j.1365-313x.2012.05074.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
During their life cycle, flowering plants must experience a transition from vegetative to reproductive growth. Here, we report that double mutations in the Arabidopsis thaliana IMITATION SWITCH (AtISWI) genes, CHROMATIN REMODELING11 (CHR11) and CHR17, and the plant-specific DDT-domain containing genes, RINGLET1 (RLT1) and RLT2, resulted in plants with similar developmental defects, including the dramatically accelerated vegetative-to-reproductive transition. We demonstrated that AtISWI physically interacts with RLTs in preventing plants from activating the vegetative-to-reproductive transition early by regulating several key genes that contribute to flower timing. In particular, AtISWI and RLTs repress FT, SEP1, SEP3, FUL, and SOC1, but promote FLC in the leaf. Furthermore, AtISWI and RLTs may directly repress FT and SEP3 through associating with the FT and SEP3 loci. Our study reveals that AtISWI and RLTs represent a previously unrecognized genetic pathway that is required for the maintenance of the plant vegetative phase.
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Affiliation(s)
- Guang Li
- National Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
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