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Thirulogachandar V, Govind G, Hensel G, Kale SM, Kuhlmann M, Eschen-Lippold L, Rutten T, Koppolu R, Rajaraman J, Palakolanu SR, Seiler C, Sakuma S, Jayakodi M, Lee J, Kumlehn J, Komatsuda T, Schnurbusch T, Sreenivasulu N. HOMEOBOX2, the paralog of SIX-ROWED SPIKE1/HOMEOBOX1, is dispensable for barley spikelet development. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2900-2916. [PMID: 38366171 DOI: 10.1093/jxb/erae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 02/14/2024] [Indexed: 02/18/2024]
Abstract
The HD-ZIP class I transcription factor Homeobox 1 (HvHOX1), also known as Vulgare Row-type Spike 1 (VRS1) or Six-rowed Spike 1, regulates lateral spikelet fertility in barley (Hordeum vulgare L.). It was shown that HvHOX1 has a high expression only in lateral spikelets, while its paralog HvHOX2 was found to be expressed in different plant organs. Yet, the mechanistic functions of HvHOX1 and HvHOX2 during spikelet development are still fragmentary. Here, we show that compared with HvHOX1, HvHOX2 is more highly conserved across different barley genotypes and Hordeum species, hinting at a possibly vital but still unclarified biological role. Using bimolecular fluorescence complementation, DNA-binding, and transactivation assays, we validate that HvHOX1 and HvHOX2 are bona fide transcriptional activators that may potentially heterodimerize. Accordingly, both genes exhibit similar spatiotemporal expression patterns during spike development and growth, albeit their mRNA levels differ quantitatively. We show that HvHOX1 delays the lateral spikelet meristem differentiation and affects fertility by aborting the reproductive organs. Interestingly, the ancestral relationship of the two genes inferred from their co-expressed gene networks suggested that HvHOX1 and HvHOX2 might play a similar role during barley spikelet development. However, CRISPR-derived mutants of HvHOX1 and HvHOX2 demonstrated the suppressive role of HvHOX1 on lateral spikelets, while the loss of HvHOX2 does not influence spikelet development. Collectively, our study shows that through the suppression of reproductive organs, lateral spikelet fertility is regulated by HvHOX1, whereas HvHOX2 is dispensable for spikelet development in barley.
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Affiliation(s)
- Venkatasubbu Thirulogachandar
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
- Research Group Abiotic Stress Genomics, Interdisciplinary Center for Crop Plant Research (IZN), Hoher Weg 8, 06120 Halle (Saale), Germany
| | - Geetha Govind
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Götz Hensel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Sandip M Kale
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Markus Kuhlmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
- Research Group Abiotic Stress Genomics, Interdisciplinary Center for Crop Plant Research (IZN), Hoher Weg 8, 06120 Halle (Saale), Germany
| | | | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Ravi Koppolu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Jeyaraman Rajaraman
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Sudhakar Reddy Palakolanu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Christiane Seiler
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Shun Sakuma
- National Institute of Agrobiological Sciences (NIAS), Plant Genome Research Unit, Tsukuba 3058602, Japan
| | - Murukarthick Jayakodi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Justin Lee
- Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, D-06120 Halle, Germany
| | - Jochen Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Takao Komatsuda
- National Institute of Agrobiological Sciences (NIAS), Plant Genome Research Unit, Tsukuba 3058602, Japan
| | - Thorsten Schnurbusch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
- Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Nese Sreenivasulu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
- Research Group Abiotic Stress Genomics, Interdisciplinary Center for Crop Plant Research (IZN), Hoher Weg 8, 06120 Halle (Saale), Germany
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Manrique S, Cavalleri A, Guazzotti A, Villarino GH, Simonini S, Bombarely A, Higashiyama T, Grossniklaus U, Mizzotti C, Pereira AM, Coimbra S, Sankaranarayanan S, Onelli E, Masiero S, Franks RG, Colombo L. HISTONE DEACETYLASE19 Controls Ovule Number Determination and Transmitting Tract Differentiation. PLANT PHYSIOLOGY 2024; 194:2117-2135. [PMID: 38060625 PMCID: PMC10980524 DOI: 10.1093/plphys/kiad629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/29/2023] [Indexed: 04/01/2024]
Abstract
The gynoecium is critical for the reproduction of flowering plants as it contains the ovules and the tissues that foster pollen germination, growth, and guidance. These tissues, known as the reproductive tract (ReT), comprise the stigma, style, and transmitting tract (TT). The ReT and ovules originate from the carpel margin meristem (CMM) within the pistil. SHOOT MERISTEMLESS (STM) is a key transcription factor for meristem formation and maintenance. In all above-ground meristems, including the CMM, local STM downregulation is required for organ formation. However, how this downregulation is achieved in the CMM is unknown. Here, we have studied the role of HISTONE DEACETYLASE 19 (HDA19) in Arabidopsis (Arabidopsis thaliana) during ovule and ReT differentiation based on the observation that the hda19-3 mutant displays a reduced ovule number and fails to differentiate the TT properly. Fluorescence-activated cell sorting coupled with RNA-sequencing revealed that in the CMM of hda19-3 mutants, genes promoting organ development are downregulated while meristematic markers, including STM, are upregulated. HDA19 was essential to downregulate STM in the CMM, thereby allowing ovule formation and TT differentiation. STM is ectopically expressed in hda19-3 at intermediate stages of pistil development, and its downregulation by RNA interference alleviated the hda19-3 phenotype. Chromatin immunoprecipitation assays indicated that STM is a direct target of HDA19 during pistil development and that the transcription factor SEEDSTICK is also required to regulate STM via histone acetylation. Thus, we identified factors required for the downregulation of STM in the CMM, which is necessary for organogenesis and tissue differentiation.
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Affiliation(s)
- Silvia Manrique
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Giovanni Celoria 26, Milan 20133, Italy
| | - Alex Cavalleri
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Giovanni Celoria 26, Milan 20133, Italy
| | - Andrea Guazzotti
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Giovanni Celoria 26, Milan 20133, Italy
| | - Gonzalo H Villarino
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27606, USA
| | - Sara Simonini
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, Zurich CH-8008, Switzerland
| | - Aureliano Bombarely
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Giovanni Celoria 26, Milan 20133, Italy
| | - Tetsuya Higashiyama
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, Zurich CH-8008, Switzerland
| | - Chiara Mizzotti
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Giovanni Celoria 26, Milan 20133, Italy
| | - Ana Marta Pereira
- Faculdade de Ciências da Universidade do Porto, Departamento de Biologia, Universidade do Porto, rua do Campo Alegre, Porto 4169-007, Portugal
- LAQV Requimte, Sustainable Chemistry, Universidade do Porto, Porto 4169-007, Portugal
| | - Silvia Coimbra
- Faculdade de Ciências da Universidade do Porto, Departamento de Biologia, Universidade do Porto, rua do Campo Alegre, Porto 4169-007, Portugal
- LAQV Requimte, Sustainable Chemistry, Universidade do Porto, Porto 4169-007, Portugal
| | - Subramanian Sankaranarayanan
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
| | - Elisabetta Onelli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Giovanni Celoria 26, Milan 20133, Italy
| | - Simona Masiero
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Giovanni Celoria 26, Milan 20133, Italy
| | - Robert G Franks
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27606, USA
| | - Lucia Colombo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Giovanni Celoria 26, Milan 20133, Italy
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Chiteri KO, Rairdin A, Sandhu K, Redsun S, Farmer A, O'Rourke JA, Cannon SB, Singh A. Combining GWAS and comparative genomics to fine map candidate genes for days to flowering in mung bean. BMC Genomics 2024; 25:270. [PMID: 38475739 DOI: 10.1186/s12864-024-10156-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND Mung bean (Vigna radiata (L.) Wilczek), is an important pulse crop in the global south. Early flowering and maturation are advantageous traits for adaptation to northern and southern latitudes. This study investigates the genetic basis of the Days-to-Flowering trait (DTF) in mung bean, combining genome-wide association studies (GWAS) in mung bean and comparisons with orthologous genes involved with control of DTF responses in soybean (Glycine max (L) Merr) and Arabidopsis (Arabidopsis thaliana). RESULTS The most significant associations for DTF were on mung bean chromosomes 1, 2, and 4. Only the SNPs on chromosomes 1 and 4 were heavily investigated using downstream analysis. The chromosome 1 DTF association is tightly linked with a cluster of locally duplicated FERONIA (FER) receptor-like protein kinase genes, and the SNP occurs within one of the FERONIA genes. In Arabidopsis, an orthologous FERONIA gene (AT3G51550), has been reported to regulate the expression of the FLOWERING LOCUS C (FLC). For the chromosome 4 DTF locus, the strongest candidates are Vradi04g00002773 and Vradi04g00002778, orthologous to the Arabidopsis PhyA and PIF3 genes, encoding phytochrome A (a photoreceptor protein sensitive to red to far-red light) and phytochrome-interacting factor 3, respectively. The soybean PhyA orthologs include the classical loci E3 and E4 (genes GmPhyA3, Glyma.19G224200, and GmPhyA2, Glyma.20G090000). The mung bean PhyA ortholog has been previously reported as a candidate for DTF in studies conducted in South Korea. CONCLUSION The top two identified SNPs accounted for a significant proportion (~ 65%) of the phenotypic variability in mung bean DTF by the six significant SNPs (39.61%), with a broad-sense heritability of 0.93. The strong associations of DTF with genes that have orthologs with analogous functions in soybean and Arabidopsis provide strong circumstantial evidence that these genes are causal for this trait. The three reported loci and candidate genes provide useful targets for marker-assisted breeding in mung beans.
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Affiliation(s)
- Kevin O Chiteri
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Ashlyn Rairdin
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | | | - Sven Redsun
- National Center for Genome Resources, Santa Fe, NM, 87505, United States
| | - Andrew Farmer
- National Center for Genome Resources, Santa Fe, NM, 87505, United States
| | - Jamie A O'Rourke
- Department of Agronomy, Iowa State University, Ames, IA, United States
- USDA - Agricultural Research Service, Corn Insects, and Crop Genetics Research Unit, Ames, IA, United States
| | - Steven B Cannon
- Department of Agronomy, Iowa State University, Ames, IA, United States.
- USDA - Agricultural Research Service, Corn Insects, and Crop Genetics Research Unit, Ames, IA, United States.
| | - Arti Singh
- Department of Agronomy, Iowa State University, Ames, IA, United States.
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Jia P, Wang Y, Sharif R, Dong QL, Liu Y, Luan HA, Zhang XM, Guo SP, Qi GH. KNOTTED1-like homeobox (KNOX) transcription factors - Hubs in a plethora of networks: A review. Int J Biol Macromol 2023; 253:126878. [PMID: 37703987 DOI: 10.1016/j.ijbiomac.2023.126878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/09/2023] [Accepted: 09/10/2023] [Indexed: 09/15/2023]
Abstract
KNOX (KNOTTED1-like HOMEOBOX) belongs to a class of important homeobox genes, which encode the homeodomain proteins binding to the specific element of target genes, and widely participate in plant development. Advancements in genetics and molecular biology research generate a large amount of information about KNOX genes in model and non-model plants, and their functions in different developmental backgrounds are gradually becoming clear. In this review, we summarize the known and presumed functions of the KNOX gene in plants, focusing on horticultural plants and crops. The classification and structural characteristics, expression characteristics and regulation, interacting protein factors, functions, and mechanisms of KNOX genes are systematically described. Further, the current research gaps and perspectives were discussed. These comprehensive data can provide a reference for the directional improvement of agronomic traits through KNOX gene regulation.
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Affiliation(s)
- Peng Jia
- College of Forestry, Hebei Agricultural University, Baoding 071000, China.
| | - Yuan Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071000, China
| | - Rahat Sharif
- Department of Horticulture, School of Horticulture and Landscape, Yangzhou University, Yangzhou 225009, China
| | - Qing-Long Dong
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
| | - Yang Liu
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
| | - Hao-An Luan
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
| | - Xue-Mei Zhang
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
| | - Sup-Ping Guo
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
| | - Guo-Hui Qi
- College of Forestry, Hebei Agricultural University, Baoding 071000, China.
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5
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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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Fu W, Yu Y, Shu J, Yu Z, Zhong Y, Zhu T, Zhang Z, Liang Z, Cui Y, Chen C, Li C. Organization, genomic targeting, and assembly of three distinct SWI/SNF chromatin remodeling complexes in Arabidopsis. THE PLANT CELL 2023; 35:2464-2483. [PMID: 37062961 PMCID: PMC10291025 DOI: 10.1093/plcell/koad111] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/21/2023] [Accepted: 03/26/2023] [Indexed: 06/19/2023]
Abstract
Switch defective/sucrose nonfermentable (SWI/SNF) complexes are evolutionarily conserved multisubunit machines that play vital roles in chromatin architecture regulation for modulating gene expression via sliding or ejection of nucleosomes in eukaryotes. In plants, perturbations of SWI/SNF subunits often result in severe developmental disorders. However, the subunit composition, pathways of assembly, and genomic targeting of the plant SWI/SNF complexes are poorly understood. Here, we report the organization, genomic targeting, and assembly of 3 distinct SWI/SNF complexes in Arabidopsis thaliana: BRAHMA-Associated SWI/SNF complexes (BAS), SPLAYED-Associated SWI/SNF complexes (SAS), and MINUSCULE-Associated SWI/SNF complexes (MAS). We show that BAS complexes are equivalent to human ncBAF, whereas SAS and MAS complexes evolve in multiple subunits unique to plants, suggesting plant-specific functional evolution of SWI/SNF complexes. We further show overlapping and specific genomic targeting of the 3 plant SWI/SNF complexes on chromatin and reveal that SAS complexes are necessary for the correct genomic localization of the BAS complexes. Finally, we define the role of the core module subunit in the assembly of plant SWI/SNF complexes and highlight that ATPase module subunit is required for global complex stability and the interaction of core module subunits in Arabidopsis SAS and BAS complexes. Together, our work highlights the divergence of SWI/SNF chromatin remodelers during eukaryote evolution and provides a comprehensive landscape for understanding plant SWI/SNF complex organization, assembly, genomic targeting, and function.
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Affiliation(s)
- Wei Fu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yaoguang Yu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jie Shu
- 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, Guangdong 510650, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zewang Yu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yixiong Zhong
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Tao Zhu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhihao Zhang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhenwei Liang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuhai Cui
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada N5V 4T3
| | - Chen Chen
- 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, Guangdong 510650, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Chenlong Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
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Wang P, Wu T, Jiang C, Huang B, Li Z. Brt9SIDA/IDALs as peptide signals mediate diverse biological pathways in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 330:111642. [PMID: 36804389 DOI: 10.1016/j.plantsci.2023.111642] [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: 11/04/2022] [Revised: 01/28/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
As signal molecules, plant peptides play key roles in intercellular communication during growth and development, as well as stress responses. The 14-amino-acid (aa) INFLORESCENCE DEFICIENT IN ABSCISSION (IDA) peptide was originally identified to play an essential role in the floral organ abscission of Arabidopsis. It is synthesized from its precursor, a small protein containing 77-aa residues with an N-terminal signal peptide sequence. Recently, the IDA/IDA-like (IDLs) genes are isolated in several angiosperms and are highly conserved in land plants. In addition, IDA/IDLs are not only involved in organ abscission but also function in multiple biological processes, including biotic and abiotic stress responses. Here, we summarize the post-translational modification and proteolytic processing, the evolutionary conservation, and the potential regulatory function of IDA/IDLs, and also present future perspectives to investigate the IDA/IDLs signaling pathway. We anticipate that this detailed knowledge will help to improve the understanding of the molecular mechanism of plant peptide signaling.
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Affiliation(s)
- Pingyu Wang
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China.
| | - Ting Wu
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China.
| | - Chen Jiang
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China.
| | - Baowen Huang
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China.
| | - Zhengguo Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China.
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Prunus Knotted-like Genes: Genome-Wide Analysis, Transcriptional Response to Cytokinin in Micropropagation, and Rootstock Transformation. Int J Mol Sci 2023; 24:ijms24033046. [PMID: 36769369 PMCID: PMC9918302 DOI: 10.3390/ijms24033046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
Knotted1-like homeobox (KNOX) transcription factors are involved in plant development, playing complex roles in aerial organs. As Prunus species include important fruit tree crops of Italy, an exhaustive investigation of KNOX genes was performed using genomic and RNA-seq meta-analyses. Micropropagation is an essential technology for rootstock multiplication; hence, we investigated KNOX transcriptional behavior upon increasing 6-benzylaminopurine (BA) doses and the effects on GF677 propagules. Moreover, gene function in Prunus spp. was assessed by Gisela 6 rootstock transformation using fluorescence and peach KNOX transgenes. Based on ten Prunus spp., KNOX proteins fit into I-II-M classes named after Arabidopsis. Gene number, class member distribution, and chromosome positions were maintained, and exceptions supported the diversification of Prunus from Cerasus subgenera, and that of Armeniaca from the other sections within Prunus. Cytokinin (CK) cis-elements occurred in peach and almond KNOX promoters, suggesting a BA regulatory role in GF677 shoot multiplication as confirmed by KNOX expression variation dependent on dose, time, and interaction. The tripled BA concentration exacerbated stress, altered CK perception genes, and modified KNOX transcriptions, which are proposed to concur in in vitro anomalies. Finally, Gisela 6 transformation efficiency varied (2.6-0.6%) with the genetic construct, with 35S:GFP being more stable than 35S:KNOPE1 lines, which showed leaf modification typical of KNOX overexpression.
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9
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BREVIPEDICELLUS Positively Regulates Salt-Stress Tolerance in Arabidopsis thaliana. Int J Mol Sci 2023; 24:ijms24021054. [PMID: 36674568 PMCID: PMC9866879 DOI: 10.3390/ijms24021054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/15/2022] [Accepted: 12/31/2022] [Indexed: 01/06/2023] Open
Abstract
Salt stress is one of the major environmental threats to plant growth and development. However, the mechanisms of plants responding to salt stress are not fully understood. Through genetic screening, we identified and characterized a salt-sensitive mutant, ses5 (sensitive to salt 5), in Arabidopsis thaliana. Positional cloning revealed that the decreased salt-tolerance of ses5 was caused by a mutation in the transcription factor BP (BREVIPEDICELLUS). BP regulates various developmental processes in plants. However, the biological function of BP in abiotic stress-signaling and tolerance are still not clear. Compared with wild-type plants, the bp mutant exhibited a much shorter primary-root and lower survival rate under salt treatment, while the BP overexpressors were more tolerant. Further analysis showed that BP could directly bind to the promoter of XTH7 (xyloglucan endotransglucosylase/hydrolase 7) and activate its expression. Resembling the bp mutant, the disruption of XTH7 gave rise to salt sensitivity. These results uncovered novel roles of BP in positively modulating salt-stress tolerance, and illustrated a putative working mechanism.
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Gastaldi V, Alem AL, Mansilla N, Ariel FD, Viola IL, Lucero LE, Gonzalez DH. BREVIPEDICELLUS/KNAT1 targets TCP15 to modulate filament elongation during Arabidopsis late stamen development. PLANT PHYSIOLOGY 2023; 191:29-34. [PMID: 36303324 PMCID: PMC9806550 DOI: 10.1093/plphys/kiac502] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/04/2022] [Indexed: 06/01/2023]
Abstract
The Arabidopsis homeodomain protein BREVIPEDICELLUS/KNAT1 represses the expression of the gene encoding the transcription factor TCP15 to limit filament growth at late stages of stamen development.
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Affiliation(s)
- Victoria Gastaldi
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Antonela L Alem
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Natanael Mansilla
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Federico D Ariel
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Ivana L Viola
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Leandro E Lucero
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Daniel H Gonzalez
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
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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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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: 16] [Impact Index Per Article: 8.0] [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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Crick J, Corrigan L, Belcram K, Khan M, Dawson JW, Adroher B, Li S, Hepworth SR, Pautot V. Floral organ abscission in Arabidopsis requires the combined activities of three TALE homeodomain transcription factors. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6150-6169. [PMID: 35689803 DOI: 10.1093/jxb/erac255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Floral organ abscission is a separation process in which sepals, petals, and stamens detach from the plant at abscission zones. Here, we investigated the collective role of three amino-acid-loop-extension (TALE) homeobox genes ARABIDOPSIS THALIANA HOMEOBOX GENE1 (ATH1), KNAT6 (for KNOTTED LIKE from Arabidopsis thaliana) and KNAT2, which form a module that patterns boundaries under the regulation of BLADE-ON-PETIOLE 1 and 2 (BOP1/2) co-activators. These TALE homeodomain transcription factors were shown to maintain boundaries in the flower, functioning as a unit to coordinate the growth, patterning, and activity of abscission zones. Together with BOP1 and BOP2, ATH1 and its partners KNAT6 and KNAT2 collectively contribute to the differentiation of lignified and separation layers of the abscission zone. The genetic interactions of BOP1/2 and ATH1 with INFLORESCENCE DEFICIENT IN ABSCISSION (IDA) were also explored. We showed that BOP1/2 co-activators and ATH1 converge with the IDA signalling pathway to promote KNAT6 and KNAT2 expression in the abscission zone and cell separation. ATH1 acts as a central regulator in floral organ abscission as it controls the expression of other TALE genes in abscission zone cells.
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Affiliation(s)
- Jennifer Crick
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Laura Corrigan
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Katia Belcram
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Madiha Khan
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Jeff W Dawson
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Bernard Adroher
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Sibei Li
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | | | - Véronique Pautot
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
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Zhang X, Jiang J, Yang Y, Ma Z, Meng L, Cui G, Yin X. Identification and responding to exogenous hormone of HB-KNOX family based on transcriptome data of Caucasian clover. Gene 2022; 828:146469. [PMID: 35413395 DOI: 10.1016/j.gene.2022.146469] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 02/12/2022] [Accepted: 03/31/2022] [Indexed: 11/17/2022]
Abstract
Caucasian clover (Trifolium ambiguum M. Bieb.) is a strongly rhizomatous, low-crowned perennial leguminous and ground-covering grass. The species is resistant to cold, arid temperatures and grazing due to a well-developed underground rhizome system and a strong clonal reproduction capacity. KNOTTED1-LIKE HOMEOBOX (KNOX) genes are a family of plant-specific homeobox transcription factors with important roles in plant development. Preliminary transcriptome analysis enabled us to understand the gene expression in five different tissues, which helped us to screen the predetermined genes of the HB-KNOX family genes for the rhizome growth and development of Caucasian clover. The study identified 41 TaKNOX genes from the Caucasian clover transcriptome database. Gene length, MW and pl of TaKNOX family transcription factors varied, but the gene structure and motifs were relatively conserved in bioinformatics analysis. Phylogenetic analyses of Arabidopsis thaliana, soybean, Medicago truncatula and Caucasian clover were performed to study the evolutionary and functional relationships in various species. Prediction and verification of the subcellular localizations revealed the diverse subcellular localization of these 41 TaKNOX proteins. The expression profile of exogenous hormones showed that the TaKNOX gene showed multiple expression regulation patterns, and was involved in 6-BA, IAA and KT signaling pathways. Our results reveal the characteristics of the TaKNOX gene family, thus laying a foundation for further functional analysis of the KNOX family in Caucasian clover.
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Affiliation(s)
- Xiaomeng Zhang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Jingwen Jiang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Yupeng Yang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Zewang Ma
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Lingdong Meng
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Guowen Cui
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China.
| | - Xiujie Yin
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China.
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Forgione I, Muto A, Woloszynska M, Chiappetta AA, Ferrari M, Van Lijsebettens M, Bitonti MB, Bruno L. Epigenetic mechanisms affect the curled leaf phenotype in the hypomethylated ddc mutant of Arabidopsis thaliana. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 319:111254. [PMID: 35487663 DOI: 10.1016/j.plantsci.2022.111254] [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: 09/21/2021] [Revised: 02/02/2022] [Accepted: 03/12/2022] [Indexed: 06/14/2023]
Abstract
The ddc mutant of Arabidopsis thaliana is characterized by pleiotropic phenotypic alterations including a curl-shaped leaf, previously explained by disturbed auxin metabolism and transport. The present study was aimed at further explore the molecular bases underlying the abnormal phenotype of the ddc leaf. We demonstrated that genes specifically related to leaf fate commitment and morphogenesis were misexpressed on developing ddc leaves, such as upregulation of CURLY LEAF (CLF) and downregulation of ASYMMETRIC LEAVES2 (AS2), KNOTTED-like gene from A. thaliana (KNAT6), TEOSINTE-LIKE1 CYCLOIDEA and PROLIFERATING CELL FACTOR 2 (TCP2) and others. The CLF gene, encoding a component of Polycomb repressive complex 2 (PRC2) which adds trimethylation marks at Lys27 of histone H3, was overexpressed in the ddc mutant and concomitantly was correlated with DNA methylation-dependent repression of its negative regulator UCL1. KNAT6, encoding a class 1 KNOX homeotic gene, had increased H3K27me3 trimethylation levels, suggesting it is a target gene of the CLF containing PRC2 complex in the ddc mutant. We postulate that different epigenetic mechanisms modulate expression of genes related to auxin pathways as well as gene targets of Polycomb repressive action, during leaf morphogenesis.
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Affiliation(s)
- Ivano Forgione
- Department of Biology, Ecology and Earth Science, University of Calabria, Ponte P. Bucci, Arcavacata di Rende, 87036 Cosenza, Italy; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center Plant Systems Biology, VIB, 9052 Ghent, Belgium.
| | - Antonella Muto
- Department of Biology, Ecology and Earth Science, University of Calabria, Ponte P. Bucci, Arcavacata di Rende, 87036 Cosenza, Italy.
| | - Magdalena Woloszynska
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center Plant Systems Biology, VIB, 9052 Ghent, Belgium; Department of Genetics, Faculty of Biology and Animal Sciences, Wroclaw University of Environmental and Life Sciences, ul. Kozuchowska 7, 51-631 Wroclaw, Poland.
| | - Adriana Ada Chiappetta
- Department of Biology, Ecology and Earth Science, University of Calabria, Ponte P. Bucci, Arcavacata di Rende, 87036 Cosenza, Italy.
| | - Michele Ferrari
- Department of Biology, Ecology and Earth Science, University of Calabria, Ponte P. Bucci, Arcavacata di Rende, 87036 Cosenza, Italy.
| | - Mieke Van Lijsebettens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center Plant Systems Biology, VIB, 9052 Ghent, Belgium.
| | - Maria Beatrice Bitonti
- Department of Biology, Ecology and Earth Science, University of Calabria, Ponte P. Bucci, Arcavacata di Rende, 87036 Cosenza, Italy.
| | - Leonardo Bruno
- Department of Biology, Ecology and Earth Science, University of Calabria, Ponte P. Bucci, Arcavacata di Rende, 87036 Cosenza, Italy.
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The Roles of BLH Transcription Factors in Plant Development and Environmental Response. Int J Mol Sci 2022; 23:ijms23073731. [PMID: 35409091 PMCID: PMC8998993 DOI: 10.3390/ijms23073731] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/16/2022] [Accepted: 03/22/2022] [Indexed: 02/04/2023] Open
Abstract
Despite recent advancements in plant molecular biology and biotechnology, providing enough, and safe, food for an increasing world population remains a challenge. The research into plant development and environmental adaptability has attracted more and more attention from various countries. The transcription of some genes, regulated by transcript factors (TFs), and their response to biological and abiotic stresses, are activated or inhibited during plant development; examples include, rooting, flowering, fruit ripening, drought, flooding, high temperature, pathogen infection, etc. Therefore, the screening and characterization of transcription factors have increasingly become a hot topic in the field of plant research. BLH/BELL (BEL1-like homeodomain) transcription factors belong to a subfamily of the TALE (three-amino-acid-loop-extension) superfamily and its members are involved in the regulation of many vital biological processes, during plant development and environmental response. This review focuses on the advances in our understanding of the function of BLH/BELL TFs in different plants and their involvement in the development of meristems, flower, fruit, plant morphogenesis, plant cell wall structure, the response to the environment, including light and plant resistance to stress, biosynthesis and signaling of ABA (Abscisic acid), IAA (Indoleacetic acid), GA (Gibberellic Acid) and JA (Jasmonic Acid). We discuss the theoretical basis and potential regulatory models for BLH/BELL TFs’ action and provide a comprehensive view of their multiple roles in modulating different aspects of plant development and response to environmental stress and phytohormones. We also present the value of BLHs in the molecular breeding of improved crop varieties and the future research direction of the BLH gene family.
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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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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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19
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Genome wide identification of StKNOX gene family and characterization of their expression in Solanum tuberosum. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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20
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Yue Z, Ma R, Cheng D, Yan X, He Y, Wang C, Pan X, Yin L, Zhang X, Wei C. Candidate gene analysis of watermelon stripe pattern locus ClSP ongoing recombination suppression. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3263-3277. [PMID: 34185107 DOI: 10.1007/s00122-021-03891-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 06/10/2021] [Indexed: 05/15/2023]
Abstract
Using two segregating population, watermelon stripe pattern underlying gene ClSP was delimited to a 611.78 Kb region, consisting of four discrete haploblocks and ongoing recombination suppression. Stripe pattern is an important commodity trait in watermelon, displaying diverse types. In this study, two segregating populations were generated for genetic mapping the single dominant locus ClSP, which was finally delimited to a 611.78 Kb interval with suppression of recombination. According to polymorphism sites detected among genotypes, four discrete haploblocks were characterized in this target region. Based on reference genomes, 81 predicted genes were annotated in the ClSP interval, including seven transcription factors namely as candidate No1-No7. Meanwhile, the ortholog gene of cucumber ist responsible for the irregular stripes was considered as candidate No8. Strikingly, gene structures of No1-No5 completely varied from their reference descriptions and subsequently re-annotated. For instance, the original adjacent distribution candidates No2 and No3 were re-annotated as No2_3, while No4 and No5 were integrated as No4_5. Sequence analysis demonstrated the third polymorphism in CDS of re-annotated No4_5 resulting in truncated proteins in non-stripe plants. Furthermore, only No4_5 was down-regulated in light green stripes relative to dark green stripes. Transcriptome analysis identified 356 DEGs between dark green striped and light green striped peels, with genes involved in photosynthesis and chloroplast development down-regulated in light green stripes but calcium ion binding related genes up-regulated. Additionally, 38 DEGs were annotated as transcription factors, with the majority up-regulated in light green stripes, such as ERFs and WRKYs. This study not only contributes to a better understanding of the molecular mechanisms underlying watermelon stripe development, but also provides new insights into the genomic structure of ClSP locus and valuable candidates.
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Affiliation(s)
- Zhen Yue
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A and F University, Yangling, 712100, Shaanxi, China
| | - Rongxue Ma
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A and F University, Yangling, 712100, Shaanxi, China
| | - Denghu Cheng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A and F University, Yangling, 712100, Shaanxi, China
| | - Xing Yan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A and F University, Yangling, 712100, Shaanxi, China
| | - Yaping He
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A and F University, Yangling, 712100, Shaanxi, China
| | - Chunxia Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A and F University, Yangling, 712100, Shaanxi, China
| | - Xiaona Pan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A and F University, Yangling, 712100, Shaanxi, China
| | - Lijuan Yin
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A and F University, Yangling, 712100, Shaanxi, China
| | - Xian Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A and F University, Yangling, 712100, Shaanxi, China
| | - Chunhua Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A and F University, Yangling, 712100, Shaanxi, China.
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21
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Li X, Shen F, Xu X, Zheng Q, Wang Y, Wu T, Li W, Qiu C, Xu X, Han Z, Zhang X. An HD-ZIP transcription factor, MxHB13, integrates auxin-regulated and juvenility-determined control of adventitious rooting in Malus xiaojinensis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1663-1680. [PMID: 34218490 DOI: 10.1111/tpj.15406] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 06/23/2021] [Indexed: 06/13/2023]
Abstract
Adventitious root (AR) formation is a critical factor in the vegetative propagation of forestry and horticultural plants. Competence for AR formation declines in many species during the miR156/SPL-mediated vegetative phase change. Auxin also plays a regulatory role in AR formation. In apple rootstock, both high miR156 expression and exogenous auxin application are prerequisites for AR formation. However, the mechanism by which the miR156/SPL module interacts with auxin in controlling AR formation is unclear. In this paper, leafy cuttings of juvenile (Mx-J) and adult (Mx-A) phase Malus xiaojinensis were used in an RNA-sequencing experiment. The results revealed that numerous genes involved in phytohormone signaling, carbohydrate metabolism, cell dedifferentiation, and reactivation were downregulated in Mx-A cuttings in response to indole butyric acid treatment. Among the differentially expressed genes, an HD-ZIP transcription factor gene, MxHB13, was found to be under negative regulation of MdSPL26 by directly binding to MxHB13 promoter. MxTIFY9 interacts with MxSPL26 and may play a role in co-repressing the expression of MxHB13. The expression of MxTIFY9 was induced by exogenous indole butyric acid. MxHB13 binds to the promoter of MxABCB19-2 and positively affects the expression. A model is proposed in which MxHB13 links juvenility-limited and auxin-limited AR recalcitrance mechanisms in Mx-A.
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Affiliation(s)
- Xu Li
- College of Horticulture, China Agricultural University, Beijing, China
| | - Fei Shen
- College of Horticulture, China Agricultural University, Beijing, China
| | - Xiaozhao Xu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Qingbo Zheng
- College of Horticulture, China Agricultural University, Beijing, China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Wei Li
- College of Horticulture, China Agricultural University, Beijing, China
| | - Changpeng Qiu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Xuefeng Xu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing, China
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing, China
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22
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Challa KR, Rath M, Sharma AN, Bajpai AK, Davuluri S, Acharya KK, Nath U. Active suppression of leaflet emergence as a mechanism of simple leaf development. NATURE PLANTS 2021; 7:1264-1275. [PMID: 34312497 DOI: 10.1038/s41477-021-00965-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 06/14/2021] [Indexed: 05/21/2023]
Abstract
Angiosperm leaves show extensive shape diversity and are broadly divided into two forms; simple leaves with intact lamina and compound leaves with lamina dissected into leaflets. The mechanistic basis of margin dissection and leaflet initiation has been inferred primarily by analysing compound-leaf architecture, and thus whether the intact lamina of simple leaves has the potential to initiate leaflets upon endogenous gene inactivation remains unclear. Here, we show that the CINCINNATA-like TEOSINTE BRANCHED1, CYCLOIDEA, PROLIFERATING CELL FACTORS (CIN-TCP) transcription factors activate the class II KNOTTED1-LIKE (KNOX-II) genes and the CIN-TCP and KNOX-II proteins together redundantly suppress leaflet initiation in simple leaves. Simultaneous downregulation of CIN-TCP and KNOX-II in Arabidopsis leads to the reactivation of the stemness genes KNOX-I and CUPSHAPED COTYLEDON (CUC) and triggers ectopic organogenesis, eventually converting the simple lamina to a super-compound form that appears to initiate leaflets indefinitely. Thus, a conserved developmental mechanism promotes simple leaf architecture in which CIN-TCP-KNOX-II forms a strong differentiation module that suppresses the KNOX-I-CUC network and leaflet initiation.
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Affiliation(s)
- Krishna Reddy Challa
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Monalisha Rath
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Anurag N Sharma
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | | | | | | | - Utpal Nath
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India.
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23
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Yu Y, Fu W, Xu J, Lei Y, Song X, Liang Z, Zhu T, Liang Y, Hao Y, Yuan L, Li C. Bromodomain-containing proteins BRD1, BRD2, and BRD13 are core subunits of SWI/SNF complexes and vital for their genomic targeting in Arabidopsis. MOLECULAR PLANT 2021; 14:888-904. [PMID: 33771698 DOI: 10.1016/j.molp.2021.03.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/08/2021] [Accepted: 03/19/2021] [Indexed: 05/26/2023]
Abstract
Switch defective/sucrose non-fermentable (SWI/SNF) chromatin remodeling complexes are multi-subunit machines that play vital roles in the regulation of chromatin structure and gene expression. However, the mechanisms by which SWI/SNF complexes recognize their target loci in plants are not fully understood. Here, we show that the Arabidopsis thaliana bromodomain-containing proteins BRD1, BRD2, and BRD13 are core subunits of SWI/SNF complexes and critical for SWI/SNF genomic targeting. These three BRDs interact directly with multiple SWI/SNF subunits, including the BRAHMA (BRM) catalytic subunit. Phenotypic and transcriptomic analyses of the brd1 brd2 brd13 triple mutant revealed that these BRDs act largely redundantly to control gene expression and developmental processes that are also regulated by BRM. Genome-wide occupancy profiling demonstrated that these three BRDs extensively colocalize with BRM on chromatin. Simultaneous loss of function of three BRD genes results in reduced BRM protein levels and decreased occupancy of BRM on chromatin across the genome. Furthermore, we demonstrated that the bromodomains of BRDs are essential for genomic targeting of the BRD subunits of SWI/SNF complexes to their target sites. Collectively, these results demonstrate that BRD1, BRD2, and BRD13 are core subunits of SWI/SNF complexes and reveal their biological roles in facilitating genomic targeting of BRM-containing SWI/SNF complexes in plants.
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Affiliation(s)
- Yaoguang Yu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Wei Fu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Jianqu Xu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Yawen Lei
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Xin Song
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Zhenwei Liang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Tao Zhu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Yuhui Liang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Yuanhao Hao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Liangbing Yuan
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Chenlong Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.
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24
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Reeger JE, Wheatley M, Yang Y, Brown KM. Targeted mutation of transcription factor genes alters metaxylem vessel size and number in rice roots. PLANT DIRECT 2021; 5:e00328. [PMID: 34142002 PMCID: PMC8204146 DOI: 10.1002/pld3.328] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 06/12/2023]
Abstract
Root metaxylem vessels are responsible for axial water transport and contribute to hydraulic architecture. Variation in metaxylem vessel size and number can impact drought tolerance in crop plants, including rice, a crop that is particularly sensitive to drought. Identifying and validating candidate genes for metaxylem development would aid breeding efforts for improved varieties for drought tolerance. We identified three transcription factor candidate genes that potentially regulate metaxylem vessel size and number in rice based on orthologous annotations, published expression data, and available root and drought-related QTL data. Single gene knockout mutants were generated for each candidate using CRISPR-Cas9 genome editing. Root metaxylem vessel area and number were analyzed in 6-week-old knockout mutants and wild-type plants under well-watered and drought conditions in the greenhouse. Compared with wild type, LONESOME HIGHWAY (OsLHW) mutants had fewer, smaller metaxylem vessels in shallow roots and more, larger vessels in deep roots in drought conditions, indicating that OsLHW may be a repressor of drought-induced metaxylem plasticity. The AUXIN RESPONSE FACTOR 15 mutants showed fewer but larger metaxylem vessel area in well-watered conditions, but phenotypes were inconsistent under drought treatment. ORYZA SATIVA HOMEBOX 6 (OSH6) mutants had fewer, smaller metaxylem vessels in well-watered conditions with greater effects on xylem number than size. OSH6 mutants had larger shoots and more, deeper roots than the wild type in well-watered conditions, but there were no differences in performance under drought between mutants and wild type. Though these candidate gene mutants did not exhibit large phenotypic effects, the identification and investigation of candidate genes related to metaxylem traits in rice deepen our understanding of metaxylem development and are needed to facilitate incorporation of favorable alleles into breeding populations to improve drought stress tolerance.
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Affiliation(s)
- Jenna E. Reeger
- Intercollege Graduate Degree Program in Plant BiologyHuck Institutes of the Life SciencesPenn State UniversityUniversity ParkPAUSA
| | - Matthew Wheatley
- Department of Plant Pathology and Environmental MicrobiologyHuck Institute of the Life SciencesThe Pennsylvania State UniversityUniversity ParkPAUSA
| | - Yinong Yang
- Department of Plant Pathology and Environmental MicrobiologyHuck Institute of the Life SciencesThe Pennsylvania State UniversityUniversity ParkPAUSA
| | - Kathleen M. Brown
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPAUSA
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25
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Song ZT, Liu JX, Han JJ. Chromatin remodeling factors regulate environmental stress responses in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:438-450. [PMID: 33421288 DOI: 10.1111/jipb.13064] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 12/23/2020] [Indexed: 05/14/2023]
Abstract
Environmental stress from climate change and agricultural activity threatens global plant biodiversity as well as crop yield and quality. As sessile organisms, plants must maintain the integrity of their genomes and adjust gene expression to adapt to various environmental changes. In eukaryotes, nucleosomes are the basic unit of chromatin around which genomic DNA is packaged by condensation. To enable dynamic access to packaged DNA, eukaryotes have evolved Snf2 (sucrose nonfermenting 2) family proteins as chromatin remodeling factors (CHRs) that modulate the position of nucleosomes on chromatin. During plant stress responses, CHRs are recruited to specific genomic loci, where they regulate the distribution or composition of nucleosomes, which in turn alters the accessibility of these loci to general transcription or DNA damage repair machinery. Moreover, CHRs interplay with other epigenetic mechanisms, including DNA methylation, histone modifications, and deposition of histone variants. CHRs are also involved in RNA processing at the post-transcriptional level. In this review, we discuss major advances in our understanding of the mechanisms by which CHRs function during plants' response to environmental stress.
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Affiliation(s)
- Ze-Ting Song
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, 650500, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
| | - Jian-Xiang Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
| | - Jia-Jia Han
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, 650500, China
- Laboratory of Ecology and Evolutionary Biology, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650500, China
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26
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Cai H, Chai M, Chen F, Huang Y, Zhang M, He Q, Liu L, Yan M, Qin Y. HBI1 acts downstream of ERECTA and SWR1 in regulating inflorescence architecture through the activation of the brassinosteroid and auxin signaling pathways. THE NEW PHYTOLOGIST 2021; 229:414-428. [PMID: 32746499 DOI: 10.1111/nph.16840] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/23/2020] [Indexed: 05/20/2023]
Abstract
Inflorescence architecture critically influences plant reproductive success and crop yield, and it reflects the activity of the inflorescence meristem and pedicel length. In Arabidopsis thaliana, the ERECTA (ER) signaling pathway and the SWR1 chromatin remodeling complex jointly regulate inflorescence architecture by promoting the expression of the PACLOBUTRAZOL RESISTANCE (PRE) gene family. However, how PREs regulate inflorescence architecture remains unclear. RNA-sequencing and chromatin immunoprecipitation coupled with quantitative PCR analyses were performed. Genetic interactions between HOMOLOG OF BEE2 INTERACTING WITH IBH1 (HBI1) and the SWR1-ER-MPK6 pathway in the control of inflorescence architecture were further studied. The present findings support that HBI1 functions downstream of PREs in the SWR1 and ER pathways to regulate inflorescence architecture by promoting pedicel elongation. Specifically, it binds to the promoters of the brassinosteroid (BR) biosynthesis gene CYP85A2 and a series of auxin-related genes, including auxin response factor ARF3, and promotes their expression. In turn, ARF3 can also bind to auxin signaling genes as well as CYP85A2 to activate their expression and promote pedicel elongation. Our study provides evidence that inflorescence architecture regulation by SWR1 and ER involves the HBI1 regulatory hub and its activation of both the BR and auxin hormone pathways.
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Affiliation(s)
- Hanyang Cai
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Agriculture, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mengnan Chai
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Agriculture, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Fangqian Chen
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Agriculture, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Youmei Huang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Agriculture, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Man Zhang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Agriculture, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qing He
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Agriculture, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liping Liu
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Agriculture, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Maokai Yan
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Agriculture, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Yuan Qin
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Agriculture, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
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27
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Yu Y, Liang Z, Song X, Fu W, Xu J, Lei Y, Yuan L, Ruan J, Chen C, Fu W, Cui Y, Huang S, Li C. BRAHMA-interacting proteins BRIP1 and BRIP2 are core subunits of Arabidopsis SWI/SNF complexes. NATURE PLANTS 2020; 6:996-1007. [PMID: 32747760 DOI: 10.1038/s41477-020-0734-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 06/29/2020] [Indexed: 05/22/2023]
Abstract
Switch defective/sucrose non-fermentable (SWI/SNF) chromatin remodelling complexes are multi-protein machineries that control gene expression by regulating chromatin structure in eukaryotes. However, the full subunit composition of SWI/SNF complexes in plants remains unclear. Here we report that in Arabidopsis thaliana, two homologous glioma tumour suppressor candidate region domain-containing proteins, named BRAHMA-interacting proteins 1 (BRIP1) and BRIP2, are core subunits of plant SWI/SNF complexes. brip1 brip2 double mutants exhibit developmental phenotypes and a transcriptome remarkably similar to those of BRAHMA (BRM) mutants. Genetic interaction tests indicated that BRIP1 and BRIP2 act together with BRM to regulate gene expression. Furthermore, BRIP1 and BRIP2 physically interact with BRM-containing SWI/SNF complexes and extensively co-localize with BRM on chromatin. Simultaneous mutation of BRIP1 and BRIP2 results in decreased BRM occupancy at almost all BRM target loci and substantially reduced abundance of the SWI/SNF assemblies. Together, our work identifies new core subunits of BRM-containing SWI/SNF complexes in plants and uncovers the essential role of these subunits in maintaining the abundance of SWI/SNF complexes in plants.
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Affiliation(s)
- Yaoguang Yu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Zhenwei Liang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Xin Song
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Wei Fu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Jianqu Xu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Yawen Lei
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Liangbing Yuan
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Jiuxiao Ruan
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Chen Chen
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada
| | - Wenqun Fu
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou, China
| | - Yuhai Cui
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada
| | - Shangzhi Huang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Chenlong Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.
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28
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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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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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30
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Zhao Z, Li T, Peng X, Wu K, Yang S. Identification and Characterization of Tomato SWI3-Like Proteins: Overexpression of SlSWIC Increases the Leaf Size in Transgenic Arabidopsis. Int J Mol Sci 2019; 20:ijms20205121. [PMID: 31623074 PMCID: PMC6829904 DOI: 10.3390/ijms20205121] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/09/2019] [Accepted: 10/10/2019] [Indexed: 02/06/2023] Open
Abstract
As the subunits of the SWI/SNF (mating-type switching (SWI) and sucrose nonfermenting (SNF)) chromatin-remodeling complexes (CRCs), Swi3-like proteins are crucial to chromatin remodeling in yeast and human. Growing evidence indicate that AtSWI3s are also essential for development and response to hormones in Arabidopsis. Nevertheless, the biological functions of Swi3-like proteins in tomato (Solanum lycopersicum) have not been investigated. Here we identified four Swi3-like proteins from tomato, namely SlSWI3A, SlSWI3B, SlSWI3C, and SlSWI3D. Subcellular localization analysis revealed that all SlSWI3s are localized in the nucleus. The expression patterns showed that all SlSWI3s are ubiquitously expressed in all tissues and organs, and SlSWI3A and SlSWI3B can be induced by cold treatment. In addition, we found that SlSWI3B can form homodimers with itself and heterodimers with SlSWI3A and SlSWI3C. SlSWI3B can also interact with SlRIN and SlCHR8, two proteins involved in tomato reproductive development. Overexpression of SlSWI3C increased the leaf size in transgenic Arabidopsis with increased expression of GROWTH REGULATING FACTORs, such as GRF3, GRF5, and GRF6. Taken together, our results indicate that SlSWI3s may play important roles in tomato growth and development.
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Affiliation(s)
- Zhongyi Zhao
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, Sichuan University, Chengdu 610064, China.
- 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 Life Sciences, China West Normal University, Nanchong 637002, China.
| | - Tao Li
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510650, China.
| | - Xiuling 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.
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, 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.
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31
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Zhu C, Yang J, Box MS, Kellogg EA, Eveland AL. A Dynamic Co-expression Map of Early Inflorescence Development in Setaria viridis Provides a Resource for Gene Discovery and Comparative Genomics. FRONTIERS IN PLANT SCIENCE 2018; 9:1309. [PMID: 30258452 PMCID: PMC6143762 DOI: 10.3389/fpls.2018.01309] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 08/20/2018] [Indexed: 05/29/2023]
Abstract
The morphological and functional diversity of plant form is governed by dynamic gene regulatory networks. In cereal crops, grain and/or pollen-bearing inflorescences exhibit vast architectural diversity and developmental complexity, yet the underlying genetic framework is only partly known. Setaria viridis is a small, rapidly growing grass species in the subfamily Panicoideae, a group that includes economically important cereal crops such as maize and sorghum. The S. viridis inflorescence displays complex branching patterns, but its early development is similar to that of other panicoid grasses, and thus is an ideal model for studying inflorescence architecture. Here we report a detailed transcriptional resource that captures dynamic transitions across six sequential stages of S. viridis inflorescence development, from reproductive onset to floral organ differentiation. Co-expression analyses identified stage-specific signatures of development, which include homologs of previously known developmental genes from maize and rice, suites of transcription factors and gene family members, and genes of unknown function. This spatiotemporal co-expression map and associated analyses provide a foundation for gene discovery in S. viridis inflorescence development, and a comparative model for exploring related architectural features in agronomically important cereals.
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32
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Vu LD, Zhu T, Verstraeten I, van de Cotte B, Gevaert K, De Smet I. Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:4609-4624. [PMID: 29939309 PMCID: PMC6117581 DOI: 10.1093/jxb/ery204] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 05/16/2018] [Indexed: 05/20/2023]
Abstract
Wheat (Triticum ssp.) is one of the most important human food sources. However, this crop is very sensitive to temperature changes. Specifically, processes during wheat leaf, flower, and seed development and photosynthesis, which all contribute to the yield of this crop, are affected by high temperature. While this has to some extent been investigated on physiological, developmental, and molecular levels, very little is known about early signalling events associated with an increase in temperature. Phosphorylation-mediated signalling mechanisms, which are quick and dynamic, are associated with plant growth and development, also under abiotic stress conditions. Therefore, we probed the impact of a short-term and mild increase in temperature on the wheat leaf and spikelet phosphoproteome. In total, 3822 (containing 5178 phosphosites) and 5581 phosphopeptides (containing 7023 phosphosites) were identified in leaf and spikelet samples, respectively. Following statistical analysis, the resulting data set provides the scientific community with a first large-scale plant phosphoproteome under the control of higher ambient temperature. This community resource on the high temperature-mediated wheat phosphoproteome will be valuable for future studies. Our analyses also revealed a core set of common proteins between leaf and spikelet, suggesting some level of conserved regulatory mechanisms. Furthermore, we observed temperature-regulated interconversion of phosphoforms, which probably impacts protein activity.
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Affiliation(s)
- Lam Dai Vu
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
| | - Tingting Zhu
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
| | - Inge Verstraeten
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Brigitte van de Cotte
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | | | - Kris Gevaert
- Department of Biochemistry, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
| | - Ive De Smet
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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33
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Simonini S, Stephenson P, Østergaard L. A molecular framework controlling style morphology in Brassicaceae. Development 2018; 145:dev.158105. [PMID: 29440299 PMCID: PMC5868994 DOI: 10.1242/dev.158105] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 01/23/2018] [Indexed: 01/04/2023]
Abstract
Organ formation in multicellular organisms depends on the coordinated activities of regulatory components that integrate developmental and hormonal cues to control gene expression and mediate cell-type specification. For example, development of the Arabidopsis gynoecium is tightly controlled by distribution and synthesis of the plant hormone auxin. The functions of several transcription factors (TFs) have been linked with auxin dynamics during gynoecium development; yet how their activities are coordinated is not known. Here, we show that five such TFs function together to ensure polarity establishment at the gynoecium apex. The auxin response factor ETTIN (ARF3; herein, ETT) is a central component of this framework. Interaction of ETT with TF partners is sensitive to the presence of auxin and our results suggest that ETT forms part of a repressive gene-regulatory complex. We show that this function is conserved between members of the Brassicaceae family and that variation in an ETT subdomain affects interaction strengths and gynoecium morphology. These results suggest that variation in affinities between conserved TFs can lead to morphological differences and thus contribute to the evolution of diverse organ shapes. Summary: Variation in interaction affinity between transcription factors of an ETTIN-containing complex underlies diversity of gynoecium style structure among members of the Brassicacea family.
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Affiliation(s)
- Sara Simonini
- Crop Genetics Department, John Innes Centre, Norwich NR4 7UH, UK
| | | | - Lars Østergaard
- Crop Genetics Department, John Innes Centre, Norwich NR4 7UH, UK
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34
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Ojolo SP, Cao S, Priyadarshani SVGN, Li W, Yan M, Aslam M, Zhao H, Qin Y. Regulation of Plant Growth and Development: A Review From a Chromatin Remodeling Perspective. FRONTIERS IN PLANT SCIENCE 2018; 9:1232. [PMID: 30186301 PMCID: PMC6113404 DOI: 10.3389/fpls.2018.01232] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 08/03/2018] [Indexed: 05/04/2023]
Abstract
In eukaryotes, genetic material is packaged into a dynamic but stable nucleoprotein structure called chromatin. Post-translational modification of chromatin domains affects the expression of underlying genes and subsequently the identity of cells by conveying epigenetic information from mother to daughter cells. SWI/SNF chromatin remodelers are ATP-dependent complexes that modulate core histone protein polypeptides, incorporate variant histone species and modify nucleotides in DNA strands within the nucleosome. The present review discusses the SWI/SNF chromatin remodeler family, its classification and recent advancements. We also address the involvement of SWI/SNF remodelers in regulating vital plant growth and development processes such as meristem establishment and maintenance, cell differentiation, organ initiation, flower morphogenesis and flowering time regulation. Moreover, the role of chromatin remodelers in key phytohormone signaling pathways is also reviewed. The information provided in this review may prompt further debate and investigations aimed at understanding plant-specific epigenetic regulation mediated by chromatin remodeling under continuously varying plant growth conditions and global climate change.
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Affiliation(s)
- Simon P. Ojolo
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shijiang Cao
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - S. V. G. N. Priyadarshani
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weimin Li
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Maokai Yan
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mohammad Aslam
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Heming Zhao
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuan Qin
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Yuan Qin, ;
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35
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Cortijo S, Charoensawan V, Brestovitsky A, Buning R, Ravarani C, Rhodes D, van Noort J, Jaeger KE, Wigge PA. Transcriptional Regulation of the Ambient Temperature Response by H2A.Z Nucleosomes and HSF1 Transcription Factors in Arabidopsis. MOLECULAR PLANT 2017; 10:1258-1273. [PMID: 28893714 PMCID: PMC6175055 DOI: 10.1016/j.molp.2017.08.014] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 08/21/2017] [Accepted: 08/24/2017] [Indexed: 05/18/2023]
Abstract
Temperature influences the distribution, range, and phenology of plants. The key transcriptional activators of heat shock response in eukaryotes, the heat shock factors (HSFs), have undergone large-scale gene amplification in plants. While HSFs are central in heat stress responses, their role in the response to ambient temperature changes is less well understood. We show here that the warm ambient temperature transcriptome is dependent upon the HSFA1 clade of Arabidopsis HSFs, which cause a rapid and dynamic eviction of H2A.Z nucleosomes at target genes. A transcriptional cascade results in the activation of multiple downstream stress-responsive transcription factors, triggering large-scale changes to the transcriptome in response to elevated temperature. H2A.Z nucleosomes are enriched at temperature-responsive genes at non-inducible temperature, and thus likely confer inducibility of gene expression and higher responsive dynamics. We propose that the antagonistic effects of H2A.Z and HSF1 provide a mechanism to activate gene expression rapidly and precisely in response to temperature, while preventing leaky transcription in the absence of an activation signal.
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Affiliation(s)
- Sandra Cortijo
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK
| | - Varodom Charoensawan
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK; Department of Biochemistry, Faculty of Science, Mahidol University, 272 Rama VI Road, Ratchathewi District, Bangkok 10400, Thailand; Integrative Computational BioScience (ICBS) Center, Mahidol University, 999 Phuttamonthon 4 Road, Salaya, Nakhon Pathom 73170, Thailand.
| | - Anna Brestovitsky
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK
| | - Ruth Buning
- Biological and Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, the Netherlands
| | - Charles Ravarani
- Medical Research Council Laboratory for Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Daniela Rhodes
- Medical Research Council Laboratory for Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Institute of Structural Biology, Nanyang Technical University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - John van Noort
- Biological and Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, the Netherlands
| | - Katja E Jaeger
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK
| | - Philip A Wigge
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK.
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36
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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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37
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Woerlen N, Allam G, Popescu A, Corrigan L, Pautot V, Hepworth SR. Repression of BLADE-ON-PETIOLE genes by KNOX homeodomain protein BREVIPEDICELLUS is essential for differentiation of secondary xylem in Arabidopsis root. PLANTA 2017; 245:1079-1090. [PMID: 28204875 DOI: 10.1007/s00425-017-2663-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 02/08/2017] [Indexed: 05/27/2023]
Abstract
Repression of boundary genes by KNOTTED1-like homeodomain transcription factor BREVIPEDICELLUS promotes the differentiation of phase II secondary xylem in Arabidopsis roots. Plant growth and development relies on the activity of meristems. Boundaries are domains of restricted growth that separate forming organs and the meristem. Class I KNOX homeodomain transcription factors are important regulators of meristem maintenance. Members of this class including BREVIDICELLUS also called KNOTTED-LIKE FROM ARABIDOPSIS THALIANA1 (BP/KNAT1) fulfill this function in part by spatially regulating boundary genes. The vascular cambium is a lateral meristem that allows for radial expansion of organs during secondary growth. We show here that BP/KNAT1 repression of boundary genes plays a crucial role in root secondary growth. In particular, exclusion of BLADE-ON-PETIOLE1/2 (BOP1/2) and other members of this module from xylem is required for the differentiation of lignified fibers and vessels during the xylem expansion phase of root thickening. These data reveal a previously undiscovered role for boundary genes in the root and shed light on mechanisms controlling wood development in trees.
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Affiliation(s)
- Natalie Woerlen
- Department of Biology and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
- Institut Jean-Pierre Bourgin, UMR1318, INRA, Agro Paris Tech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France
| | - Gamalat Allam
- Department of Biology and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Adina Popescu
- Department of Biology and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
- Institut Jean-Pierre Bourgin, UMR1318, INRA, Agro Paris Tech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France
| | - Laura Corrigan
- Department of Biology and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Véronique Pautot
- Institut Jean-Pierre Bourgin, UMR1318, INRA, Agro Paris Tech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France
| | - Shelley R Hepworth
- Department of Biology and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada.
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38
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Cai H, Zhao L, Wang L, Zhang M, Su Z, Cheng Y, Zhao H, Qin Y. ERECTA signaling controls Arabidopsis inflorescence architecture through chromatin-mediated activation of PRE1 expression. THE NEW PHYTOLOGIST 2017; 214:1579-1596. [PMID: 28295392 DOI: 10.1111/nph.14521] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 02/09/2017] [Indexed: 05/02/2023]
Abstract
Flowering plants display a remarkable diversity in inflorescence architecture, and pedicel length is one of the key contributors to this diversity. In Arabidopsis thaliana, the receptor-like kinase ERECTA (ER) mediated signaling pathway plays important roles in regulating inflorescence architecture by promoting cell proliferation. However, the regulating mechanism remains elusive in the pedicel. Genetic interactions between ERECTA signaling and the chromatin remodeling complex SWR1 in the control of inflorescence architecture were studied. Comparative transcriptome analysis was applied to identify downstream components. Chromatin immunoprecipitation and nucleosome occupancy was further investigated. The results indicated that the chromatin remodeler SWR1 coordinates with ERECTA signaling in regulating inflorescence architecture by activating the expression of PRE1 family genes and promoting pedicel elongation. It was found that SWR1 is required for the incorporation of the H2A.Z histone variant into nucleosomes of the whole PRE1 gene family and the ERECTA controlled expression of PRE1 gene family through regulating nucleosome dynamics. We propose that utilization of a chromatin remodeling complex to regulate gene expression is a common theme in developmental control across kingdoms. These findings shed light on the mechanisms through which chromatin remodelers orchestrate complex transcriptional regulation of gene expression in coordination with a developmental cue.
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Affiliation(s)
- Hanyang Cai
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education & Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China
| | - Lihua Zhao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education & Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China
| | - Lulu Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education & Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China
| | - Man Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education & Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China
| | - Zhenxia Su
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education & Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China
| | - Yan Cheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education & Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China
| | - Heming Zhao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education & Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China
| | - Yuan Qin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education & Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China
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Douglas SJ, Li B, Kliebenstein DJ, Nambara E, Riggs CD. A novel Filamentous Flower mutant suppresses brevipedicellus developmental defects and modulates glucosinolate and auxin levels. PLoS One 2017; 12:e0177045. [PMID: 28493925 PMCID: PMC5426679 DOI: 10.1371/journal.pone.0177045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 04/23/2017] [Indexed: 12/02/2022] Open
Abstract
BREVIPEDICELLUS (BP) encodes a class-I KNOTTED1-like homeobox (KNOX) transcription factor that plays a critical role in conditioning a replication competent state in the apical meristem, and it also governs growth and cellular differentiation in internodes and pedicels. To search for factors that modify BP signaling, we conducted a suppressor screen on bp er (erecta) plants and identified a mutant that ameliorates many of the pleiotropic defects of the parent line. Map based cloning and complementation studies revealed that the defect lies in the FILAMENTOUS FLOWER (FIL) gene, a member of the YABBY family of transcriptional regulators that contribute to meristem organization and function, phyllotaxy, leaf and floral organ growth and polarity, and are also known to repress KNOX gene expression. Genetic and cytological analyses of the fil-10 suppressor line indicate that the role of FIL in promoting growth is independent of its previously characterized influences on meristem identity and lateral organ polarity, and likely occurs non-cell-autonomously from superior floral organs. Transcription profiling of inflorescences revealed that FIL downregulates numerous transcription factors which in turn may subordinately regulate inflorescence architecture. In addition, FIL, directly or indirectly, activates over a dozen genes involved in glucosinolate production in part by activating MYB28, a known activator of many aliphatic glucosinolate biosynthesis genes. In the bp er fil-10 suppressor mutant background, enhanced expression of CYP71A13, AMIDASE1 (AMI) and NITRILASE genes suggest that auxin levels can be modulated by shunting glucosinolate metabolites into the IAA biosynthetic pathway, and increased IAA levels in the bp er fil-10 suppressor accompany enhanced internode and pedicel elongation. We propose that FIL acts to oppose KNOX1 gene function through a complex regulatory network that involves changes in secondary metabolites and auxin.
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Affiliation(s)
- Scott J. Douglas
- Department of Biological Sciences, University of Toronto-Scarborough, Scarborough, Ontario, Canada
| | - Baohua Li
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Daniel J. Kliebenstein
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
- DynaMo Center of Excellence, Copenhagen Plant Science Centre, University of Copenhagen, Denmark
| | - Eiji Nambara
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Centre for the Analysis of Gene Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - C. Daniel Riggs
- Department of Biological Sciences, University of Toronto-Scarborough, Scarborough, Ontario, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Centre for the Analysis of Gene Evolution and Function, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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40
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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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He C, Wu K, Zhang J, Liu X, Zeng S, Yu Z, Zhang X, Teixeira da Silva JA, Deng R, Tan J, Luo J, Duan J. Cytochemical Localization of Polysaccharides in Dendrobium officinale and the Involvement of DoCSLA6 in the Synthesis of Mannan Polysaccharides. FRONTIERS IN PLANT SCIENCE 2017; 8:173. [PMID: 28261235 PMCID: PMC5306395 DOI: 10.3389/fpls.2017.00173] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 01/27/2017] [Indexed: 05/25/2023]
Abstract
Dendrobium officinale is a precious traditional Chinese medicinal plant because of its abundant polysaccharides found in stems. We determined the composition of water-soluble polysaccharides and starch content in D. officinale stems. The extracted water-soluble polysaccharide content was as high as 35% (w/w). Analysis of the composition of monosaccharides showed that the water-soluble polysaccharides were dominated by mannose, to a lesser extent glucose, and a small amount of galactose, in a molar ratio of 223:48:1. Although starch was also found, its content was less than 10%. This result indicated that the major polysaccharides in D. officinale stems were non-starch polysaccharides, which might be mannan polysaccharides. The polysaccharides formed granules and were stored in plastids similar to starch grains, were localized in D. officinale stems by semi-thin and ultrathin sections. CELLULOSE SYNTHASE-LIKE A (CSLA) family members encode mannan synthases that catalyze the formation of mannan polysaccharides. To determine whether the CSLA gene from D. officinale was responsible for the synthesis of mannan polysaccharides, 35S:DoCSLA6 transgenic lines were generated and characterized. Our results suggest that the CSLA family genes from D. officinale play an important role in the biosynthesis of mannan polysaccharides.
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Affiliation(s)
- Chunmei He
- Key Laboratory of South China Agricultural Plant Molecular Analysis, Gene Improvement, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Kunlin Wu
- Key Laboratory of South China Agricultural Plant Molecular Analysis, Gene Improvement, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Jianxia Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis, Gene Improvement, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Xuncheng Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis, Gene Improvement, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Songjun Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis, Gene Improvement, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Zhenming Yu
- Key Laboratory of South China Agricultural Plant Molecular Analysis, Gene Improvement, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Xinghua Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis, Gene Improvement, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | | | - Rufang Deng
- Key Laboratory of South China Agricultural Plant Molecular Analysis, Gene Improvement, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Jianwen Tan
- Key Laboratory of South China Agricultural Plant Molecular Analysis, Gene Improvement, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Jianping Luo
- School of Food Science and Engineering, Hefei University of TechnologyHefei, China
| | - Jun Duan
- Key Laboratory of South China Agricultural Plant Molecular Analysis, Gene Improvement, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
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DoGMP1 from Dendrobium officinale contributes to mannose content of water-soluble polysaccharides and plays a role in salt stress response. Sci Rep 2017; 7:41010. [PMID: 28176760 PMCID: PMC5296857 DOI: 10.1038/srep41010] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 12/14/2016] [Indexed: 12/20/2022] Open
Abstract
GDP-mannose pyrophosphorylase (GMP) catalyzed the formation of GDP-mannose, which serves as a donor for the biosynthesis of mannose-containing polysaccharides. In this study, three GMP genes from Dendrobium officinale (i.e., DoGMPs) were cloned and analyzed. The putative 1000 bp upstream regulatory region of these DoGMPs was isolated and cis-elements were identified, which indicates their possible role in responses to abiotic stresses. The DoGMP1 protein was shown to be localized in the cytoplasm. To further study the function of the DoGMP1 gene, 35S:DoGMP1 transgenic A. thaliana plants with an enhanced expression level of DoGMP1 were generated. Transgenic plants were indistinguishable from wild-type (WT) plants in tissue culture or in soil. However, the mannose content of the extracted water-soluble polysaccharides increased 67%, 96% and 92% in transgenic lines #1, #2 and #3, respectively more than WT levels. Germination percentage of seeds from transgenic lines was higher than WT seeds and the growth of seedlings from transgenic lines was better than WT seedlings under salinity stress (150 mM NaCl). Our results provide genetic evidence for the involvement of GMP genes in the biosynthesis of mannose-containing polysaccharides and the mediation of GMP genes in the response to salt stress during seed germination and seedling growth.
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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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He C, Wu K, Zhang J, Liu X, Zeng S, Yu Z, Zhang X, Teixeira da Silva JA, Deng R, Tan J, Luo J, Duan J. Cytochemical Localization of Polysaccharides in Dendrobium officinale and the Involvement of DoCSLA6 in the Synthesis of Mannan Polysaccharides. FRONTIERS IN PLANT SCIENCE 2017. [PMID: 28261235 DOI: 10.3389/fpls.2017.00173/1664-462x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Dendrobium officinale is a precious traditional Chinese medicinal plant because of its abundant polysaccharides found in stems. We determined the composition of water-soluble polysaccharides and starch content in D. officinale stems. The extracted water-soluble polysaccharide content was as high as 35% (w/w). Analysis of the composition of monosaccharides showed that the water-soluble polysaccharides were dominated by mannose, to a lesser extent glucose, and a small amount of galactose, in a molar ratio of 223:48:1. Although starch was also found, its content was less than 10%. This result indicated that the major polysaccharides in D. officinale stems were non-starch polysaccharides, which might be mannan polysaccharides. The polysaccharides formed granules and were stored in plastids similar to starch grains, were localized in D. officinale stems by semi-thin and ultrathin sections. CELLULOSE SYNTHASE-LIKE A (CSLA) family members encode mannan synthases that catalyze the formation of mannan polysaccharides. To determine whether the CSLA gene from D. officinale was responsible for the synthesis of mannan polysaccharides, 35S:DoCSLA6 transgenic lines were generated and characterized. Our results suggest that the CSLA family genes from D. officinale play an important role in the biosynthesis of mannan polysaccharides.
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Affiliation(s)
- Chunmei He
- Key Laboratory of South China Agricultural Plant Molecular Analysis, Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences Guangzhou, China
| | - Kunlin Wu
- Key Laboratory of South China Agricultural Plant Molecular Analysis, Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences Guangzhou, China
| | - Jianxia Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis, Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences Guangzhou, China
| | - Xuncheng Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis, Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences Guangzhou, China
| | - Songjun Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis, Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences Guangzhou, China
| | - Zhenming Yu
- Key Laboratory of South China Agricultural Plant Molecular Analysis, Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences Guangzhou, China
| | - Xinghua Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis, Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences Guangzhou, China
| | | | - Rufang Deng
- Key Laboratory of South China Agricultural Plant Molecular Analysis, Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences Guangzhou, China
| | - Jianwen Tan
- Key Laboratory of South China Agricultural Plant Molecular Analysis, Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences Guangzhou, China
| | - Jianping Luo
- School of Food Science and Engineering, Hefei University of Technology Hefei, China
| | - Jun Duan
- Key Laboratory of South China Agricultural Plant Molecular Analysis, Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences Guangzhou, China
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45
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Chen W, Zhu Q, Liu Y, Zhang Q. Chromatin Remodeling and Plant Immunity. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2016; 106:243-260. [PMID: 28057214 DOI: 10.1016/bs.apcsb.2016.08.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Chromatin remodeling, an important facet of the regulation of gene expression in eukaryotes, is performed by two major types of multisubunit complexes, covalent histone- or DNA-modifying complexes, and ATP-dependent chromosome remodeling complexes. Snf2 family DNA-dependent ATPases constitute the catalytic subunits of ATP-dependent chromosome remodeling complexes, which accounts for energy supply during chromatin remodeling. Increasing evidence indicates a critical role of chromatin remodeling in the establishment of long-lasting, even transgenerational immune memory in plants, which is supported by the findings that DNA methylation, histone deacetylation, and histone methylation can prime the promoters of immune-related genes required for disease defense. So what are the links between Snf2-mediated ATP-dependent chromosome remodeling and plant immunity, and what mechanisms might support its involvement in disease resistance?
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Affiliation(s)
- W Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Q Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Y Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Q Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China; Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, College of Life Sciences, South China Agricultural University, Guangzhou, China.
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46
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Sarnowska E, Gratkowska DM, Sacharowski SP, Cwiek P, Tohge T, Fernie AR, Siedlecki JA, Koncz C, Sarnowski TJ. The Role of SWI/SNF Chromatin Remodeling Complexes in Hormone Crosstalk. TRENDS IN PLANT SCIENCE 2016; 21:594-608. [PMID: 26920655 DOI: 10.1016/j.tplants.2016.01.017] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 12/14/2015] [Accepted: 01/21/2016] [Indexed: 05/20/2023]
Abstract
SWI/SNF-type ATP-dependent chromatin remodeling complexes (CRCs) are evolutionarily conserved multiprotein machineries controlling DNA accessibility by regulating chromatin structure. We summarize here recent advances highlighting the role of SWI/SNF in the regulation of hormone signaling pathways and their crosstalk in Arabidopsis thaliana. We discuss the functional interdependences of SWI/SNF complexes and key elements regulating developmental and hormone signaling pathways by indicating intriguing similarities and differences in plants and humans, and summarize proposed mechanisms of SWI/SNF action on target loci. We postulate that, given their viability, several plant SWI/SNF mutants may serve as an attractive model for searching for conserved functions of SWI/SNF CRCs in hormone signaling, cell cycle control, and other regulatory pathways.
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Affiliation(s)
| | | | | | - Pawel Cwiek
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Takayuki Tohge
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | | | - Csaba Koncz
- Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany; Institute of Plant Biology, Biological Research Center of Hungarian Academy, Temesvári Körút 62, 6724 Szeged, Hungary
| | - Tomasz J Sarnowski
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland.
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47
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Li C, Gu L, Gao L, Chen C, Wei CQ, Qiu Q, Chien CW, Wang S, Jiang L, Ai LF, Chen CY, Yang S, Nguyen V, Qi Y, Snyder MP, Burlingame AL, Kohalmi SE, Huang S, Cao X, Wang ZY, Wu K, Chen X, Cui Y. Concerted genomic targeting of H3K27 demethylase REF6 and chromatin-remodeling ATPase BRM in Arabidopsis. Nat Genet 2016; 48:687-93. [PMID: 27111034 DOI: 10.1038/ng.3555] [Citation(s) in RCA: 161] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 04/01/2016] [Indexed: 12/13/2022]
Abstract
SWI/SNF-type chromatin remodelers, such as BRAHMA (BRM), and H3K27 demethylases both have active roles in regulating gene expression at the chromatin level, but how they are recruited to specific genomic sites remains largely unknown. Here we show that RELATIVE OF EARLY FLOWERING 6 (REF6), a plant-unique H3K27 demethylase, targets genomic loci containing a CTCTGYTY motif via its zinc-finger (ZnF) domains and facilitates the recruitment of BRM. Genome-wide analyses showed that REF6 colocalizes with BRM at many genomic sites with the CTCTGYTY motif. Loss of REF6 results in decreased BRM occupancy at BRM-REF6 co-targets. Furthermore, REF6 directly binds to the CTCTGYTY motif in vitro, and deletion of the motif from a target gene renders it inaccessible to REF6 in vivo. Finally, we show that, when its ZnF domains are deleted, REF6 loses its genomic targeting ability. Thus, our work identifies a new genomic targeting mechanism for an H3K27 demethylase and demonstrates its key role in recruiting the BRM chromatin remodeler.
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Affiliation(s)
- Chenlong Li
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada.,Department of Biology, Western University, London, Ontario, Canada
| | - Lianfeng Gu
- Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou, China.,Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, California, USA.,State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Lei Gao
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, California, USA
| | - Chen Chen
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada.,Department of Biology, Western University, London, Ontario, Canada
| | - Chuang-Qi Wei
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA.,Life Science College, Hebei Normal University, Shijiazhuang, China
| | - Qi Qiu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Chih-Wei Chien
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA
| | - Suikang Wang
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, California, USA.,State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Lihua Jiang
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Lian-Feng Ai
- Hebei Entry-Exit Inspection and Quarantine Bureau, Shijiazhuang, China
| | - Chia-Yang Chen
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Songguang Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Vi Nguyen
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada
| | - Yanhua Qi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Michael P Snyder
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | | | - Shangzhi Huang
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-sen University, Guangzhou, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.,Collaborative Innovation Center of Genetics and Development, Shanghai, China.,CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Zhi-Yong Wang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA
| | - Keqiang Wu
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, California, USA.,Howard Hughes Medical Institute, University of California, Riverside, Riverside, California, USA
| | - Yuhai Cui
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada.,Department of Biology, Western University, London, Ontario, Canada
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48
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Roy S. Function of MYB domain transcription factors in abiotic stress and epigenetic control of stress response in plant genome. PLANT SIGNALING & BEHAVIOR 2016; 11:e1117723. [PMID: 26636625 PMCID: PMC4871670 DOI: 10.1080/15592324.2015.1117723] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 11/02/2015] [Indexed: 05/18/2023]
Abstract
Plants have developed highly efficient and remarkable mechanisms to survive under frequent and extreme environmental stress conditions. Exposure of plants to various stress factors is associated with coordinated changes in gene expression at the transcriptional level and hence transcription factors, such as those belonging to the MYB family play a central role in triggering the right responses. MYB transcription factors have been extensively studied in regard of their involvement in the regulation of a number of such stress responses in plants. Genetic and molecular biological studies, primarily in Arabidopsis, have also begun to unravel the role of MYB transcription factors in the epigenetic regulation of stress responses in plants. This review focuses on the role of MYB transcription factors in the regulation of various stress responses in general, highlighting on recent advances in our understanding of the involvement of this class of transcription factors in epigenetic regulation of stress response in plant genome.
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Affiliation(s)
- Sujit Roy
- Department of Botany, UGC Center of Advanced Studies, Golapbag, The University of Burdwan, Burdwan, West Bengal, India
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49
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Khan M, Ragni L, Tabb P, Salasini BC, Chatfield S, Datla R, Lock J, Kuai X, Després C, Proveniers M, Yongguo C, Xiang D, Morin H, Rullière JP, Citerne S, Hepworth SR, Pautot V. Repression of Lateral Organ Boundary Genes by PENNYWISE and POUND-FOOLISH Is Essential for Meristem Maintenance and Flowering in Arabidopsis. PLANT PHYSIOLOGY 2015; 169:2166-86. [PMID: 26417006 PMCID: PMC4634066 DOI: 10.1104/pp.15.00915] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 09/25/2015] [Indexed: 05/20/2023]
Abstract
In the model plant Arabidopsis (Arabidopsis thaliana), endogenous and environmental signals acting on the shoot apical meristem cause acquisition of inflorescence meristem fate. This results in changed patterns of aerial development seen as the transition from making leaves to the production of flowers separated by elongated internodes. Two related BEL1-like homeobox genes, PENNYWISE (PNY) and POUND-FOOLISH (PNF), fulfill this transition. Loss of function of these genes impairs stem cell maintenance and blocks internode elongation and flowering. We show here that pny pnf apices misexpress lateral organ boundary genes BLADE-ON-PETIOLE1/2 (BOP1/2) and KNOTTED-LIKE FROM ARABIDOPSIS THALIANA6 (KNAT6) together with ARABIDOPSIS THALIANA HOMEOBOX GENE1 (ATH1). Inactivation of genes in this module fully rescues pny pnf defects. We further show that BOP1 directly activates ATH1, whereas activation of KNAT6 is indirect. The pny pnf restoration correlates with renewed accumulation of transcripts conferring floral meristem identity, including FD, SQUAMOSA PROMOTER-BINDING PROTEIN LIKE genes, LEAFY, and APETALA1. To gain insight into how this module blocks flowering, we analyzed the transcriptome of BOP1-overexpressing plants. Our data suggest a central role for the microRNA156-SQUAMOSA PROMOTER BINDING PROTEIN-LIKE-microRNA172 module in integrating stress signals conferred in part by promotion of jasmonic acid biosynthesis. These data reveal a potential mechanism by which repression of lateral organ boundary genes by PNY-PNF is essential for flowering.
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Affiliation(s)
- Madiha Khan
- Department of Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6 (M.K., P.T., B.C.S., S.Ch., J.L., S.R.H.);Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-AgroParisTech, Bâtiment 2, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, 78026 Versailles cedex, France (L.R., H.M., J.-P.R., S.Ci., V.P.); Plant Biotechnology Institute,National Research Council Canada, Saskatoon, Saskatchewan, Canada S7N 0W9 (R.D., C.Y., D.X.);Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada L2S 3A1 (X.K, C.D.); andMolecular Plant Physiology, Department of Biology, Faculty of Sciences, Utrecht University, CH-3584 Utrecht, The Netherlands (M.P.)
| | - Laura Ragni
- Department of Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6 (M.K., P.T., B.C.S., S.Ch., J.L., S.R.H.);Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-AgroParisTech, Bâtiment 2, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, 78026 Versailles cedex, France (L.R., H.M., J.-P.R., S.Ci., V.P.); Plant Biotechnology Institute,National Research Council Canada, Saskatoon, Saskatchewan, Canada S7N 0W9 (R.D., C.Y., D.X.);Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada L2S 3A1 (X.K, C.D.); andMolecular Plant Physiology, Department of Biology, Faculty of Sciences, Utrecht University, CH-3584 Utrecht, The Netherlands (M.P.)
| | - Paul Tabb
- Department of Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6 (M.K., P.T., B.C.S., S.Ch., J.L., S.R.H.);Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-AgroParisTech, Bâtiment 2, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, 78026 Versailles cedex, France (L.R., H.M., J.-P.R., S.Ci., V.P.); Plant Biotechnology Institute,National Research Council Canada, Saskatoon, Saskatchewan, Canada S7N 0W9 (R.D., C.Y., D.X.);Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada L2S 3A1 (X.K, C.D.); andMolecular Plant Physiology, Department of Biology, Faculty of Sciences, Utrecht University, CH-3584 Utrecht, The Netherlands (M.P.)
| | - Brenda C Salasini
- Department of Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6 (M.K., P.T., B.C.S., S.Ch., J.L., S.R.H.);Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-AgroParisTech, Bâtiment 2, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, 78026 Versailles cedex, France (L.R., H.M., J.-P.R., S.Ci., V.P.); Plant Biotechnology Institute,National Research Council Canada, Saskatoon, Saskatchewan, Canada S7N 0W9 (R.D., C.Y., D.X.);Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada L2S 3A1 (X.K, C.D.); andMolecular Plant Physiology, Department of Biology, Faculty of Sciences, Utrecht University, CH-3584 Utrecht, The Netherlands (M.P.)
| | - Steven Chatfield
- Department of Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6 (M.K., P.T., B.C.S., S.Ch., J.L., S.R.H.);Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-AgroParisTech, Bâtiment 2, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, 78026 Versailles cedex, France (L.R., H.M., J.-P.R., S.Ci., V.P.); Plant Biotechnology Institute,National Research Council Canada, Saskatoon, Saskatchewan, Canada S7N 0W9 (R.D., C.Y., D.X.);Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada L2S 3A1 (X.K, C.D.); andMolecular Plant Physiology, Department of Biology, Faculty of Sciences, Utrecht University, CH-3584 Utrecht, The Netherlands (M.P.)
| | - Raju Datla
- Department of Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6 (M.K., P.T., B.C.S., S.Ch., J.L., S.R.H.);Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-AgroParisTech, Bâtiment 2, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, 78026 Versailles cedex, France (L.R., H.M., J.-P.R., S.Ci., V.P.); Plant Biotechnology Institute,National Research Council Canada, Saskatoon, Saskatchewan, Canada S7N 0W9 (R.D., C.Y., D.X.);Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada L2S 3A1 (X.K, C.D.); andMolecular Plant Physiology, Department of Biology, Faculty of Sciences, Utrecht University, CH-3584 Utrecht, The Netherlands (M.P.)
| | - John Lock
- Department of Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6 (M.K., P.T., B.C.S., S.Ch., J.L., S.R.H.);Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-AgroParisTech, Bâtiment 2, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, 78026 Versailles cedex, France (L.R., H.M., J.-P.R., S.Ci., V.P.); Plant Biotechnology Institute,National Research Council Canada, Saskatoon, Saskatchewan, Canada S7N 0W9 (R.D., C.Y., D.X.);Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada L2S 3A1 (X.K, C.D.); andMolecular Plant Physiology, Department of Biology, Faculty of Sciences, Utrecht University, CH-3584 Utrecht, The Netherlands (M.P.)
| | - Xiahezi Kuai
- Department of Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6 (M.K., P.T., B.C.S., S.Ch., J.L., S.R.H.);Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-AgroParisTech, Bâtiment 2, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, 78026 Versailles cedex, France (L.R., H.M., J.-P.R., S.Ci., V.P.); Plant Biotechnology Institute,National Research Council Canada, Saskatoon, Saskatchewan, Canada S7N 0W9 (R.D., C.Y., D.X.);Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada L2S 3A1 (X.K, C.D.); andMolecular Plant Physiology, Department of Biology, Faculty of Sciences, Utrecht University, CH-3584 Utrecht, The Netherlands (M.P.)
| | - Charles Després
- Department of Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6 (M.K., P.T., B.C.S., S.Ch., J.L., S.R.H.);Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-AgroParisTech, Bâtiment 2, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, 78026 Versailles cedex, France (L.R., H.M., J.-P.R., S.Ci., V.P.); Plant Biotechnology Institute,National Research Council Canada, Saskatoon, Saskatchewan, Canada S7N 0W9 (R.D., C.Y., D.X.);Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada L2S 3A1 (X.K, C.D.); andMolecular Plant Physiology, Department of Biology, Faculty of Sciences, Utrecht University, CH-3584 Utrecht, The Netherlands (M.P.)
| | - Marcel Proveniers
- Department of Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6 (M.K., P.T., B.C.S., S.Ch., J.L., S.R.H.);Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-AgroParisTech, Bâtiment 2, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, 78026 Versailles cedex, France (L.R., H.M., J.-P.R., S.Ci., V.P.); Plant Biotechnology Institute,National Research Council Canada, Saskatoon, Saskatchewan, Canada S7N 0W9 (R.D., C.Y., D.X.);Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada L2S 3A1 (X.K, C.D.); andMolecular Plant Physiology, Department of Biology, Faculty of Sciences, Utrecht University, CH-3584 Utrecht, The Netherlands (M.P.)
| | - Cao Yongguo
- Department of Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6 (M.K., P.T., B.C.S., S.Ch., J.L., S.R.H.);Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-AgroParisTech, Bâtiment 2, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, 78026 Versailles cedex, France (L.R., H.M., J.-P.R., S.Ci., V.P.); Plant Biotechnology Institute,National Research Council Canada, Saskatoon, Saskatchewan, Canada S7N 0W9 (R.D., C.Y., D.X.);Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada L2S 3A1 (X.K, C.D.); andMolecular Plant Physiology, Department of Biology, Faculty of Sciences, Utrecht University, CH-3584 Utrecht, The Netherlands (M.P.)
| | - Daoquan Xiang
- Department of Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6 (M.K., P.T., B.C.S., S.Ch., J.L., S.R.H.);Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-AgroParisTech, Bâtiment 2, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, 78026 Versailles cedex, France (L.R., H.M., J.-P.R., S.Ci., V.P.); Plant Biotechnology Institute,National Research Council Canada, Saskatoon, Saskatchewan, Canada S7N 0W9 (R.D., C.Y., D.X.);Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada L2S 3A1 (X.K, C.D.); andMolecular Plant Physiology, Department of Biology, Faculty of Sciences, Utrecht University, CH-3584 Utrecht, The Netherlands (M.P.)
| | - Halima Morin
- Department of Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6 (M.K., P.T., B.C.S., S.Ch., J.L., S.R.H.);Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-AgroParisTech, Bâtiment 2, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, 78026 Versailles cedex, France (L.R., H.M., J.-P.R., S.Ci., V.P.); Plant Biotechnology Institute,National Research Council Canada, Saskatoon, Saskatchewan, Canada S7N 0W9 (R.D., C.Y., D.X.);Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada L2S 3A1 (X.K, C.D.); andMolecular Plant Physiology, Department of Biology, Faculty of Sciences, Utrecht University, CH-3584 Utrecht, The Netherlands (M.P.)
| | - Jean-Pierre Rullière
- Department of Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6 (M.K., P.T., B.C.S., S.Ch., J.L., S.R.H.);Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-AgroParisTech, Bâtiment 2, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, 78026 Versailles cedex, France (L.R., H.M., J.-P.R., S.Ci., V.P.); Plant Biotechnology Institute,National Research Council Canada, Saskatoon, Saskatchewan, Canada S7N 0W9 (R.D., C.Y., D.X.);Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada L2S 3A1 (X.K, C.D.); andMolecular Plant Physiology, Department of Biology, Faculty of Sciences, Utrecht University, CH-3584 Utrecht, The Netherlands (M.P.)
| | - Sylvie Citerne
- Department of Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6 (M.K., P.T., B.C.S., S.Ch., J.L., S.R.H.);Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-AgroParisTech, Bâtiment 2, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, 78026 Versailles cedex, France (L.R., H.M., J.-P.R., S.Ci., V.P.); Plant Biotechnology Institute,National Research Council Canada, Saskatoon, Saskatchewan, Canada S7N 0W9 (R.D., C.Y., D.X.);Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada L2S 3A1 (X.K, C.D.); andMolecular Plant Physiology, Department of Biology, Faculty of Sciences, Utrecht University, CH-3584 Utrecht, The Netherlands (M.P.)
| | - Shelley R Hepworth
- Department of Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6 (M.K., P.T., B.C.S., S.Ch., J.L., S.R.H.);Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-AgroParisTech, Bâtiment 2, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, 78026 Versailles cedex, France (L.R., H.M., J.-P.R., S.Ci., V.P.); Plant Biotechnology Institute,National Research Council Canada, Saskatoon, Saskatchewan, Canada S7N 0W9 (R.D., C.Y., D.X.);Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada L2S 3A1 (X.K, C.D.); andMolecular Plant Physiology, Department of Biology, Faculty of Sciences, Utrecht University, CH-3584 Utrecht, The Netherlands (M.P.)
| | - Véronique Pautot
- Department of Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6 (M.K., P.T., B.C.S., S.Ch., J.L., S.R.H.);Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique-AgroParisTech, Bâtiment 2, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, 78026 Versailles cedex, France (L.R., H.M., J.-P.R., S.Ci., V.P.); Plant Biotechnology Institute,National Research Council Canada, Saskatoon, Saskatchewan, Canada S7N 0W9 (R.D., C.Y., D.X.);Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada L2S 3A1 (X.K, C.D.); andMolecular Plant Physiology, Department of Biology, Faculty of Sciences, Utrecht University, CH-3584 Utrecht, The Netherlands (M.P.)
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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: 103] [Impact Index Per Article: 11.4] [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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