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Li Y, Kamiyama Y, Minegishi F, Tamura Y, Yamashita K, Katagiri S, Takase H, Otani M, Tojo R, Rupp GE, Suzuki T, Kawakami N, Peck SC, Umezawa T. Group C MAP kinases phosphorylate MBD10 to regulate ABA-induced leaf senescence in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1747-1759. [PMID: 38477703 DOI: 10.1111/tpj.16706] [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: 10/01/2023] [Revised: 02/15/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024]
Abstract
Abscisic acid (ABA) is a phytohormone that promotes leaf senescence in response to environmental stress. We previously identified methyl CpG-binding domain 10 (MBD10) as a phosphoprotein that becomes differentially phosphorylated after ABA treatment in Arabidopsis. ABA-induced leaf senescence was delayed in mbd10 knockout plants but accelerated in MBD10-overexpressing plants, suggesting that MBD10 positively regulates ABA-induced leaf senescence. ABA-induced phosphorylation of MBD10 occurs in planta on Thr-89, and our results demonstrated that Thr-89 phosphorylation is essential for MBD10's function in leaf senescence. The in vivo phosphorylation of Thr-89 in MBD10 was significantly downregulated in a quadruple mutant of group C MAPKs (mpk1/2/7/14), and group C MAPKs directly phosphorylated MBD10 in vitro. Furthermore, mpk1/2/7/14 showed a similar phenotype as seen in mbd10 for ABA-induced leaf senescence, suggesting that group C MAPKs are the cognate kinases of MBD10 for Thr-89. Because group C MAPKs have been reported to function downstream of SnRK2s, our results indicate that group C MAPKs and MBD10 constitute a regulatory pathway for ABA-induced leaf senescence.
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Grants
- KAKENHI JP21H05654 Ministry of Education, Culture, Sports, Science and Technology
- KAKENHI JP22K19170 Ministry of Education, Culture, Sports, Science and Technology
- KAKENHI JP23H02497 Ministry of Education, Culture, Sports, Science and Technology
- KAKENHI JP23H04192 Ministry of Education, Culture, Sports, Science and Technology
- 20350427 Moonshot Research and Development Program
- JP21J10962 Japan Society for the Promotion of Science
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Affiliation(s)
- Yangdan Li
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, 184-8588, Tokyo, Japan
| | - Yoshiaki Kamiyama
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, 184-8588, Tokyo, Japan
| | - Fuko Minegishi
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, 184-8588, Tokyo, Japan
| | - Yuki Tamura
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, 184-8588, Tokyo, Japan
| | - Kota Yamashita
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, 184-8588, Tokyo, Japan
| | - Sotaro Katagiri
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, 184-8588, Tokyo, Japan
| | - Hinano Takase
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, 184-8588, Tokyo, Japan
| | - Masahiko Otani
- School of Agriculture, Meiji University, Kawasaki, 214-8571, Kanagawa, Japan
| | - Ryo Tojo
- School of Agriculture, Meiji University, Kawasaki, 214-8571, Kanagawa, Japan
| | - Gabrielle E Rupp
- Department of Biochemistry, University of Missouri, Columbia, 65211, Missouri, USA
| | - Takamasa Suzuki
- College of Bioscience and Biotechnology, Chubu University, Kasugai, 487-8501, Aichi, Japan
| | - Naoto Kawakami
- School of Agriculture, Meiji University, Kawasaki, 214-8571, Kanagawa, Japan
| | - Scott C Peck
- Department of Biochemistry, University of Missouri, Columbia, 65211, Missouri, USA
| | - Taishi Umezawa
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, 184-8588, Tokyo, Japan
- Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, 183-8538, Tokyo, Japan
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Shu J, Yin X, Liu Y, Mi Y, Zhang B, Zhang A, Guo H, Dong J. MBD3 Regulates Male Germ Cell Division and Sperm Fertility in Arabidopsis thaliana. PLANTS (BASEL, SWITZERLAND) 2023; 12:2654. [PMID: 37514268 PMCID: PMC10384339 DOI: 10.3390/plants12142654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/03/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023]
Abstract
DNA methylation plays important roles through the methyl-CpG-binding domain (MBD) to realize epigenetic modifications. Thirteen AtMBD proteins have been identified from the Arabidopsis thaliana genome, but the functions of some members are unclear. AtMBD3 was found to be highly expressed in pollen and seeds and it preferably binds methylated CG, CHG, and unmethylated DNA sequences. Then, two mutant alleles at the AtMBD3 locus were obtained in order to further explore its function using CRISPR/Cas9. When compared with 92.17% mature pollen production in the wild type, significantly lower percentages of 84.31% and 78.91% were observed in the mbd3-1 and mbd3-2 mutants, respectively. About 16-21% of pollen from the mbd3 mutants suffered a collapse in reproductive transmission, whereas the other pollen was found to be normal. After pollination, about 16% and 24% of mbd3-1 and mbd3-2 mutant seeds underwent early or late abortion, respectively. Among all the late abortion seeds in mbd3-2 plants, 25% of the abnormal seeds were at the globular stage, 31.25% were at the transition stage, and 43.75% were at the heart stage. A transcriptome analysis of the seeds found 950 upregulated genes and 1128 downregulated genes between wild type and mbd3-2 mutants. Some transcriptional factors involved in embryo development were selected to be expressed, and we found significant differences between wild type and mbd3 mutants, such as WOXs, CUC1, AIB4, and RGL3. Furthermore, we found a gene that is specifically expressed in pollen, named PBL6. PBL6 was found to directly interact with AtMBD3. Our results provide insights into the function of AtMBD3 in plants, especially in sperm fertility.
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Affiliation(s)
- Jia Shu
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Xiaochang Yin
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Yannan Liu
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Yingjie Mi
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Bin Zhang
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Aoyuan Zhang
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Hongbo Guo
- College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China
| | - Juane Dong
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
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3
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Methyl-CpG binding proteins (MBD) family evolution and conservation in plants. Gene 2022; 824:146404. [PMID: 35278634 DOI: 10.1016/j.gene.2022.146404] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 02/17/2022] [Accepted: 03/04/2022] [Indexed: 11/20/2022]
Abstract
DNA methylation is an epigenetic mechanism that acts on cytosine residues. The methyl-CpG-binding domain proteins (MBD) are involved in the recognition of methyl-cytosines by activating a signaling cascade that induces the formation of heterochromatin or euchromatin, thereby regulating gene expression. In this study, we analyzed the evolution and conservation of MBD proteins in plants. First, we performed a genome-wide identification and analysis of the MBD family in common bean and soybean, since they have experienced one and two whole-genome duplication events, respectively. We found one pair of MBD paralogs in soybean (GmMBD2) has subfunctionalized after their recent divergence, which was corroborated with their expression profile. Phylogenetic analysis revealed that classes of MBD proteins clustered with human MBD. Interestingly, the MBD9 may have emerged after the hexaploidization event in eudicots. We found that plants and humans share a great similarity in MBDs' binding affinity in the mCpG context. MBD2 and MBD4 from different plant species have the conserved four amino acid residues -Arg (R), Asp (D), Tyr (Y) and Arg (R)- reported to be responsible for MBD-binding in the mCpG. However, MBD8, MBD9, MBD10, and MBD11 underwent substitutions in these residues, suggesting the non-interaction in the mCpG context, but a heterochromatin association as MBD5 and MBD6 from human. This study represents the first genome-wide analysis of the MBD gene family in eurosids I - soybean and common bean. The data presented here contribute towards understanding the evolution of MBDs proteins in plants and their specific binding affinity on mCpG site.
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Liang J, Li X, Wen Y, Wu X, Wang H, Li D, Song F. Genome-Wide Characterization of the Methyl CpG Binding Domain-Containing Proteins in Watermelon and Functional Analysis of Their Roles in Disease Resistance Through Ectopic Overexpression in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2022; 13:886965. [PMID: 35615127 PMCID: PMC9125323 DOI: 10.3389/fpls.2022.886965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/20/2022] [Indexed: 06/15/2023]
Abstract
Methyl-CPG-Binding Domain (MBD) proteins play important roles in plant growth, development, and stress responses. The present study characterized the MBD families in watermelon and other cucurbit plants regarding the gene numbers and structures, phylogenetic and syntenic relationships, evolution events, and conserved domain organization of the MBD proteins. The watermelon ClMBD proteins were found to be localized in nucleus, and ClMBD2 and ClMBD3 interacted with ClIDM2 and ClIDM3. ClMBD2 bound to DNA harboring methylated CG sites but not to DNA with methylated CHG and CHH sites in vitro. The ClMBD genes exhibited distinct expression patterns in watermelon plants after SA and MeJA treatment and after infection by fungal pathogens Fusarium oxysporum f.sp. niveum and Didymella bryoniae. Overexpression of ClMBD2, ClMBD3, or ClMBD5 in Arabidopsis resulted in attenuated resistance against Botrytis cinerea, accompanied by down-regulated expression of AtPDF1.2 and increased accumulation of H2O2 upon B. cinerea infection. Overexpression of ClMBD1 and ClMBD2 led to down-regulated expression of AtPR1 and decreased resistance while overexpression of ClMBD5 resulted in up-regulated expression of AtPR1 and increased resistance against Pseudomonas syringae pv. tomato DC3000. Transcriptome analysis revealed that overexpression of ClMBD2 in Arabidopsis up-regulated the expression of a small set of genes that negatively regulate Arabidopsis immunity. These data suggest the importance of some ClMBD genes in plant immunity and provide the possibility to improve plant immunity through modification of specific ClMBD genes.
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Affiliation(s)
- Jiayu Liang
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Molecular Biology of Crop Pathogens and Insects, College of Agriculture and Biotechnology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Xiaodan Li
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Molecular Biology of Crop Pathogens and Insects, College of Agriculture and Biotechnology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Ya Wen
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Molecular Biology of Crop Pathogens and Insects, College of Agriculture and Biotechnology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Xinyi Wu
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Molecular Biology of Crop Pathogens and Insects, College of Agriculture and Biotechnology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Hui Wang
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Molecular Biology of Crop Pathogens and Insects, College of Agriculture and Biotechnology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Dayong Li
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Molecular Biology of Crop Pathogens and Insects, College of Agriculture and Biotechnology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Fengming Song
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Molecular Biology of Crop Pathogens and Insects, College of Agriculture and Biotechnology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
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Exploration of the Potential Transcriptional Regulatory Mechanisms of DNA Methyltransferases and MBD Genes in Petunia Anther Development and Multi-Stress Responses. Genes (Basel) 2022; 13:genes13020314. [PMID: 35205359 PMCID: PMC8872020 DOI: 10.3390/genes13020314] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/28/2022] [Accepted: 02/01/2022] [Indexed: 02/01/2023] Open
Abstract
Cytosine-5 DNA methyltransferases (C5-MTases) and methyl-CpG-binding-domain (MBD) genes can be co-expressed. They directly control target gene expression by enhancing their DNA methylation levels in humans; however, the presence of this kind of cooperative relationship in plants has not been determined. A popular garden plant worldwide, petunia (Petunia hybrida) is also a model plant in molecular biology. In this study, 9 PhC5-MTase and 11 PhMBD proteins were identified in petunia, and they were categorized into four and six subgroups, respectively, on the basis of phylogenetic analyses. An expression correlation analysis was performed to explore the co-expression relationships between PhC5-MTases and PhMBDs using RNA-seq data, and 11 PhC5-MTase/PhMBD pairs preferentially expressed in anthers were identified as having the most significant correlations (Pearson’s correlation coefficients > 0.9). Remarkably, the stability levels of the PhC5-MTase and PhMBD pairs significantly decreased in different tissues and organs compared with that in anthers, and most of the selected PhC5-MTases and PhMBDs responded to the abiotic and hormonal stresses. However, highly correlated expression relationships between most pairs were not observed under different stress conditions, indicating that anther developmental processes are preferentially influenced by the co-expression of PhC5-MTases and PhMBDs. Interestingly, the nuclear localization genes PhDRM2 and PhMBD2 still had higher correlations under GA treatment conditions, implying that they play important roles in the GA-mediated development of petunia. Collectively, our study suggests a regulatory role for DNA methylation by C5-MTase and MBD genes in petunia anther maturation processes and multi-stress responses, and it provides a framework for the functional characterization of C5-MTases and MBDs in the future.
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6
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Mahana Y, Ohki I, Walinda E, Morimoto D, Sugase K, Shirakawa M. Structural Insights into Methylated DNA Recognition by the Methyl-CpG Binding Domain of MBD6 from Arabidopsis thaliana. ACS OMEGA 2022; 7:3212-3221. [PMID: 35128234 PMCID: PMC8811898 DOI: 10.1021/acsomega.1c04917] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 11/24/2021] [Indexed: 06/01/2023]
Abstract
Cytosine methylation is an epigenetic modification essential for formation of mature heterochromatin, gene silencing, and genomic stability. In plants, methylation occurs not only at cytosine bases in CpG but also in CpHpG and CpHpH contexts, where H denotes A, T, or C. Methyl-CpG binding domain (MBD) proteins, which recognize symmetrical methyl-CpG dinucleotides and act as gene repressors in mammalian cells, are also present in plant cells, although their structural and functional properties still remain poorly understood. To fill this gap, in this study, we determined the solution structure of the MBD domain of the MBD6 protein from Arabidopsis thaliana and investigated its binding properties to methylated DNA by binding assays and an in-depth NMR spectroscopic analysis. The AtMBD6 MBD domain folds into a canonical MBD structure in line with its binding specificity toward methyl-CpG and possesses a DNA binding interface similar to mammalian MBD domains. Intriguingly, however, the binding affinity of the AtMBD6 MBD domain toward methyl-CpG-containing DNA was found to be much lower than that of known mammalian MBD domains. The main difference arises from the absence of positively charged residues in AtMBD6 that supposedly interact with the DNA backbone as seen in mammalian MBD/methyl-CpG-containing DNA complexes. Taken together, we have established a structural basis for methyl-CpG recognition by AtMBD6 to develop a deeper understanding how MBD proteins work as mediators of epigenetic signals in plant cells.
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Affiliation(s)
- Yutaka Mahana
- Department
of Molecular Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto 615-8510, Japan
| | - Izuru Ohki
- Institute
for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Erik Walinda
- Graduate
School of Medicine, Kyoto University, Yoshida Konoe-Cho, Sakyo-Ku, Kyoto 606-8501, Japan
| | - Daichi Morimoto
- Department
of Molecular Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto 615-8510, Japan
| | - Kenji Sugase
- Department
of Molecular Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto 615-8510, Japan
| | - Masahiro Shirakawa
- Department
of Molecular Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto 615-8510, Japan
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7
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Wu Z, Chen S, Zhou M, Jia L, Li Z, Zhang X, Min J, Liu K. Family-wide Characterization of Methylated DNA Binding Ability of Arabidopsis MBDs. J Mol Biol 2021; 434:167404. [PMID: 34919920 DOI: 10.1016/j.jmb.2021.167404] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/15/2021] [Accepted: 12/07/2021] [Indexed: 01/28/2023]
Abstract
13 MBD-containing genes (AtMBD1-13) have been identified in Arabidopsis thaliana so far, however, their DNA binding ability is still controversial. Here, we systematically measured the DNA binding affinities of these MBDs by ITC and EMSA binding assays, except for those of pseudogenes AtMBD3 and AtMBD13, and found that only AtMBD6 and AtMBD7 function as methylated DNA readers. We also found that the MBD of AtMBD5 exhibits very weak binding to methylated DNA compared to that of AtMBD6. To further investigate the structural basis of AtMBDs in binding to methylated DNA, we determined the complex structure of the AtMBD6 MBD with a 12mer mCG DNA and the apo structure of the AtMBD5 MBD. Structural analysis coupled with mutagenesis studies indicated that, in addition to the conserved arginine fingers contributing to the DNA binding specificity, the residues located in the loop1 and α1 are also essential for the methylated DNA binding of these MBDs in Arabidopsis thaliana, which explains why AtMBD5 MBD and the other AtMBDs display very weak or no binding to methylated DNA. Thus, our study here systematically demonstrates the DNA binding ability of the MBDs in Arabidopsis thaliana, which also provides a general guideline in understanding the DNA binding ability of the MBDs in other plants as a whole.
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Affiliation(s)
- Zhibin Wu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Sizhuo Chen
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Mengqi Zhou
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Lingbo Jia
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Zhenhua Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Xiyou Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Jinrong Min
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China.
| | - Ke Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China.
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8
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Ichino L, Boone BA, Strauskulage L, Harris CJ, Kaur G, Gladstone MA, Tan M, Feng S, Jami-Alahmadi Y, Duttke SH, Wohlschlegel JA, Cheng X, Redding S, Jacobsen SE. MBD5 and MBD6 couple DNA methylation to gene silencing through the J-domain protein SILENZIO. Science 2021; 372:eabg6130. [PMID: 34083448 PMCID: PMC8639832 DOI: 10.1126/science.abg6130] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 05/20/2021] [Indexed: 01/02/2023]
Abstract
DNA methylation is associated with transcriptional repression of eukaryotic genes and transposons, but the downstream mechanism of gene silencing is largely unknown. Here we describe two Arabidopsis methyl-CpG binding domain proteins, MBD5 and MBD6, that are recruited to chromatin by recognition of CG methylation, and redundantly repress a subset of genes and transposons without affecting DNA methylation levels. These methyl-readers recruit a J-domain protein, SILENZIO, that acts as a transcriptional repressor in loss-of-function and gain-of-function experiments. J-domain proteins often serve as co-chaperones with HSP70s. Indeed, we found that SILENZIO's conserved J-domain motif was required for its interaction with HSP70s and for its silencing function. These results uncover an unprecedented role of a molecular chaperone J-domain protein in gene silencing downstream of DNA methylation.
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Affiliation(s)
- Lucia Ichino
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Brandon A Boone
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Luke Strauskulage
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94143, USA
- Tetrad Graduate Program, University of California San Francisco, San Francisco, CA 94143, USA
| | - C Jake Harris
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Gundeep Kaur
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Matthew A Gladstone
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Maverick Tan
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Suhua Feng
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edyth Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Sascha H Duttke
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - James A Wohlschlegel
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sy Redding
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Steven E Jacobsen
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA.
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edyth Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA
- Howard Hughes Medical Institute (HHMI), UCLA, Los Angeles, CA 90095, USA
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9
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Qu M, Zhang Z, Liang T, Niu P, Wu M, Chi W, Chen ZQ, Chen ZJ, Zhang S, Chen S. Overexpression of a methyl-CpG-binding protein gene OsMBD707 leads to larger tiller angles and reduced photoperiod sensitivity in rice. BMC PLANT BIOLOGY 2021; 21:100. [PMID: 33602126 PMCID: PMC7893954 DOI: 10.1186/s12870-021-02880-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/04/2021] [Indexed: 05/19/2023]
Abstract
BACKGROUND Methyl-CpG-binding domain (MBD) proteins play important roles in epigenetic gene regulation, and have diverse molecular, cellular, and biological functions in plants. MBD proteins have been functionally characterized in various plant species, including Arabidopsis, wheat, maize, and tomato. In rice, 17 sequences were bioinformatically predicted as putative MBD proteins. However, very little is known regarding the function of MBD proteins in rice. RESULTS We explored the expression patterns of the rice OsMBD family genes and identified 13 OsMBDs with active expression in various rice tissues. We further characterized the function of a rice class I MBD protein OsMBD707, and demonstrated that OsMBD707 is constitutively expressed and localized in the nucleus. Transgenic rice overexpressing OsMBD707 displayed larger tiller angles and reduced photoperiod sensitivity-delayed flowering under short day (SD) and early flowering under long day (LD). RNA-seq analysis revealed that overexpression of OsMBD707 led to reduced photoperiod sensitivity in rice and to expression changes in flowering regulator genes in the Ehd1-Hd3a/RFT1 pathway. CONCLUSION The results of this study suggested that OsMBD707 plays important roles in rice growth and development, and should lead to further studies on the functions of OsMBD proteins in growth, development, or other molecular, cellular, and biological processes in rice.
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Affiliation(s)
- Mengyu Qu
- Marine and Agricultural Biotechnology Laboratory, Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
| | - Zhujian Zhang
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Tingmin Liang
- Marine and Agricultural Biotechnology Laboratory, Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
| | - Peipei Niu
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mingji Wu
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
| | - Wenchao Chi
- Marine and Agricultural Biotechnology Laboratory, Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
| | - Zi-Qiang Chen
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
| | - Zai-Jie Chen
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
| | - Shubiao Zhang
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Songbiao Chen
- Marine and Agricultural Biotechnology Laboratory, Institute of Oceanography, Minjiang University, Fuzhou, 350108, China.
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10
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Cheng Y, Cheng L, Cao Q, Zou J, Li X, Ma X, Zhou J, Zhai F, Sun Z, Lan Y, Han L. Heterologous Expression of SvMBD5 from Salix viminalis L. Promotes Flowering in Arabidopsis thaliana L. Genes (Basel) 2020; 11:genes11030285. [PMID: 32156087 PMCID: PMC7140845 DOI: 10.3390/genes11030285] [Citation(s) in RCA: 4] [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: 02/07/2020] [Revised: 02/21/2020] [Accepted: 03/04/2020] [Indexed: 11/23/2022] Open
Abstract
Methyl-CpG-binding domain (MBD) proteins have diverse molecular and biological functions in plants. Most studies of MBD proteins in plants have focused on the model plant Arabidopsis thaliana L. Here we cloned SvMBD5 from the willow Salix viminalis L. by reverse transcription-polymerase chain reaction (RT-PCR) and analyzed the structure of SvMBD5 and its evolutionary relationships with proteins in other species. The coding sequence of SvMBD5 is 645 bp long, encoding a 214 amino acid protein with a methyl-CpG-binding domain. SvMBD5 belongs to the same subfamily as AtMBD5 and AtMBD6 from Arabidopsis. Subcellular localization analysis showed that SvMBD5 is only expressed in the nucleus. We transformed Arabidopsis plants with a 35S::SvMBD5 expression construct to examine SvMBD5 function. The Arabidopsis SvMBD5-expressing line flowered earlier than the wild type. In the transgenic plants, the expression of FLOWERING LOCUS T and CONSTANS significantly increased, while the expression of FLOWERING LOCUS C greatly decreased. In addition, heterologously expressing SvMBD5 in Arabidopsis significantly inhibited the establishment and maintenance of methylation of CHROMOMETHYLASE 3 and METHYLTRANSFERASE 1, as well as their expression, and significantly increased the expression of the demethylation-related genes REPRESSOR OF SILENCING1 and DEMETER-LIKE PROTEIN3. Our findings suggest that SvMBD5 participates in the flowering process by regulating the methylation levels of flowering genes, laying the foundation for further studying the role of SvMBD5 in regulating DNA demethylation.
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Affiliation(s)
- Yunhe Cheng
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100193, China; (Y.C.); (J.Z.); (X.L.); (X.M.); (J.Z.); (Z.S.)
- Beijing Academy of Forestry and Pomology Sciences, Beijing 100093, China; (L.C.); (Q.C.)
| | - Lili Cheng
- Beijing Academy of Forestry and Pomology Sciences, Beijing 100093, China; (L.C.); (Q.C.)
| | - Qingchang Cao
- Beijing Academy of Forestry and Pomology Sciences, Beijing 100093, China; (L.C.); (Q.C.)
| | - Junzhu Zou
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100193, China; (Y.C.); (J.Z.); (X.L.); (X.M.); (J.Z.); (Z.S.)
- Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Beijing 100193, China
| | - Xia Li
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100193, China; (Y.C.); (J.Z.); (X.L.); (X.M.); (J.Z.); (Z.S.)
- Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Beijing 100193, China
- College of Agriculture and Bioengineering, Heze University, Heze 274000, China
| | - Xiaodong Ma
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100193, China; (Y.C.); (J.Z.); (X.L.); (X.M.); (J.Z.); (Z.S.)
- Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Beijing 100193, China
| | - Jingjing Zhou
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100193, China; (Y.C.); (J.Z.); (X.L.); (X.M.); (J.Z.); (Z.S.)
- Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Beijing 100193, China
| | - Feifei Zhai
- School of Architectural and Artistic Design, Henan Polytechnic University, Jiaozuo 454000, China;
| | - Zhenyuan Sun
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100193, China; (Y.C.); (J.Z.); (X.L.); (X.M.); (J.Z.); (Z.S.)
- Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Beijing 100193, China
| | - Yanping Lan
- Beijing Academy of Forestry and Pomology Sciences, Beijing 100093, China; (L.C.); (Q.C.)
- Correspondence: (Y.L.); (L.H.); Tel.: +86-010-827-596-103 (Y.L.); +86-010-62-889-652 (L.H.)
| | - Lei Han
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100193, China; (Y.C.); (J.Z.); (X.L.); (X.M.); (J.Z.); (Z.S.)
- Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Beijing 100193, China
- Correspondence: (Y.L.); (L.H.); Tel.: +86-010-827-596-103 (Y.L.); +86-010-62-889-652 (L.H.)
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11
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Dobrovolska O, Brilkov M, Madeleine N, Ødegård-Fougner Ø, Strømland Ø, Martin SR, De Marco V, Christodoulou E, Teigen K, Isaksson J, Underhaug J, Reuter N, Aalen RB, Aasland R, Halskau Ø. The Arabidopsis (ASHH2) CW domain binds monomethylated K4 of the histone H3 tail through conformational selection. FEBS J 2020; 287:4458-4480. [PMID: 32083791 DOI: 10.1111/febs.15256] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 12/17/2019] [Accepted: 02/20/2020] [Indexed: 12/27/2022]
Abstract
Chromatin post-translational modifications are thought to be important for epigenetic effects on gene expression. Methylation of histone N-terminal tail lysine residues constitutes one of many such modifications, executed by families of histone lysine methyltransferase (HKMTase). One such protein is ASHH2 from the flowering plant Arabidopsis thaliana, equipped with the interaction domain, CW, and the HKMTase domain, SET. The CW domain of ASHH2 is a selective binder of monomethylation at lysine 4 on histone H3 (H3K4me1) and likely helps the enzyme dock correctly onto chromatin sites. The study of CW and related interaction domains has so far been emphasizing lock-key models, missing important aspects of histone-tail CW interactions. We here present an analysis of the ASHH2 CW-H3K4me1 complex using NMR and molecular dynamics, as well as mutation and affinity studies of flexible coils. β-augmentation and rearrangement of coils coincide with changes in the flexibility of the complex, in particular the η1, η3 and C-terminal coils, but also in the β1 and β2 strands and the C-terminal part of the ligand. Furthermore, we show that mutating residues with outlier dynamic behaviour affect the complex binding affinity despite these not being in direct contact with the ligand. Overall, the binding process is consistent with conformational selection. We propose that this binding mechanism presents an advantage when searching for the correct post-translational modification state among the highly modified and flexible histone tails, and also that the binding shifts the catalytic SET domain towards the nucleosome. DATABASES: Structural data are available in the PDB database under the accession code 6QXZ. Resonance assignments for CW42 in its apo- and holo-forms are available in the BMRB database under the accession code 27251.
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Affiliation(s)
- Olena Dobrovolska
- Department of Biological Sciences, University of Bergen, Norway, Bergen
| | - Maxim Brilkov
- Department of Biological Sciences, University of Bergen, Norway, Bergen
| | - Noelly Madeleine
- Department of Biological Sciences, University of Bergen, Norway, Bergen.,Department of Biomedicine, University of Bergen, Norway, Bergen
| | - Øyvind Ødegård-Fougner
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Stephen R Martin
- Structural Biology Science Technology Platform, Francis Crick Institute, London, UK
| | | | | | - Knut Teigen
- Department of Biomedicine, University of Bergen, Norway, Bergen
| | - Johan Isaksson
- Department of Chemistry, The Arctic University of Tromsø, Norway
| | - Jarl Underhaug
- Department of Chemistry, University of Bergen, Norway, Bergen
| | - Nathalie Reuter
- Department of Chemistry, University of Bergen, Norway, Bergen
| | | | - Rein Aasland
- Department of Biosciences, University of Oslo, Norway, Oslo
| | - Øyvind Halskau
- Department of Biological Sciences, University of Bergen, Norway, Bergen
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12
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Sijacic P, Holder DH, Bajic M, Deal RB. Methyl-CpG-binding domain 9 (MBD9) is required for H2A.Z incorporation into chromatin at a subset of H2A.Z-enriched regions in the Arabidopsis genome. PLoS Genet 2019; 15:e1008326. [PMID: 31381567 PMCID: PMC6695207 DOI: 10.1371/journal.pgen.1008326] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 08/15/2019] [Accepted: 07/22/2019] [Indexed: 12/01/2022] Open
Abstract
The SWR1 chromatin remodeling complex, which deposits the histone variant H2A.Z into nucleosomes, has been well characterized in yeast and animals, but its composition in plants has remained uncertain. We used the conserved SWR1 subunit ACTIN RELATED PROTEIN 6 (ARP6) as bait in tandem affinity purification experiments to isolate associated proteins from Arabidopsis thaliana. We identified all 11 subunits found in yeast SWR1 and the homologous mammalian SRCAP complexes, demonstrating that this complex is conserved in plants. We also identified several additional proteins not previously associated with SWR1, including Methyl-CpG-BINDING DOMAIN 9 (MBD9) and three members of the Alfin1-like protein family, all of which have been shown to bind modified histone tails. Since mbd9 mutant plants were phenotypically similar to arp6 mutants, we explored a potential role for MBD9 in H2A.Z deposition. We found that MBD9 is required for proper H2A.Z incorporation at thousands of discrete sites, which represent a subset of the genomic regions normally enriched with H2A.Z. We also discovered that MBD9 preferentially interacts with acetylated histone H4 peptides, as well as those carrying mono- or dimethylated H3 lysine 4, or dimethylated H3 arginine 2 or 8. Considering that MBD9-dependent H2A.Z sites show a distinct histone modification profile, we propose that MBD9 recognizes particular nucleosome modifications via its PHD- and Bromo-domains and thereby guides SWR1 to these sites for H2A.Z deposition. Our data establish the SWR1 complex as being conserved across eukaryotes and suggest that MBD9 may be involved in targeting the complex to specific genomic sites through nucleosomal interactions. The finding that MBD9 does not appear to be a core subunit of the Arabidopsis SWR1 complex, along with the synergistic phenotype of arp6;mbd9 double mutants, suggests that MBD9 also has important roles beyond H2A.Z deposition. The histone H2A variant, H2A.Z, is found in all known eukaryotes and plays important roles in transcriptional regulation. H2A.Z is selectively incorporated into nucleosomes within many genes by the activity of a conserved ATP-dependent chromatin remodeling complex in yeast, insects, and mammals. Whether this complex exists in the same form in plants, and how the complex is targeted to specific genomic locations have remained open questions. In this study we demonstrate that plants do indeed utilize a complex analogous to those of fungi and animals to deposit H2A.Z, and we also identify several new proteins that interact with this complex. We found that one such interactor, Methyl-CpG-BINDING DOMAIN 9 (MBD9), is required for H2A.Z incorporation at thousands of genomic sites that share a distinct histone modification profile. The histone binding properties of MBD9 suggest that it may guide H2A.Z deposition to specific sites by interacting with modified nucleosomes and with the H2A.Z deposition complex. We hypothesize that this represents a general paradigm for the targeting of H2A.Z to specific sites.
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Affiliation(s)
- Paja Sijacic
- Department of Biology, Emory University, Atlanta, GA, United States of America
| | - Dylan H. Holder
- Department of Biology, Emory University, Atlanta, GA, United States of America
- Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, GA, United States of America
| | - Marko Bajic
- Department of Biology, Emory University, Atlanta, GA, United States of America
- Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, GA, United States of America
| | - Roger B. Deal
- Department of Biology, Emory University, Atlanta, GA, United States of America
- * E-mail:
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13
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Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition. Nat Commun 2019; 10:3352. [PMID: 31350403 PMCID: PMC6659704 DOI: 10.1038/s41467-019-11291-w] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 07/05/2019] [Indexed: 11/08/2022] Open
Abstract
Deposition of the histone variant H2A.Z by the SWI2/SNF2-Related 1 chromatin remodeling complex (SWR1-C) is important for gene regulation in eukaryotes, but the composition of the Arabidopsis SWR1-C has not been thoroughly characterized. Here, we aim to identify interacting partners of a conserved Arabidopsis SWR1 subunit ACTIN-RELATED PROTEIN 6 (ARP6). We isolate nine predicted components and identify additional interactors implicated in histone acetylation and chromatin biology. One of the interacting partners, methyl-CpG-binding domain 9 (MBD9), also strongly interacts with the Imitation SWItch (ISWI) chromatin remodeling complex. MBD9 is required for deposition of H2A.Z at a distinct subset of ARP6-dependent loci. MBD9 is preferentially bound to nucleosome-depleted regions at the 5’ ends of genes containing high levels of activating histone marks. These data suggest that MBD9 is a SWR1-C interacting protein required for H2A.Z deposition at a subset of actively transcribing genes. The SWI2/SNF2-Related 1 chromatin remodeling complex (SWR1-C) is important for gene regulation, but its composition remains largely uncharacterized in plants. Here, the authors report that methyl-CpG-binding domain 9 (MBD9) is a SWR1-C interacting protein required for histone H2A.Z deposition in Arabidopsis.
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14
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Parida AP, Sharma A, Sharma AK. AtMBD4: A methylated DNA binding protein negatively regulates a subset of phosphate starvation genes. J Biosci 2019; 44:14. [PMID: 30837365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
DNA methylation is an important epigenetic modification that governs transcriptional regulation. The methylation mark is read by a special class of proteins called methyl-CpG-binding domain proteins. The role of DNA methylation has been found in X-chromosome inactivation, genomic imprinting, transposon silencing, and self-incompatibility. Recently, remodeling of global DNA methylation was demonstrated in Arabidopsis during low phosphate availability. The present study reports that AtMBD4 gene of Arabidopsis negatively regulates phosphate starvation. The T-DNA insertion mutation at the AtMBD4 locus exhibited altered root architecture as compared to wild-type plants. Using microarray hybridization and analysis, an increased transcript accumulation of 242 genes was observed in the mutant. Many of these genes were related to phosphate transporters and transcription factors, involved in phosphate starvation response. Comparison of data of atmbd4 mutant with publicly available microarray data of phosphate starvation response indicated the role of AtMBD4 protein in phosphate starvation response. Further, promoter analysis of up-regulated genes suggested that cis-regulatory elements like MBS, W-box, and B1BS are more prominent in the promoters of up-regulated genes. Upon performing a methylation-specific PCR, a decreased DNA methylation in the promoter regions of up-regulated genes was observed. The accumulation of anthocyanin and inorganic phosphate in the atmbd4 mutant was found to be higher than the wild-type plant. Altered root morphology, up-regulation of phosphate starvation-induced genes in atmbd4 mutant suggests that AtMBD4 negatively regulates the phosphate starvation response.
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15
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AtMBD4: A methylated DNA binding protein negatively regulates a subset of phosphate starvation genes. J Biosci 2019. [DOI: 10.1007/s12038-018-9843-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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16
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Parida AP, Raghuvanshi U, Pareek A, Singh V, Kumar R, Sharma AK. Genome-wide analysis of genes encoding MBD domain-containing proteins from tomato suggest their role in fruit development and abiotic stress responses. Mol Biol Rep 2018; 45:2653-2669. [PMID: 30350236 DOI: 10.1007/s11033-018-4435-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/10/2018] [Indexed: 01/25/2023]
Abstract
In tomato, DNA methylation has an inhibitory effect on fruit ripening. The inhibition of DNA methyltransferase by 5-azacytidine results in premature fruit ripening. Methyl CpG binding domain (MBD) proteins are the readers of DNA methylation marks and help in the recruitment of chromatin-modifying enzymes which affect gene expression. Therefore, we investigate their contribution during fruit development. In this study, we identified and analyzed 18 putative genes of Solanum lycopersicum and Solanum pimpinellifolium encoding MBD proteins. We also identified tomato MBD syntelogs in Capsicum annum and Solanum tuberosum. Sixty-three MBD genes identified from four different species of solanaceae were classified into three groups. An analysis of the conserved domains in these proteins identified additional domains along with MBD motif. The transcript profiling of tomato MBDs in wild-type and two non-ripening mutants, rin and Nr, indicated constructive information regarding their involvement during fruit development. When we performed a stage-specific expression analysis during fruit ripening, a gradual decrease in transcript accumulation in the wild-type fruit was detected. However, a very low expression was observed in the ripening mutants. Furthermore, many ethylene-responsive cis-elements were found in SlMBD gene promoters, and some of them were induced in the presence of exogenous ethylene. Further, we detected the possible role of these MBDs in abiotic stresses. We found that few genes were differentially expressed under various abiotic stress conditions. Our results provide an evidence of the involvement of the tomato MBDs in fruit ripening and abiotic stress responses, which would be helpful in further studies on these genes in tomato fruit ripening.
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Affiliation(s)
- Adwaita Prasad Parida
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Utkarsh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Amit Pareek
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Vijendra Singh
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Rahul Kumar
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India
| | - Arun Kumar Sharma
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India.
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Shi R, Zhang J, Li J, Wang K, Jia H, Zhang L, Wang P, Yin J, Meng F, Li Y. Cloning and characterization of TaMBD6 homeologues encoding methyl-CpG-binding domain proteins in wheat. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 109:1-8. [PMID: 27611240 DOI: 10.1016/j.plaphy.2016.08.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 08/30/2016] [Accepted: 08/31/2016] [Indexed: 06/06/2023]
Abstract
DNA methylation is a major epigenetic marker in plants that plays a crucial role in transcriptional and developmental regulation. The DNA methylation 'code' is thought to be 'read' by a set of proteins containing methyl-CpG-binding domain (MBD). However, little is known about MBD genes in common wheat (Triticum aestivum L.). Here, we report the isolation and characterization of TaMBD6 and its homeologues (TaMBD6_A, TaMBD6_B, and TaMBD6_D) in hexaploid wheat. The cDNA was quite different among the three homeologues and InDel mutations were detected in 5'-UTR and coding region. Two types of TRs (tandem repeats) -- TR1 (57 bp) and TR2 (39 bp) -- occurred in the coding region. TaMBD6_B harbored five copies of TR1 and two copies of TR2. In contrast, TaMBD6_A lacked 30 bp between the 2nd and 3rd copy of TR1, while TaMBD6_D was missing two copies of TR1 but had three copies of TR2. TaMBD6_A, TaMBD6_B, and TaMBD6_D encoded 435, 446, and 420 amino acids, respectively. Structural analysis of TaMBD6 protein indicated that each of the three homeologues had an identical MBD domain at the N-terminal, as well as a typical nuclear localization signal. Although genomics analysis showed that two introns were included, the length of the first intron varied from 3100 bp to 3471 bp and their sequences were very different. Expression analysis demonstrated that the transcription level of TaMBD6 began to increase gradually in developing grains at 15 days after pollination while decreasing significantly in endosperm and embryo tissues during germination. Expression of TaMBD6 appeared to be positively correlated with starch metabolism in the endosperm but was negatively correlated with embryo formation and sprouting. We were also interested to learn that TaMBD6 homeologues were differentially expressed in developing wheat plants and that their expression patterns were variously affected by vernalization treatment. Further investigation revealed that TaMBD6 was induced by prolonged chilling, indicating that the protein is potentially involved in regulating the developmental transition from vegetative to reproductive stages. Although the homeologues generally showed similar differential expression patterns, TaMBD6_D and TaMBD6_B contribute more to the processes of grain development and germination while TaMBD6_A is predominant in mature plants.
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Affiliation(s)
- Ruijie Shi
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China; College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Jiahui Zhang
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China; College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Jingyuan Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Ketao Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Haiying Jia
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Lin Zhang
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Putong Wang
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China; College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Jun Yin
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China; College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Fanrong Meng
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China; College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China.
| | - Yongchun Li
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China; College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China.
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18
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Li Y, Deng H, Miao M, Li H, Huang S, Wang S, Liu Y. Tomato MBD5, a methyl CpG binding domain protein, physically interacting with UV-damaged DNA binding protein-1, functions in multiple processes. THE NEW PHYTOLOGIST 2016; 210:208-26. [PMID: 26551231 DOI: 10.1111/nph.13745] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 10/02/2015] [Indexed: 05/22/2023]
Abstract
In tomato (Solanum lycopersicum), high pigment mutations (hp-1 and hp-2) were mapped to genes encoding UV-damaged DNA binding protein 1 (DDB1) and de-etiolated-1 (DET1), respectively. Here we characterized a tomato methyl-CpG-binding domain protein SlMBD5 identified by yeast two-hybrid screening using SlDDB1 as a bait. Yeast two-hybrid assay demonstrated that the physical interaction of SlMBD5 with SlDDB1 is mediated by the C-termini of SlMBD5 and the β-propeller-C (BPC) of SlDDB1. Co-immunoprecipitation analyses revealed that SlMBD5 associates with SlDDB1-interacting partners including SlDET1, SlCUL4, SlRBX1a and SlRBX1b in vivo. SlMBD5 was shown to target to nucleus and dimerizes via its MBD motif. Electrophoresis mobility shift analysis suggested that the MBD of SlMBD5 specifically binds to methylated CpG dinucleotides but not to methylated CpHpG or CpHpH dinucleotides. SlMBD5 expressed in protoplast is capable of activating transcription of CG islands, whereas CUL4/DDB1 antagonizes this effect. Overexpressing SlMBD5 resulted in diverse developmental alterations including darker green fruits with increased plastid level and elevated pigmentation, as well as enhanced expression of SlGLK2, a key regulator of plastid biogenesis. Taken together, we hypothesize that the physical interaction of SlMBD5 with the CUL4-DDB1-DET1 complex component may affect its binding activity to methylated DNA and subsequently attenuate its transcription activation of downstream genes.
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Affiliation(s)
- Yuxiang Li
- Ministry of education Key Laboratory for Bio-resource and Eco-environment, State key laboratory of Hydraulics and mountain River Engineering, College of Life Science, Sichuan University, Chengdu, 610064, China
| | - Heng Deng
- Ministry of education Key Laboratory for Bio-resource and Eco-environment, State key laboratory of Hydraulics and mountain River Engineering, College of Life Science, Sichuan University, Chengdu, 610064, China
| | - Min Miao
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Huirong Li
- Ministry of education Key Laboratory for Bio-resource and Eco-environment, State key laboratory of Hydraulics and mountain River Engineering, College of Life Science, Sichuan University, Chengdu, 610064, China
| | - Shengxiong Huang
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Songhu Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Yongsheng Liu
- Ministry of education Key Laboratory for Bio-resource and Eco-environment, State key laboratory of Hydraulics and mountain River Engineering, College of Life Science, Sichuan University, Chengdu, 610064, China
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China
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19
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Baute J, Herman D, Coppens F, De Block J, Slabbinck B, Dell'Acqua M, Pè ME, Maere S, Nelissen H, Inzé D. Combined Large-Scale Phenotyping and Transcriptomics in Maize Reveals a Robust Growth Regulatory Network. PLANT PHYSIOLOGY 2016; 170:1848-67. [PMID: 26754667 PMCID: PMC4775144 DOI: 10.1104/pp.15.01883] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 01/07/2016] [Indexed: 05/20/2023]
Abstract
Leaves are vital organs for biomass and seed production because of their role in the generation of metabolic energy and organic compounds. A better understanding of the molecular networks underlying leaf development is crucial to sustain global requirements for food and renewable energy. Here, we combined transcriptome profiling of proliferative leaf tissue with in-depth phenotyping of the fourth leaf at later stages of development in 197 recombinant inbred lines of two different maize (Zea mays) populations. Previously, correlation analysis in a classical biparental mapping population identified 1,740 genes correlated with at least one of 14 traits. Here, we extended these results with data from a multiparent advanced generation intercross population. As expected, the phenotypic variability was found to be larger in the latter population than in the biparental population, although general conclusions on the correlations among the traits are comparable. Data integration from the two diverse populations allowed us to identify a set of 226 genes that are robustly associated with diverse leaf traits. This set of genes is enriched for transcriptional regulators and genes involved in protein synthesis and cell wall metabolism. In order to investigate the molecular network context of the candidate gene set, we integrated our data with publicly available functional genomics data and identified a growth regulatory network of 185 genes. Our results illustrate the power of combining in-depth phenotyping with transcriptomics in mapping populations to dissect the genetic control of complex traits and present a set of candidate genes for use in biomass improvement.
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Affiliation(s)
- Joke Baute
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.); andInstitute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (M.D., M.E.P.)
| | - Dorota Herman
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.); andInstitute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (M.D., M.E.P.)
| | - Frederik Coppens
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.); andInstitute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (M.D., M.E.P.)
| | - Jolien De Block
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.); andInstitute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (M.D., M.E.P.)
| | - Bram Slabbinck
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.); andInstitute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (M.D., M.E.P.)
| | - Matteo Dell'Acqua
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.); andInstitute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (M.D., M.E.P.)
| | - Mario Enrico Pè
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.); andInstitute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (M.D., M.E.P.)
| | - Steven Maere
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.); andInstitute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (M.D., M.E.P.)
| | - Hilde Nelissen
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.); andInstitute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (M.D., M.E.P.)
| | - Dirk Inzé
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (J.B., D.H., F.C., J.D.B., B.S., S.M., H.N., D.I.); andInstitute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (M.D., M.E.P.)
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Questa JI, Rius SP, Casadevall R, Casati P. ZmMBD101 is a DNA-binding protein that maintains Mutator elements chromatin in a repressive state in maize. PLANT, CELL & ENVIRONMENT 2016; 39:174-184. [PMID: 26147461 DOI: 10.1111/pce.12604] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 06/25/2015] [Accepted: 06/26/2015] [Indexed: 06/04/2023]
Abstract
In maize (Zea mays), as well as in other crops, transposable elements (TEs) constitute a great proportion of the genome. Chromatin modifications play a vital role in establishing transposon silencing and perpetuating the acquired repressive state. Nucleosomes associated with TEs are enriched for dimethylation of histone H3 at lysine 9 and 27 (H3K9me2 and H3K27me2, respectively), signals of repressive chromatin. Here, we describe a chromatin protein, ZmMBD101, involved in the regulation of Mutator (Mu) genes in maize. ZmMBD101 is localized to the nucleus and contains a methyl-CpG-binding domain (MBD) and a zinc finger CW (CW) domain. Transgenic lines with reduced levels of ZmMBD101 transcript present enhanced induction of Mu genes when plants are irradiated with UV-B. Chromatin immunoprecipitation analysis with H3K9me2 and H3K27me2 antibodies indicated that ZmMBD101 is required to maintain the levels of these histone repressive marks at Mu terminal inverted repeats (TIRs) under UV-B conditions. Although Mutator inactivity is associated with DNA methylation, cytosine methylation at Mu TIRs is not affected in ZmMBD101 deficient plants. Several plant proteins are predicted to share the simple CW-MBD domain architecture present in ZmMBD101. We hypothesize that plant CW-MBD proteins may also function to protect plant genomes from deleterious transposition.
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Affiliation(s)
- Julia I Questa
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Sebastián P Rius
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Romina Casadevall
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Paula Casati
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
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Nazemof N, Couroux P, Rampitsch C, Xing T, Robert LS. Proteomic profiling reveals insights into Triticeae stigma development and function. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:6069-80. [PMID: 25170101 PMCID: PMC4203142 DOI: 10.1093/jxb/eru350] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
To our knowledge, this study represents the first high-throughput characterization of a stigma proteome in the Triticeae. A total of 2184 triticale mature stigma proteins were identified using three different gel-based approaches combined with mass spectrometry. The great majority of these proteins are described in a Triticeae stigma for the first time. These results revealed many proteins likely to play important roles in stigma development and pollen-stigma interactions, as well as protection against biotic and abiotic stresses. Quantitative comparison of the triticale stigma transcriptome and proteome showed poor correlation, highlighting the importance of having both types of analysis. This work makes a significant contribution towards the elucidation of the Triticeae stigma proteome and provides novel insights into its role in stigma development and function.
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Affiliation(s)
- Nazila Nazemof
- Agriculture and Agri-Food Canada, Eastern Cereal and Oilseed Research Centre, 960 Carling Avenue, Ottawa, ON, Canada K1A 0C6 Carleton University, Department of Biology, 1125 Colonel By Drive, Ottawa, ON, Canada K1S 5B6
| | - Philippe Couroux
- Agriculture and Agri-Food Canada, Eastern Cereal and Oilseed Research Centre, 960 Carling Avenue, Ottawa, ON, Canada K1A 0C6
| | - Christof Rampitsch
- Agriculture and Agri-Food Canada, Cereal Research Centre, 101 Route 100, Morden, MB, Canada R6M 1Y5
| | - Tim Xing
- Carleton University, Department of Biology, 1125 Colonel By Drive, Ottawa, ON, Canada K1S 5B6
| | - Laurian S Robert
- Agriculture and Agri-Food Canada, Eastern Cereal and Oilseed Research Centre, 960 Carling Avenue, Ottawa, ON, Canada K1A 0C6
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22
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Grafi G, Ohad N. Plant Epigenetics: A Historical Perspective. EPIGENETIC MEMORY AND CONTROL IN PLANTS 2013. [DOI: 10.1007/978-3-642-35227-0_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Yaish MW, Colasanti J, Rothstein SJ. The role of epigenetic processes in controlling flowering time in plants exposed to stress. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:3727-35. [PMID: 21633082 DOI: 10.1093/jxb/err177] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Plants interact with their environment by modifying gene expression patterns. One mechanism for this interaction involves epigenetic modifications that affect a number of aspects of plant growth and development. Thus, the epigenome is highly dynamic in response to environmental cues and developmental changes. Flowering is controlled by a set of genes that are affected by environmental conditions through an alteration in their expression pattern. This ensures the production of flowers even when plants are growing under adverse conditions, and thereby enhances transgenerational seed production. In this review recent findings on the epigenetic changes associated with flowering in Arabidopsis thaliana grown under abiotic stress conditions such as cold, drought, and high salinity are discussed. These epigenetic modifications include DNA methylation, histone modifications, and the production of micro RNAs (miRNAs) that mediate epigenetic modifications. The roles played by the phytohormones abscisic acid (ABA) and auxin in chromatin remodelling are also discussed. It is shown that there is a crucial relationship between the epigenetic modifications associated with floral initiation and development and modifications associated with stress tolerance. This relationship is demonstrated by the common epigenetic pathways through which plants control both flowering and stress tolerance, and can be used to identify new epigenomic players.
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Affiliation(s)
- Mahmoud W Yaish
- Department of Biology, College of Science, Sultan Qaboos University, Muscat, Oman.
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Thorstensen T, Grini PE, Aalen RB. SET domain proteins in plant development. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1809:407-20. [PMID: 21664308 DOI: 10.1016/j.bbagrm.2011.05.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Revised: 05/08/2011] [Accepted: 05/10/2011] [Indexed: 10/18/2022]
Abstract
Post-translational methylation of lysine residues on histone tails is an epigenetic modification crucial for regulation of chromatin structure and gene expression in eukaryotes. The majority of the histone lysine methyltransferases (HKMTases) conferring such modifications are proteins with a conserved SET domain responsible for the enzymatic activity. The SET domain proteins in the model plant Arabidopsis thaliana can be assigned to evolutionarily conserved classes with different specificities allowing for different outcomes on chromatin structure. Here we review the present knowledge of the biochemical and biological functions of plant SET domain proteins in developmental processes. This article is part of a Special Issue entitled: Epigenetic control of cellular and developmental processes in plants.
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Affiliation(s)
- Tage Thorstensen
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
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Hoppmann V, Thorstensen T, Kristiansen PE, Veiseth SV, Rahman MA, Finne K, Aalen RB, Aasland R. The CW domain, a new histone recognition module in chromatin proteins. EMBO J 2011; 30:1939-52. [PMID: 21522130 DOI: 10.1038/emboj.2011.108] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Accepted: 03/11/2011] [Indexed: 12/28/2022] Open
Abstract
Post-translational modifications of the N-terminal histone tails, including lysine methylation, have key roles in regulation of chromatin and gene expression. A number of protein modules have been identified that recognize differentially modified histone tails and provide their proteins with the capacity to sense such modifications. Here, we identify the CW domain of plant and animal chromatin-related proteins as a novel module that recognizes different methylated states of lysine 4 on histone H3 (H3K4me). The solution structure of the CW domain of the Arabidopsis ASH1 HOMOLOG2 (ASHH2) histone methyltransferase provides insight into how different CW domains can distinguish different methylated histone tails. We provide evidence that ASHH2 is acting on H3K4me-marked genes, allowing for ASHH2-dependent H3K36 tri-methylation, which contributes to sustained expression of tissue-specific and developmentally regulated genes. This suggests that ASHH2 is a combined 'reader' and 'writer' of the histone code. We propose that different CW domains, dependent on their specificity for different H3K4 methylations, are important for epigenetic memory or participate in switching between permissive and repressive chromatin states.
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Affiliation(s)
- Verena Hoppmann
- Department of Molecular Biology, University of Bergen, Bergen, Norway
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Hu Z, Yu Y, Wang R, Yao Y, Peng H, Ni Z, Sun Q. Expression divergence of TaMBD2 homoeologous genes encoding methyl CpG-binding domain proteins in wheat (Triticum aestivum L.). Gene 2010; 471:13-8. [PMID: 20951189 DOI: 10.1016/j.gene.2010.10.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Revised: 10/03/2010] [Accepted: 10/05/2010] [Indexed: 11/27/2022]
Abstract
Most hexaploid wheat genes are present as triplicate homoeologs derived from the ancestral species. Previously, we isolated six wheat cDNAs with open reading frame, encoding methyl CpG-binding domain proteins (MBDs). In this study, the genomic and cDNA sequences of three TaMBD2 homoeologous genes were obtained and mapped on chromosomes 5A, 5B and 5D, respectively. These sequences showed a very high conservation in the coding region and the exon/intron structure, but the cDNA sequences are distinguishable by a 9-bp insertion in coding region and a size polymorphism in the 3'-untranslated region (UTR). The expression patterns of each homeologous gene in different tissues of various developmental stages and in response to abiotic stress were analyzed by using real-time PCR. Relative mRNA abundance of the three homoeologs varied considerably in different developmental stages from seedling to developing seeds. Most notably, TaMBD2-5B and TaMBD2-5D were highly responsive to salt stress and TaMBD2-5B was specifically upregulated by low temperature in the seedling leaves. These results provide further evidence for the expression variation of genes duplicated in allopolyploids. Moreover, the variation of TaMBD2 homoeologous gene expression in response to environmental stress may enable plants to better cope with stresses in their natural environments.
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Affiliation(s)
- Zhaorong Hu
- Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing 100193, China
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Zhang M, Kimatu JN, Xu K, Liu B. DNA cytosine methylation in plant development. J Genet Genomics 2010; 37:1-12. [PMID: 20171573 DOI: 10.1016/s1673-8527(09)60020-5] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2009] [Revised: 11/15/2009] [Accepted: 11/30/2009] [Indexed: 10/19/2022]
Abstract
Cytosine bases of the nuclear genome in higher plants are often extensively methylated. Cytosine methylation has been implicated in the silencing of both transposable elements (TEs) and endogenous genes, and loss of methylation may have severe functional consequences. The recent methylation profiling of the entire Arabidopsis genome has provided novel insights into the extent and pattern of cytosine methylation and its relationships with gene activity. In addition, the fresh studies also revealed the more dynamic nature of this epigenetic modification across plant development than previously believed. Cytosine methylation of gene promoter regions usually inhibits transcription, but methylation in coding regions (gene-body methylation) does not generally affect gene expression. Active demethylation (though probably act synergistically with passive loss of methylation) of promoters by the 5-methyl cytosine DNA glycosylase or DEMETER (DME) is required for the uni-parental expression of imprinting genes in endosperm, which is essential for seed viability. The opinion that cytosine methylation is indispensible for normal plant development has been reinforced by using single or combinations of diverse loss-of-function mutants for DNA methyltransferases, DNA glycosylases, components involved in siRNA biogenesis and chromatin remodeling factors. Patterns of cytosine methylation in plants are usually faithfully maintained across organismal generations by the concerted action of epigenetic inheritance and progressive correction of strayed patterns. However, some variant methylation patterns may escape from being corrected and hence produce novel epialleles in the affected somatic cells. This, coupled with the unique property of plants to produce germline cells late during development, may enable the newly acquired epialleles to be inherited to future generations, which if visible to selection may contribute to adaptation and evolution.
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Affiliation(s)
- Meishan Zhang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China
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Yaish MWF, Peng M, Rothstein SJ. AtMBD9 modulates Arabidopsis development through the dual epigenetic pathways of DNA methylation and histone acetylation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 59:123-135. [PMID: 19419532 DOI: 10.1111/j.1365-313x.2009.03860.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Mutations within the Arabidopsis METHYL-CpG BINDING DOMAIN 9 gene (AtMBD9) cause pleotropic phenotypes including early flowering and multiple lateral branches. Early flowering was previously attributed to the repression of flowering locus C (FLC) due to a reduction in histone acetylation. However, the reasons for other phenotypic variations remained obscure. Recent studies suggest an important functional correlation between DNA methylation and histone modifications. By investigating this relationship, we found that the global genomic DNA of atmbd9 was over-methylated, including the FLC gene region. Recombinant AtMBD9 does not have detectable DNA demethylation activity in vitro, but instead has histone acetylation activity. Ectopic over-expression of AtMBD9 and transient DNA demethylation promotes flowering and causes partial recovery of the normal branching phenotype. Co-immunoprecipitation assays suggest that AtMBD9 interacts in vivo with some regions of the FLC gene and binds to histone 4 (H4). Gene expression profile analysis revealed earlier up-regulation of some flower-specific transcriptional factors and alteration of potential hormonal and signal transducer axillary branching regulatory genes. In accordance with this result, AtMBD9 itself was found to be localized in the nucleus and expressed in the flower and axillary buds. Together, these results suggest that AtMBD9 controls flowering time and axillary branching by modulating gene expression through DNA methylation and histone acetylation, and reveal another component of the epigenetic mechanism controlling gene expression.
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Affiliation(s)
- Mahmoud W F Yaish
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G2W1, Canada
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Stangeland B, Rosenhave EM, Winge P, Berg A, Amundsen SS, Karabeg M, Mandal A, Bones AM, Grini PE, Aalen RB. AtMBD8 is involved in control of flowering time in the C24 ecotype of Arabidopsis thaliana. PHYSIOLOGIA PLANTARUM 2009; 136:110-26. [PMID: 19374717 DOI: 10.1111/j.1399-3054.2009.01218.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The Arabidopsis thaliana accession C24 is a vernalization-responsive, moderately late flowering ecotype. We report that a mutation in AtMBD8, which encodes a protein with a putative Methyl-CpG-Binding Domain (MBD), in C24 background, results in a delay in flowering time during both long and short days. The atmbd8-1 mutant responded to vernalization as wild type (wt) plants. Consistent with a role in modulation of flowering time, an AtMBD8::GUS-reporter construct was expressed in the shoot meristem region and developing leaves. Full-genome transcriptional profiling revealed very few changes in gene expression between atmbd8-1 and wt plants. The expression level of FLC, the major repressor of transition to flowering, was unchanged in atmbd8-1, and in accordance with that, genes upstream of FLC were unaffected by the mutation. The expression level of CONSTANS, involved in photoperiodic control of flowering, was very similar in atmbd8-1 and wt plants. In contrast, the major promoters of flowering, FT and SOC1, were both downregulated. As FT is a regulator of SOC1, we conclude that AtMBD8 is a novel promoter of flowering that acts upstream of FT in the C24 accession. In contrast to atmbd8-1, the Colombia (Col) SALK T-DNA insertion line, atmbd8-2, did not display a delayed transition to flowering. Transcriptional profiling revealed that a substantial number of genes were differentially expressed between C24 and Col wt seedlings. Several of these genes are also differentially expressed in late flowering mutants. We suggest that these differences contribute to the contrasting effect of a mutation in AtMBD8 in the two ecotypes.
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Affiliation(s)
- Biljana Stangeland
- Department of Molecular Biosciences, University of Oslo, Blindern, N-0316 Oslo, Norway
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Three SRA-domain methylcytosine-binding proteins cooperate to maintain global CpG methylation and epigenetic silencing in Arabidopsis. PLoS Genet 2008; 4:e1000156. [PMID: 18704160 PMCID: PMC2491724 DOI: 10.1371/journal.pgen.1000156] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2008] [Accepted: 07/08/2008] [Indexed: 12/20/2022] Open
Abstract
Methylcytosine-binding proteins decipher the epigenetic information encoded by DNA methylation and provide a link between DNA methylation, modification of chromatin structure, and gene silencing. VARIANT IN METHYLATION 1 (VIM1) encodes an SRA (SET- and RING-associated) domain methylcytosine-binding protein in Arabidopsis thaliana, and loss of VIM1 function causes centromere DNA hypomethylation and centromeric heterochromatin decondensation in interphase. In the Arabidopsis genome, there are five VIM genes that share very high sequence similarity and encode proteins containing a PHD domain, two RING domains, and an SRA domain. To gain further insight into the function and potential redundancy among the VIM proteins, we investigated strains combining different vim mutations and transgenic vim knock-down lines that down-regulate multiple VIM family genes. The vim1 vim3 double mutant and the transgenic vim knock-down lines showed decreased DNA methylation primarily at CpG sites in genic regions, as well as repeated sequences in heterochromatic regions. In addition, transcriptional silencing was released in these plants at most heterochromatin regions examined. Interestingly, the vim1 vim3 mutant and vim knock-down lines gained ectopic CpHpH methylation in the 5S rRNA genes against a background of CpG hypomethylation. The vim1 vim2 vim3 triple mutant displayed abnormal morphological phenotypes including late flowering, which is associated with DNA hypomethylation of the 5' region of FWA and release of FWA gene silencing. Our findings demonstrate that VIM1, VIM2, and VIM3 have overlapping functions in maintenance of global CpG methylation and epigenetic transcriptional silencing.
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The Arabidopsis SET-domain protein ASHR3 is involved in stamen development and interacts with the bHLH transcription factor ABORTED MICROSPORES (AMS). PLANT MOLECULAR BIOLOGY 2007; 66:47-59. [PMID: 17978851 DOI: 10.1007/s11103-007-9251-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2007] [Accepted: 10/04/2007] [Indexed: 12/24/2022]
Abstract
The Arabidopsis thaliana genome contains more than 30 genes encoding SET-domain proteins that are thought to be epigenetic regulators of gene expression and chromatin structure. SET-domain proteins can be divided into subgroups, and members of the Polycomb group (PcG) and trithorax group (trxG) have been shown to be important regulators of development. Both in animals and plants some of these proteins are components of multimeric protein complexes. Here, we have analyzed the Arabidopsis trxG protein ASHR3 which has a SET domain and pre- and post-SET domains similar to that of Ash1 in Drosophila. In addition to the SET domain, a divergent PHD finger is found in the N-terminus of the ASHR3 protein. As expected from SET-domain proteins involved in transcriptional activation, ASHR3 (coupled to GFP) localizes to euchromatin. A yeast two-hybrid screening revealed that the ASHR3 protein interacts with the putative basic helix-loop-helix (bHLH) transcription factor ABORTED MICROSPORES (AMS), which is involved in anther and stamen development in Arabidopsis. Deletion mapping indicated that both the PHD finger and the SET domain mediate the interaction between the two proteins. Overexpression of ASHR3 led in general to growth arrest, and specifically to degenerated anthers and male sterility. Expression analyses demonstrated that ASHR3 like AMS is expressed in the anther and in stamen filaments. We therefore propose that AMS can target ASHR3 to chromatin and regulate genes involved in stamen development and function.
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Grafi G, Zemach A, Pitto L. Methyl-CpG-binding domain (MBD) proteins in plants. ACTA ACUST UNITED AC 2007; 1769:287-94. [PMID: 17407793 DOI: 10.1016/j.bbaexp.2007.02.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2006] [Revised: 02/01/2007] [Accepted: 02/16/2007] [Indexed: 11/18/2022]
Abstract
Cytosine methylation is the most prevalent epigenetic modification of plant nuclear DNA, which occurs in symmetrical CpG or CpNpG as well as in non-symmetrical contexts. Intensive studies demonstrated the central role played by cytosine methylation in genome organization, gene expression and in plant growth and development. However, the way by which the methyl group is interpreted into a functional state has only recently begun to be explored with the isolation and characterization of methylated DNA binding proteins capable of binding 5-methylcytosine. These proteins belong to an evolutionary conserved protein family initially described in animals termed methyl-CpG-binding domain (MBD) proteins. Here, we highlight recent advances and present new prospects concerning plant MBD proteins and their possible role in controlling chromatin structure mediated by CpG methylation.
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Affiliation(s)
- Gideon Grafi
- Albert Katz Department of Dryland Biotechnologies, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion 84990, Israel.
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Zemach A, Grafi G. Methyl-CpG-binding domain proteins in plants: interpreters of DNA methylation. TRENDS IN PLANT SCIENCE 2007; 12:80-5. [PMID: 17208509 DOI: 10.1016/j.tplants.2006.12.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2006] [Revised: 11/06/2006] [Accepted: 12/20/2006] [Indexed: 05/09/2023]
Abstract
The effect of DNA methylation on various aspects of plant cellular and developmental processes has been well documented over the past 35 years. However, the underlying molecular mechanism interpreting the methylation signal has only recently been explored with the isolation and characterization of the Arabidopsis methyl-CpG-binding domain (MBD) proteins. In this review, we highlight recent advances and present new models concerning Arabidopsis MBD proteins and their possible role in controlling chromatin structure mediated by CpG methylation.
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Affiliation(s)
- Assaf Zemach
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
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YANO AIKO, KODAMA YUTAKA, KOIKE AKIKO, SHINYA TOMOTAKA, KIM HYUNJUNG, MATSUMOTO MARI, OGITA SHINJIRO, WADA YUKO, OHAD NIR, SANO HIROSHI. Interaction between methyl CpG-binding protein and ran GTPase during cell division in tobacco cultured cells. ANNALS OF BOTANY 2006; 98:1179-87. [PMID: 17008347 PMCID: PMC3292272 DOI: 10.1093/aob/mcl211] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2006] [Revised: 08/02/2006] [Accepted: 08/21/2006] [Indexed: 05/12/2023]
Abstract
BACKGROUND AND AIMS Methyl CpG-binding proteins are considered to play critical roles in epigenetic control of gene expression by recognizing and interacting with 5-methylcytosine (m(5)C) in eukaryotes. However, among 13 corresponding genes in Arabidopsis thaliana, designated as featuring a methyl-binding domain (MBD), only four have so far been shown actually to bind to m(5)C. One example, AtMBD5, was selected here to screen for interacting proteins. METHODS Yeast two-hybrid assays were used for screening, and physical interaction was confirmed by pull-down and bimolecular fluorescence complementation (BiFC) assays. Cellular localization was analysed by fluorescence-tagged fusion proteins using tobacco (Nicotiana tabacum) cultured bright yellow 2 cells. KEY RESULTS A gene finally identified was found to encode AtRAN3, a protein that belongs to the Ran GTPase family, which plays a critical role in nucleocytoplasmic transport and spindle bipolarization during cell division. AtMBD5 and AtRAN3 were clearly shown to interact in the nucleus by BiFC. On co-expression of AtMBD5-cyan fluorescence protein and yellow fluorescence protein-AtRAN3 in tobacco cells, both localized to the nucleus in the resting stage, migrating to the cytoplasm, primarily around chromatin, during mitosis, particularly at metaphase. CONCLUSIONS These results suggest that AtMBD5 becomes localized to the vicinity of chromosomes with the aid of AtRAN3 during cell division, and may play an important role not only in maintenance of chromatin structures by binding to m(5)C, but also in progress through mitosis by detaching from m(5)C. The present findings also shed light on the physiological function of Ran GTPases, direct target proteins of which have not thus far been well defined, suggesting their key role in chromatin movements in plant cells.
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Affiliation(s)
- AIKO YANO
- Research and Education Center for Genetic Information, Nara Institute of Science and Technology Nara 630-0192, Japan
| | - YUTAKA KODAMA
- Research and Education Center for Genetic Information, Nara Institute of Science and Technology Nara 630-0192, Japan
| | - AKIKO KOIKE
- Research and Education Center for Genetic Information, Nara Institute of Science and Technology Nara 630-0192, Japan
| | - TOMOTAKA SHINYA
- Research and Education Center for Genetic Information, Nara Institute of Science and Technology Nara 630-0192, Japan
| | - HYUN-JUNG KIM
- Research and Education Center for Genetic Information, Nara Institute of Science and Technology Nara 630-0192, Japan
| | - MARI MATSUMOTO
- Research and Education Center for Genetic Information, Nara Institute of Science and Technology Nara 630-0192, Japan
| | - SHINJIRO OGITA
- Biotechnology Research Center, Toyama Prefectural University Toyama 939-0398, Japan
| | - YUKO WADA
- Research and Education Center for Genetic Information, Nara Institute of Science and Technology Nara 630-0192, Japan
| | - NIR OHAD
- Department of Plant Sciences, Tel Aviv University Tel Aviv 69978, Israel
| | - HIROSHI SANO
- Research and Education Center for Genetic Information, Nara Institute of Science and Technology Nara 630-0192, Japan
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Thorstensen T, Fischer A, Sandvik SV, Johnsen SS, Grini PE, Reuter G, Aalen RB. The Arabidopsis SUVR4 protein is a nucleolar histone methyltransferase with preference for monomethylated H3K9. Nucleic Acids Res 2006; 34:5461-70. [PMID: 17020925 PMCID: PMC1636477 DOI: 10.1093/nar/gkl687] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Proteins containing the evolutionarily conserved SET domain are involved in regulation of eukaryotic gene expression and chromatin structure through their histone lysine methyltransferase (HMTase) activity. The Drosophila SU(VAR)3-9 protein and related proteins of other organisms have been associated with gene repression and heterochromatinization. In Arabidopsis there are 10 SUVH and 5 SUVR genes encoding proteins similar to SU(VAR)3-9, and 4 SUVH proteins have been shown to control heterochromatic silencing by its HMTase activity and by directing DNA methylation. The SUVR proteins differ from the SUVH proteins in their domain structure, and we show that the closely related SUVR1, SUVR2 and SUVR4 proteins contain a novel domain at their N-terminus, and a SUVR specific region preceding the SET domain. Green fluorescent protein (GFP)-fusions of these SUVR proteins preferably localize to the nucleolus, suggesting involvement in regulation of rRNA expression, in contrast to other SET-domain proteins studied so far. A novel HMTase specificity was demonstrated for SUVR4, in that monomethylated histone H3K9 is its preferred substrate in vitro.
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Affiliation(s)
| | - Andreas Fischer
- Institute of Genetics, Biologicum, Martin Luther University HalleHalle, Germany
| | | | | | | | - Gunter Reuter
- Institute of Genetics, Biologicum, Martin Luther University HalleHalle, Germany
| | - Reidunn B. Aalen
- To whom correspondence should be addressed. Tel: +47 22857297; Fax: +47 22856041;
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Peng M, Cui Y, Bi YM, Rothstein SJ. AtMBD9: a protein with a methyl-CpG-binding domain regulates flowering time and shoot branching in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2006; 46:282-96. [PMID: 16623890 DOI: 10.1111/j.1365-313x.2006.02691.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The functional characterization of mammalian proteins containing a methyl-CpG-binding domain (MBD) has revealed that MBD proteins can decipher the epigenetic information encoded by DNA methylation, and integrate DNA methylation, modification of chromatin structure and repression of gene expression. The Arabidopsis genome has 13 putative genes encoding MBD proteins, and no specific biological function has been defined for any AtMBD genes. In this study, we identified three T-DNA insertion mutant alleles at the AtMBD9 locus, and found that all of them exhibited obvious developmental abnormalities. First, the atmbd9 mutants flowered significantly earlier than wild-type plants. The expression of FLOWERING LOCUS C (FLC), a major repressor of Arabidopsis flowering, was markedly attenuated by the AtMBD9 mutations. This FLC transcription reduction was associated with a significant decrease in the acetylation level in histone H3 and H4 of FLC chromatin in the atmbd9 mutants. Secondly, the atmbd9 mutants produced more shoot branches by increasing the outgrowth of axillary buds when compared with wild-type plants. The two known major factors controlling the outgrowth of axillary buds in Arabidopsis, auxin and the more axillary growth (MAX) pathway, were found not to be involved in producing this enhanced shoot branching phenotype in atmbd9 mutants, indicating that AtMBD9 may regulate a novel pathway to control shoot branching. This pathway is not related to FLC expression as over-expression of FLC in atmbd9-2 restored its flowering time to one similar to that of the wild type, but did not alter the shoot branching phenotype.
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Affiliation(s)
- Mingsheng Peng
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada N1G 2W1
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Abstract
DNA in plants is highly methylated, containing 5-methylcytosine (m5C) and N6-methyladenine (m6A); m5C is located mainly in symmetrical CG and CNG sequences but it may occur also in other non-symmetrical contexts. m6A but not m5C was found in plant mitochondrial DNA. DNA methylation in plants is species-, tissue-, organelle- and age-specific. It is controlled by phytohormones and changes on seed germination, flowering and under the influence of various pathogens (viral, bacterial, fungal). DNA methylation controls plant growth and development, with particular involvement in regulation of gene expression and DNA replication. DNA replication is accompanied by the appearance of under-methylated, newly formed DNA strands including Okazaki fragments; asymmetry of strand DNA methylation disappears until the end of the cell cycle. A model for regulation of DNA replication by methylation is suggested. Cytosine DNA methylation in plants is more rich and diverse compared with animals. It is carried out by the families of specific enzymes that belong to at least three classes of DNA methyltransferases. Open reading frames (ORF) for adenine DNA methyltransferases are found in plant and animal genomes, and a first eukaryotic (plant) adenine DNA methyltransferase (wadmtase) is described; the enzyme seems to be involved in regulation of the mitochondria replication. Like in animals, DNA methylation in plants is closely associated with histone modifications and it affects binding of specific proteins to DNA and formation of respective transcription complexes in chromatin. The same gene (DRM2) in Arabidopsis thaliana is methylated both at cytosine and adenine residues; thus, at least two different, and probably interdependent, systems of DNA modification are present in plants. Plants seem to have a restriction-modification (R-M) system. RNA-directed DNA methylation has been observed in plants; it involves de novo methylation of almost all cytosine residues in a region of siRNA-DNA sequence identity; therefore, it is mainly associated with CNG and non-symmetrical methylations (rare in animals) in coding and promoter regions of silenced genes. Cytoplasmic viral RNA can affect methylation of homologous nuclear sequences and it maybe one of the feedback mechanisms between the cytoplasm and the nucleus to control gene expression.
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Affiliation(s)
- B F Vanyushin
- Belozersky Institute of Physical and Chemical Biology, Lomonosov Moscow State University, Russia.
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GRANT-DOWNTON RT, DICKINSON HG. Epigenetics and its implications for plant biology. 1. The epigenetic network in plants. ANNALS OF BOTANY 2005; 96:1143-64. [PMID: 16254022 PMCID: PMC4247072 DOI: 10.1093/aob/mci273] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
BACKGROUND Epigenetics has rapidly evolved in the past decade to form an exciting new branch of biology. In modern terms, 'epigenetics' studies molecular pathways regulating how the genes are packaged in the chromosome and expressed, with effects that are heritable between cell divisions and even across generations. CONTEXT Epigenetic mechanisms often conflict with Mendelian models of genetics, and many components of the epigenetic systems in plants appeared anomalous. However, it is now clear that these systems govern how the entire genome operates and evolves. SCOPE In the first part of a two-part review, how epigenetic systems in plants were elucidated is addressed. Also there is a discussion on how the different components of the epigenetic system--regulating DNA methylation, histones and their post-translational modification, and pathways recognizing aberrant transcripts--may work together.
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Chan SWL, Henderson IR, Jacobsen SE. Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat Rev Genet 2005; 6:351-60. [PMID: 15861207 DOI: 10.1038/nrg1601] [Citation(s) in RCA: 678] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
DNA methylation has two essential roles in plants and animals - defending the genome against transposons and regulating gene expression. Recent experiments in Arabidopsis thaliana have begun to address crucial questions about how DNA methylation is established and maintained. One cardinal insight has been the discovery that DNA methylation can be guided by small RNAs produced through RNA-interference pathways. Plants and mammals use a similar suite of DNA methyltransferases to propagate DNA methylation, but plants have also developed a glycosylase-based mechanism for removing DNA methylation, and there are hints that similar processes function in other organisms.
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Affiliation(s)
- Simon W-L Chan
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California 90095, USA
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Springer NM, Kaeppler SM. Evolutionary divergence of monocot and dicot methyl-CpG-binding domain proteins. PLANT PHYSIOLOGY 2005; 138:92-104. [PMID: 15888682 PMCID: PMC1104165 DOI: 10.1104/pp.105.060566] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The covalent modification of eukaryotic DNA by methylation of the 5' carbon of cytosine residues is frequently associated with transcriptional silencing. In mammals, a potential mechanism for transducing DNA methylation patterns into altered transcription levels occurs via binding of methyl-CpG-binding domain (MBD) proteins. Mammalian MBD-containing proteins bind specifically to methylated DNA and recruit chromatin-modifying complexes containing histone deacetylase activities. Sequence similarity searches reveal the presence of multiple proteins in plants containing a putative MBD. Outside of the MBD itself, there is no sequence relationship between plant and mammalian MBD proteins. The plant MBD proteins can be divided into eight classes based on sequence similarity and phylogenetic analyses of sequences obtained from two complete genomes (rice [Oryza sativa] and Arabidopsis [Arabidopsis thaliana]) and from maize (Zea mays). Two classes of MBD proteins are only represented in dicot species. The striking divergence of plant and animal MBD-containing proteins is in stark contrast to the amino acid conservation of DNA methyltransferases across plants, animals, and fungi. This observation suggests the possibility that while plants and mammals have retained similar mechanisms for the establishment and maintenance of DNA methylation patterns, they may have evolved distinct mechanisms for the interpretation of these patterns.
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Affiliation(s)
- Nathan M Springer
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin 53706, USA.
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Zemach A, Li Y, Wayburn B, Ben-Meir H, Kiss V, Avivi Y, Kalchenko V, Jacobsen SE, Grafi G. DDM1 binds Arabidopsis methyl-CpG binding domain proteins and affects their subnuclear localization. THE PLANT CELL 2005; 17:1549-58. [PMID: 15805479 PMCID: PMC1091773 DOI: 10.1105/tpc.105.031567] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2005] [Accepted: 03/14/2005] [Indexed: 05/21/2023]
Abstract
Methyl-CpG binding domain (MBD) proteins in Arabidopsis thaliana bind in vitro methylated CpG sites. Here, we aimed to characterize the binding properties of AtMBDs to chromatin in Arabidopsis nuclei. By expressing in wild-type cells AtMBDs fused to green fluorescent protein (GFP), we showed that AtMBD7 was evenly distributed at all chromocenters, whereas AtMBD5 and 6 showed preference for two perinucleolar chromocenters adjacent to nucleolar organizing regions. AtMBD2, previously shown to be incapable of binding in vitro-methylated CpG, was dispersed within the nucleus, excluding chromocenters and the nucleolus. Recruitment of AtMBD5, 6, and 7 to chromocenters was disrupted in ddm1 and met1 mutant cells, where a significant reduction in cytosine methylation occurs. In these mutant cells, however, AtMBD2 accumulated at chromocenters. No effect on localization was observed in the chromomethylase3 mutant showing reduced CpNpG methylation or in kyp-2 displaying a reduction in Lys 9 histone H3 methylation. Transient expression of DDM1 fused to GFP showed that DDM1 shares common sites with AtMBD proteins. Glutathione S-transferase pull-down assays demonstrated that AtMBDs bind DDM1; the MBD motif was sufficient for this interaction. Our results suggest that the subnuclear localization of AtMBD is not solely dependent on CpG methylation; DDM1 may facilitate localization of AtMBDs at specific nuclear domains.
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Affiliation(s)
- Assaf Zemach
- Department of Plant Sciences, Weizman Institute of Science, Rehovot 76100, Israel
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Abstract
During the development of a multicellular organism, cell differentiation involves activation and repression of transcription programs that must be stably maintained during subsequent cell divisions. Chromatin remodeling plays a crucial role in regulating chromatin states that conserve transcription programs and provide a mechanism for chromatin states to be maintained as cells proliferate, a process referred to as epigenetic inheritance. A large number of factors and protein complexes are now known to be involved in regulating the dynamic states of chromatin structure. Their biological functions and molecular mechanisms are beginning to be revealed.
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Affiliation(s)
- Tzung-Fu Hsieh
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102, USA.
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