110 results on '"Jiamu Du"'
Search Results
2. A histone H3K4me1-specific binding protein is required for siRNA accumulation and DNA methylation at a subset of loci targeted by RNA-directed DNA methylation
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Qingfeng Niu, Zhe Song, Kai Tang, Lixian Chen, Lisi Wang, Ting Ban, Zhongxin Guo, Chanhong Kim, Heng Zhang, Cheng-Guo Duan, Huiming Zhang, Jian-Kang Zhu, Jiamu Du, and Zhaobo Lang
- Subjects
Science - Abstract
In plants, RNA-directed DNA methylation (RdDM) is a de novo DNA methylation pathway that is responsible for transcriptional silencing of repetitive elements. Here, the authors characterized a new RdDM factor, RDM15, and show that it is required for RdDM-dependent DNA methylation and siRNA accumulation at a subset of RdDM target loci.
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- 2021
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3. A SYBR Gold-based Label-free in vitro Dicing Assay
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Qian Wang, Yan Xue, Laixing Zhang, Zhenhui Zhong, Suhua Feng, Changshi Wang, Lifan Xiao, Zhenlin Yang, C. Harris, Zhe Wu, Jixian Zhai, Maojun Yang, Sisi Li, Steven Jacobsen, and Jiamu Du
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Biology (General) ,QH301-705.5 - Abstract
In Arabidopsis, DICER-LIKE PROTEIN 3 (DCL3) cuts the substrate pre-siRNA into a product siRNA duplex, encompassing one 23-nt strand and one 24-nt strand. To monitor the separation of the siRNA duplex with only 1-nt difference, we developed this protocol to evaluate the in vitro dicing activity of DCL3. The method can be applied for measuring the lengths of single-stranded RNA separated through denaturing urea polyacrylamide gel electrophoresis (urea PAGE), which are visualized by a label-free fluorescence SYBR Gold, and quantified in a multi-function imager. This label-free method is easy to conduct, has low cost, and lacks the hazard of the traditional radio-labeled method. This method can also be adapted to the other Dicers and small RNAs.
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- 2022
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4. Coupling of H3K27me3 recognition with transcriptional repression through the BAH-PHD-CPL2 complex in Arabidopsis
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Yi-Zhe Zhang, Jianlong Yuan, Lingrui Zhang, Chunxiang Chen, Yuhua Wang, Guiping Zhang, Li Peng, Si-Si Xie, Jing Jiang, Jian-Kang Zhu, Jiamu Du, and Cheng-Guo Duan
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Science - Abstract
Histone 3 Lys 27 trimethylation (H3K27me3) mediates epigenetic silencing of gene expression. Here, Zhang et al. show that in Arabidopsis, the BAH-domain H3K27me3-reader protein AIPP3 forms a complex with PHD proteins and CPL2, a plant-specific Pol II phosphatase, to inhibit Pol II activity by dephosphorylation.
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- 2020
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5. The Arabidopsis H3K27me3 demethylase JUMONJI 13 is a temperature and photoperiod dependent flowering repressor
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Shuzhi Zheng, Hongmiao Hu, Huimin Ren, Zhenlin Yang, Qi Qiu, Weiwei Qi, Xinye Liu, Xiaomei Chen, Xiekui Cui, Sisi Li, Bing Zhou, Daye Sun, Xiaofeng Cao, and Jiamu Du
- Subjects
Science - Abstract
Jumonji domain-containing histone demethylases regulate flowering in plants. Here Zheng et al. show that Arabidopsis JMJ13 is an H3K27me3 demethylase that recognizes H3K27me3 via hydrogen bonding and hydrophobic interactions and affects both photoperiod and temperature-dependent flowering responses.
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- 2019
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6. Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin
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Cuijun Zhang, Xuan Du, Kai Tang, Zhenlin Yang, Li Pan, Peipei Zhu, Jinyan Luo, Yuwei Jiang, Hui Zhang, Huafang Wan, Xingang Wang, Fengkai Wu, W. Andy Tao, Xin-Jian He, Heng Zhang, Ray A. Bressan, Jiamu Du, and Jian-Kang Zhu
- Subjects
Science - Abstract
DNA methylation and H3K9 dimethylation are two linked epigenetic marks of silenced chromatin in plants that depend on the activity of CMT3/2 and SUVH4/5/6. Here the authors identify AGDP1 as an H3K9me2-binding protein required for heterochromatic non-CG DNA methylation, H3K9 dimethylation, and transcriptional silencing.
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- 2018
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7. Dual recognition of H3K4me3 and H3K27me3 by a plant histone reader SHL
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Shuiming Qian, Xinchen Lv, Ray N. Scheid, Li Lu, Zhenlin Yang, Wei Chen, Rui Liu, Melissa D. Boersma, John M. Denu, Xuehua Zhong, and Jiamu Du
- Subjects
Science - Abstract
Histone mark reader proteins bind to particular histone modifications and regulate chromatin state. Here, Qian et al. show that the SHORT LIFE reader has a unique ability to recognize both activating and repressive histone marks and that these interactions enable SHORT LIFE to repress flowering in plants.
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- 2018
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8. Combining chemical and genetic approaches to increase drought resistance in plants
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Min-Jie Cao, Yu-Lu Zhang, Xue Liu, Huan Huang, X. Edward Zhou, Wen-Long Wang, Ai Zeng, Chun-Zhao Zhao, Tong Si, Jiamu Du, Wen-Wu Wu, Fu-Xing Wang, H. Eric Xu, and Jian-Kang Zhu
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Science - Abstract
Plants respond to abiotic stress via the phytohormone ABA. Here, Cao et al. report a series of new ABA receptor agonists, named AMFs, which have higher receptor-binding affinities and show that, when employed in tandem with ABA receptor overexpression, can significantly increase drought resistance
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- 2017
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9. Cofactor-assisted dicing: insights from structural snapshots
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Jiamu Du and Dinshaw J. Patel
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Cell Biology ,Molecular Biology - Published
- 2023
10. Structure and mechanism of the plant RNA polymerase V
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Guohui Xie, Xuan Du, Hongmiao Hu, Sisi Li, Xiaofeng Cao, Steven E. Jacobsen, and Jiamu Du
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Multidisciplinary ,Article - Abstract
In addition to the conserved RNA polymerases I to III (Pols I to III) in eukaryotes, two atypical polymerases, Pols IV and V, specifically produce noncoding RNA in the RNA-directed DNA methylation pathway in plants. Here, we report on the structures of cauliflower Pol V in the free and elongation conformations. A conserved tyrosine residue of NRPE2 stacks with a double-stranded DNA branch of the transcription bubble to potentially attenuate elongation by inducing transcription stalling. The nontemplate DNA strand is captured by NRPE2 to enhance backtracking, thereby increasing 3′-5′ cleavage, which likely underpins Pol V’s high fidelity. The structures also illuminate the mechanism of Pol V transcription stalling and enhanced backtracking, which may be important for Pol V’s retention on chromatin to serve its function in tethering downstream factors for RNA-directed DNA methylation.
- Published
- 2023
11. Molecular basis of the plant ROS1-mediated active DNA demethylation
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Xuan Du, Zhenlin Yang, Guohui Xie, Changshi Wang, Laixing Zhang, Kaige Yan, Maojun Yang, Sisi Li, Jian-Kang Zhu, and Jiamu Du
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Plant Science - Published
- 2023
12. The H3K9me2‐binding protein AGDP3 limits DNA methylation and transcriptional gene silencing in Arabidopsis
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Xuelin Zhou, Mengwei Wei, Wenfeng Nie, Yue Xi, Li Peng, Qijie Zheng, Kai Tang, Viswanathan Satheesh, Yuhua Wang, Jinyan Luo, Xuan Du, Rui Liu, Zhenlin Yang, Honggui La, Yingli Zhong, Yu Yang, Jian‐Kang Zhu, Jiamu Du, and Mingguang Lei
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Arabidopsis Proteins ,Proto-Oncogene Proteins ,Arabidopsis ,Nuclear Proteins ,Gene Silencing ,DNA ,Plant Science ,DNA Methylation ,Protein-Tyrosine Kinases ,Carrier Proteins ,Biochemistry ,General Biochemistry, Genetics and Molecular Biology - Abstract
DNA methylation, a conserved epigenetic mark, is critical for tuning temporal and spatial gene expression. The Arabidopsis thaliana DNA glycosylase/lyase REPRESSOR OF SILENCING 1 (ROS1) initiates active DNA demethylation and is required to prevent DNA hypermethylation at thousands of genomic loci. However, how ROS1 is recruited to specific loci is not well understood. Here, we report the discovery of Arabidopsis AGENET Domain Containing Protein 3 (AGDP3) as a cellular factor that is required to prevent gene silencing and DNA hypermethylation. AGDP3 binds to H3K9me2 marks in its target DNA via its AGD12 cassette. Analysis of the crystal structure of the AGD12 cassette of AGDP3 in complex with an H3K9me2 peptide revealed that dimethylated H3K9 and unmodified H3K4 are specifically anchored into two different surface pockets. A histidine residue located in the methyllysine binding aromatic cage provides AGDP3 with pH-dependent H3K9me2 binding capacity. Our results uncover a molecular mechanism for the regulation of DNA demethylation by the gene silencing mark H3K9me2.
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- 2022
13. Progressive chromatin silencing of ABA biosynthesis genes permits seed germination in Arabidopsis
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Deyue Yang, Fengli Zhao, Danling Zhu, Xi Chen, Xiangxiong Kong, Yufeng Wu, Min Chen, Jiamu Du, Li-Jia Qu, and Zhe Wu
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Arabidopsis Proteins ,Gene Expression Regulation, Plant ,Seeds ,Germination ,Cell Biology ,Plant Science ,Research Articles ,Chromatin ,Abscisic Acid - Abstract
Seed germination represents a major developmental switch in plants that is vital to agriculture, but how this process is controlled at the chromatin level remains obscure. Here we demonstrate that successful germination in Arabidopsis thaliana requires a chromatin mechanism that progressively silences 9-CIS-EPOXYCAROTENOID DIOXYGENASE 6 (NCED6), which encodes a rate-limiting enzyme in abscisic acid (ABA) biosynthesis, through the cooperative action of the RNA-binding protein RZ-1 and the polycomb repressive complex 2 (PRC2). Simultaneous inactivation of RZ-1 and PRC2 blocked germination and synergistically derepressed NCEDs and hundreds of genes. At NCED6, in part by promoting H3 deacetylation and suppressing H3K4me3, RZ-1 facilitates transcriptional silencing and also an H3K27me3 accumulation process that occurs during seed germination and early seedling growth. Genome-wide analysis revealed that RZ-1 is preferentially required for transcriptional silencing of many PRC2 targets early during seed germination, when H3K27me3 is not yet established. We propose RZ-1 confers a novel silencing mechanism to compensate for and synergize with PRC2. Our work highlights the progressive chromatin silencing of ABA biosynthesis genes via the RNA-binding protein RZ-1 and PRC2 acting in synergy, a process that is vital for seed germination.
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- 2022
14. Molecular basis of CONSTANS oligomerization in FLOWERING LOCUS T activation
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Xiaolin Zeng, Xinchen Lv, Rui Liu, Hang He, Shiqi Liang, Lixian Chen, Fan Zhang, Liu Chen, Yuehui He, and Jiamu Du
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DNA-Binding Proteins ,Arabidopsis Proteins ,Gene Expression Regulation, Plant ,Photoperiod ,Arabidopsis ,Flowers ,Plant Science ,Biochemistry ,General Biochemistry, Genetics and Molecular Biology - Abstract
The transcription factor CONSTANS (CO) integrates day-length information to induce the expression of florigen FLOWERING LOCUS T (FT) in Arabidopsis. We recently reported that the C-terminal CCT domain of CO forms a complex with NUCLEAR FACTOR-YB/YC to recognize multiple cis-elements in the FT promoter, and the N-terminal tandem B-box domains form a homomultimeric assembly. However, the mechanism and biological function of CO multimerization remained unclear. Here, we report that CO takes on a head-to-tail oligomeric configuration via its B-boxes to mediate FT activation in long days. The crystal structure of B-boxes
- Published
- 2022
15. Structure of plant RNA-DEPENDENT RNA POLYMERASE 2, an enzyme involved in small interfering RNA production
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Xuan Du, Zhenlin Yang, Alfredo Jose Florez Ariza, Qian Wang, Guohui Xie, Sisi Li, and Jiamu Du
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Arabidopsis Proteins ,Arabidopsis ,Cell Biology ,Plant Science ,Breakthrough Report ,RNA, Small Interfering ,RNA-Dependent RNA Polymerase ,Zea mays ,RNA, Double-Stranded - Abstract
In plants, the biogenesis of small interfering RNA (siRNA) requires a family of RNA-dependent RNA polymerases that convert single-stranded RNA (ssRNA) into double-stranded RNA (dsRNA), which is subsequently cleaved into defined lengths by Dicer endonucleases. Here, we determined the structure of maize (Zea mays) RNA-DEPENDENT RNA POLYMERASE 2 (ZmRDR2) in the closed and open conformations. The core catalytic region of ZmRDR2 possesses the canonical DNA-dependent RNA polymerase (DdRP) catalytic sites, pointing to a shared RNA production mechanism between DdRPs and plant RDR-family proteins. Apo-ZmRDR2 adopts a highly compact structure, representing an inactive closed conformation. By contrast, adding RNA induced a significant conformational change in the ZmRDR2 Head domain that opened the RNA binding tunnel, suggesting this is an active elongation conformation of ZmRDR2. Overall, our structural studies trapped both the active and inactive conformations of ZmRDR2, providing insights into the molecular mechanism of dsRNA synthesis during plant siRNA production.
- Published
- 2022
16. Mechanistic insight into the chromatin retention of plant RNA polymerase V
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Xuan Du and Jiamu Du
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Multidisciplinary - Published
- 2023
17. Mechanism of siRNA production by a plant Dicer-RNA complex in dicing-competent conformation
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Laixing Zhang, Steven E. Jacobsen, Jiamu Du, Zhe Wu, C. Jake Harris, Sisi Li, Zhenhui Zhong, Qian Wang, Maojun Yang, Changshi Wang, Zhenlin Yang, Suhua Feng, Jixian Zhai, Yan Xue, and Lifan Xiao
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Models, Molecular ,Ribonuclease III ,Protein Conformation ,Arabidopsis ,Article ,Protein Domains ,Phosphorylation ,RNA, Small Interfering ,Multidisciplinary ,biology ,Arabidopsis Proteins ,Chemistry ,Mechanism (biology) ,Cryoelectron Microscopy ,RNA ,Cell biology ,enzymes and coenzymes (carbohydrates) ,Mutagenesis ,RNA, Plant ,Transfer RNA ,biology.protein ,Nucleic Acid Conformation ,Wafer dicing ,Biogenesis ,Protein Binding ,Dicer - Abstract
In eukaryotes, small RNAs (sRNAs) play critical roles in multiple biological processes. Dicer endonucleases are a central part of sRNA biogenesis. In plants, DICER-LIKE PROTEIN 3 (DCL3) produces 24-nucleotide (nt) small interfering RNAs (siRNAs) that determine the specificity of the RNA-directed DNA methylation pathway. Here, we determined the structure of a DCL3–pre-siRNA complex in an active dicing-competent state. The 5′-phosphorylated A1 of the guide strand and the 1-nt 3′ overhang of the complementary strand are specifically recognized by a positively charged pocket and an aromatic cap, respectively. The 24-nt siRNA length dependence relies on the separation between the 5′-phosphorylated end of the guide RNA and dual cleavage sites formed by the paired ribonuclease III domains. These structural studies, complemented by functional data, provide insight into the dicing principle for Dicers in general.
- Published
- 2021
18. Molecular basis of locus-specific H3K9 methylation catalyzed by SUVH6 in plants
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Jian Zhang, Jianlong Yuan, Juncheng Lin, Lixian Chen, Li-Yuan You, Shuling Chen, Li Peng, Chun-Han Wang, Jiamu Du, and Cheng-Guo Duan
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Multidisciplinary - Abstract
Dimethylated histone H3 Lys9 (H3K9me2) is a conserved heterochromatic mark catalyzed by SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG (SUVH) methyltransferases in plants. However, the mechanism underlying the locus specificity of SUVH enzymes has long been elusive. Here, we show that a conserved N-terminal motif is essential for SUVH6-mediated H3K9me2 deposition in planta. The SUVH6 N-terminal peptide can be recognized by the bromo-adjacent homology (BAH) domain of the RNA- and chromatin-binding protein ANTI-SILENCING 1 (ASI1), which has been shown to function in a complex to confer gene expression regulation. Structural data indicate that a classic aromatic cage of ASI1-BAH domain specifically recognizes an arginine residue of SUVH6 through extensive hydrogen bonding interactions. A classic aromatic cage of ASI1 specifically recognizes an arginine residue of SUVH6 through extensive cation-π interactions, playing a key role in recognition. The SUVH6-ASI1 module confers locus-specific H3K9me2 deposition at most SUVH6 target loci and gives rise to distinct regulation of gene expression depending on the target loci, either conferring transcriptional silencing or posttranscriptional processing of mRNA. More importantly, such mechanism is conserved in multiple plant species, indicating a coordinated evolutionary process between SUVH6 and ASI1. In summary, our findings uncover a conserved mechanism for the locus specificity of H3K9 methylation in planta. These findings provide mechanistic insights into the delicate regulation of H3K9 methylation homeostasis in plants.
- Published
- 2022
19. A histone H3K4me1-specific binding protein is required for siRNA accumulation and DNA methylation at a subset of loci targeted by RNA-directed DNA methylation
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Heng Zhang, Lisi Wang, Cheng-Guo Duan, Chanhong Kim, Ting Ban, Zhe Song, Huiming Zhang, Zhongxin Guo, Jian-Kang Zhu, Jiamu Du, Zhaobo Lang, Kai Tang, Qingfeng Niu, and Lixian Chen
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0301 basic medicine ,Tudor domain ,Protein Conformation ,Science ,Arabidopsis ,General Physics and Astronomy ,Methylation ,General Biochemistry, Genetics and Molecular Biology ,Article ,Histones ,03 medical and health sciences ,Methyllysine ,chemistry.chemical_compound ,0302 clinical medicine ,Gene Expression Regulation, Plant ,RNA, Small Interfering ,RNA-Directed DNA Methylation ,Regulation of gene expression ,Multidisciplinary ,DNA methylation ,biology ,Whole Genome Sequencing ,Chemistry ,Arabidopsis Proteins ,Lysine ,General Chemistry ,DNA-Directed RNA Polymerases ,Plants, Genetically Modified ,Chromatin ,Cell biology ,030104 developmental biology ,Histone ,biology.protein ,Chromatin Immunoprecipitation Sequencing ,RNA Interference ,Structural biology ,030217 neurology & neurosurgery ,DNA ,Protein Binding - Abstract
In plants, RNA-directed DNA methylation (RdDM) is a well-known de novo DNA methylation pathway that involves two plant-specific RNA polymerases, Pol IV and Pol V. In this study, we discovered and characterized an RdDM factor, RDM15. Through DNA methylome and genome-wide siRNA analyses, we show that RDM15 is required for RdDM-dependent DNA methylation and siRNA accumulation at a subset of RdDM target loci. We show that RDM15 contributes to Pol V-dependent downstream siRNA accumulation and interacts with NRPE3B, a subunit specific to Pol V. We also show that the C-terminal tudor domain of RDM15 specifically recognizes the histone 3 lysine 4 monomethylation (H3K4me1) mark. Structure analysis of RDM15 in complex with the H3K4me1 peptide showed that the RDM15 tudor domain specifically recognizes the monomethyllysine through an aromatic cage and a specific hydrogen bonding network; this chemical feature-based recognition mechanism differs from all previously reported monomethyllysine recognition mechanisms. RDM15 and H3K4me1 have similar genome-wide distribution patterns at RDM15-dependent RdDM target loci, establishing a link between H3K4me1 and RDM15-mediated RdDM in vivo. In summary, we have identified and characterized a histone H3K4me1-specific binding protein as an RdDM component, and structural analysis of RDM15 revealed a chemical feature-based lower methyllysine recognition mechanism., In plants, RNA-directed DNA methylation (RdDM) is a de novo DNA methylation pathway that is responsible for transcriptional silencing of repetitive elements. Here, the authors characterized a new RdDM factor, RDM15, and show that it is required for RdDM-dependent DNA methylation and siRNA accumulation at a subset of RdDM target loci.
- Published
- 2021
20. Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1.
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Julie A. Law, Jiamu Du, Christopher J. Hale, Suhua Feng, Krzysztof Krajewski 0002, Ana Marie S. Palanca, Brian D. Strahl, Dinshaw J. Patel, and Steven E. Jacobsen
- Published
- 2013
- Full Text
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21. Dysfunction of histone demethylase IBM1 in Arabidopsis causes autoimmunity and reshapes the root microbiome
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Suhui Lv, Yu Yang, Gang Yu, Li Peng, Shuai Zheng, Sunil Kumar Singh, Juan Ignacio Vílchez, Richa Kaushal, Hailing Zi, Dian Yi, Yuhua Wang, Shaofan Luo, Xiaoxuan Wu, Ziwei Zuo, Weichang Huang, Renyi Liu, Jiamu Du, Alberto P. Macho, Kai Tang, and Huiming Zhang
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Histone Demethylases ,Jumonji Domain-Containing Histone Demethylases ,Arabidopsis Proteins ,Microbiota ,Arabidopsis ,Pseudomonas syringae ,Autoimmunity ,DNA ,DNA Methylation ,Microbiology ,Epigenesis, Genetic ,Soil ,Gene Expression Regulation, Plant ,Mutation ,Salicylic Acid ,Ecology, Evolution, Behavior and Systematics ,Plant Diseases - Abstract
Root microbiota is important for plant growth and fitness. Little is known about whether and how the assembly of root microbiota may be controlled by epigenetic regulation, which is crucial for gene transcription and genome stability. Here we show that dysfunction of the histone demethylase IBM1 (INCREASE IN BONSAI METHYLATION 1) in Arabidopsis thaliana substantially reshaped the root microbiota, with the majority of the significant amplicon sequence variants (ASVs) being decreased. Transcriptome analyses of plants grown in soil and in sterile growth medium jointly disclosed salicylic acid (SA)-mediated autoimmunity and production of the defense metabolite camalexin in the ibm1 mutants. Analyses of genome-wide histone modifications and DNA methylation highlighted epigenetic modifications permissive for transcription at several important defense regulators. Consistently, ibm1 mutants showed increased resistance to the pathogen Pseudomonas syringae DC3000 with stronger immune responses. In addition, ibm1 showed substantially impaired plant growth promotion in response to beneficial bacteria; the impairment was partially mimicked by exogenous application of SA to wild-type plants, and by a null mutation of AGP19 that is important for cell expansion and that is repressed with DNA hypermethylation in ibm1. IBM1-dependent epigenetic regulation imposes strong and broad impacts on plant-microbe interactions and thereby shapes the assembly of root microbiota.
- Published
- 2022
22. Structure and mechanism of histone methylation dynamics in Arabidopsis
- Author
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Hongmiao Hu and Jiamu Du
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Histones ,Arabidopsis Proteins ,Arabidopsis ,Plant Science ,Methylation ,Chromatin - Abstract
Histone methylation plays a central role in regulating chromatin state and gene expression in Arabidopsis and is involved in a variety of physiological and developmental processes. Dynamic regulation of histone methylation relies on both histone methyltransferase "writer" and histone demethylases "eraser" proteins. In this review, we focus on the four major histone methylation modifications in Arabidopsis H3, H3K4, H3K9, H3K27, and H3K36, and summarize current knowledge of the dynamic regulation of these modifications, with an emphasis on the biochemical and structural perspectives of histone methyltransferases and demethylases.
- Published
- 2022
23. Acetylproteomics analyses reveal critical features of lysine-ε-acetylation in Arabidopsis and a role of 14-3-3 protein acetylation in alkaline response
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Jianfei Guo, Xiaoqiang Chai, Yuchao Mei, Jiamu Du, Haining Du, Huazhong Shi, Jian-Kang Zhu, and Heng Zhang
- Abstract
Lysine-ε-acetylation (Kac) is a post-translational modification (PTM) that is critical for metabolic regulation and cell signaling in mammals. However, its prevalence and importance in plants remain to be determined. Employing high-resolution tandem mass spectrometry, we analyzed protein lysine acetylation in five representative Arabidopsis organs with 2 ~ 3 biological replicates per organ. A total of 2887 Kac proteins and 5929 Kac sites were identified. This comprehensive catalog allows us to analyze proteome-wide features of lysine acetylation. We found that Kac proteins tend to be more uniformly expressed in different organs, and the acetylation status exhibits little correlation with the gene expression level, indicating that acetylation is unlikely caused by stochastic processes. Kac preferentially targets evolutionarily conserved proteins and lysine residues, but only a small percentage of Kac proteins are orthologous between rat and Arabidopsis. A large portion of Kac proteins overlap with proteins modified by other PTMs including ubiquitination, SUMOylation and phosphorylation. Although acetylation, ubiquitination and SUMOylation all modify lysine residues, our analyses show that they rarely target the same sites. In addition, we found that “reader” proteins for acetylation and phosphorylation, i.e., bromodomain-containing proteins and GRF (General Regulatory Factor)/14-3-3 proteins, are intensively modified by the two PTMs, suggesting that they are main crosstalk nodes between acetylation and phosphorylation signaling. Analyses of GRF6/14-3-3λ reveal that the Kac level of GRF6 is decreased under alkaline stress, suggesting that acetylation represses plant alkaline response. Indeed, K56ac of GRF6 inhibits its binding to and subsequent activation of the plasma membrane H+-ATPase AHA2, leading to hypersensitivity to alkaline stress. These results provide valuable resources for protein acetylation studies in plants and reveal that protein acetylation suppresses phosphorylation output by acetylating GRF/14-3-3 proteins.
- Published
- 2022
24. Molecular basis of locus-specific H3K9 methylation catalyzed by SUVH6 in plants.
- Author
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Jian Zhang, Jianlong Yuan, Juncheng Lin, Lixian Chen, Li-Yuan You, Shuling Chen, Li Peng, Chun-Han Wanga, Jiamu Du, and Cheng-Guo Duan
- Subjects
GENETIC regulation ,ENZYME specificity ,METHYLATION ,HYDROGEN bonding interactions ,PEPTIDES - Abstract
Dimethylated histone H3 Lys9 (H3K9me2) is a conserved heterochromatic mark catalyzed by SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG (SUVH) methyltransferases in plants. However, the mechanism underlying the locus specificity of SUVH enzymes has long been elusive. Here, we show that a conserved N-terminal motif is essential for SUVH6-mediated H3K9me2 deposition in planta. The SUVH6 N-terminal peptide can be recognized by the bromo-adjacent homology (BAH) domain of the RNA- and chromatin-binding protein ANTI-SILENCING 1 (ASI1), which has been shown to function in a complex to confer gene expression regulation. Structural data indicate that a classic aromatic cage of ASI1-BAH domain specifically recognizes an arginine residue of SUVH6 through extensive hydrogen bonding interactions. A classic aromatic cage of ASI1 specifically recognizes an arginine residue of SUVH6 through extensive cation-p interactions, playing a key role in recognition. The SUVH6-ASI1 module confers locus-specific H3K9me2 deposition at most SUVH6 target loci and gives rise to distinct regulation of gene expression depending on the target loci, either conferring transcriptional silencing or posttranscriptional processing of mRNA. More importantly, such mechanism is conserved in multiple plant species, indicating a coordinated evolutionary process between SUVH6 and ASI1. In summary, our findings uncover a conserved mechanism for the locus specificity of H3K9 methylation in planta. These findings provide mechanistic insights into the delicate regulation of H3K9 methylation homeostasis in plants. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
25. Progressive chromatin silencing of ABA biosynthesis gene permits seed germination in Arabidopsis
- Author
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Xiangxiong Kong, Jiamu Du, Yufeng Wu, Fengli Zhao, Xi Chen, Danling Zhu, Li-Jia Qu, Min Chen, Deyue Yang, and Zhe Wu
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biology ,Chromatin silencing ,macromolecular substances ,biology.organism_classification ,Chromatin ,Cell biology ,chemistry.chemical_compound ,chemistry ,Seedling ,Germination ,Arabidopsis ,biology.protein ,Gene silencing ,PRC2 ,Abscisic acid - Abstract
Seed germination represents a major developmental switch in plants that is vital to agricultural, but how this process is controlled at the chromatin level remains obscure. Here we demonstrate that successful germination in Arabidopsis requires a chromatin mechanism that progressively silences NCED6, which encodes a rate-limiting enzyme for abscisic acid (ABA) biosynthesis, through the cooperative action of the RNA-binding protein RZ-1 and the polycomb repressive complex 2 (PRC2). Simultaneous inactivation of RZ-1 and PRC2 blocks germination and synergistically derepresses NCEDs and hundreds of genes. At NCED6, by promoting H3 deacetylation and suppressing H3K4me3, RZ-1 facilitates transcriptional silencing and also a H3K27me3 accumulation process that occurs during seed germination and early seedling growth. Genome-wide analysis reveals RZ-1 is preferentially required for transcriptional silencing of many PRC2 targets early during seed germination when H3K27me3 is not yet established. We propose RZ-1 confers a novel silencing mechanism to compensate and coordinate with PRC2. Our work highlights the progressive chromatin silencing of ABA biosynthesis genes via synergized action of the RNA-binding protein RZ1 and PRC2, which is vital for seed germination.
- Published
- 2021
26. Making a 6mA demethylase
- Author
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Jiamu Du and Sisi Li
- Subjects
Adenine ,Cell Biology ,DNA Methylation ,Molecular Biology ,Epigenesis, Genetic - Published
- 2022
27. TEM1 combinatorially binds to
- Author
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Hongmiao, Hu, Shu, Tian, Guohui, Xie, Rui, Liu, Nana, Wang, Sisi, Li, Yuehui, He, and Jiamu, Du
- Subjects
Arabidopsis Proteins ,Gene Expression Regulation, Plant ,Photoperiod ,Arabidopsis ,food and beverages ,Polycomb-Group Proteins ,Flowers ,Biological Sciences ,Transcription Factors - Abstract
Arabidopsis TEMPRANILLO 1 (TEM1) is a transcriptional repressor that participates in multiple flowering pathways and negatively regulates the juvenile-to-adult transition and the flowering transition. To understand the molecular basis for the site-specific regulation of FLOWERING LOCUS T (FT) by TEM1, we determined the structures of the two plant-specific DNA-binding domains in TEM1, AP2 and B3, in complex with their target DNA sequences from the FT gene 5′-untranslated region (5′-UTR), revealing the molecular basis for TEM1 specificity for its DNA targets. In vitro binding assays revealed that the combination of the AP2 and B3 binding sites greatly enhanced the overall binding of TEM1 to the FT 5′-UTR, indicating TEM1 combinatorically recognizes the FT gene 5′-UTR. We further showed that TEM1 recruits the Polycomb repressive complex 2 (PRC2) to the FT 5′-UTR. The simultaneous binding of the TEM1 AP2 and B3 domains to FT is necessary for deposition of H3K27me3 at the FT 5′-UTR and for the flowering repressor function of TEM1. Overall, our data suggest that the combinatorial recognition of FT 5′-UTR by TEM1 ensures H3K27me3 deposition to precisely regulate the floral transition.
- Published
- 2021
28. TEM1 combinatorially binds to FLOWERING LOCUS T and recruits a Polycomb factor to repress the floral transition in Arabidopsis
- Author
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Rui Liu, Shu Tian, Guohui Xie, Jiamu Du, Nana Wang, Yuehui He, Sisi Li, and Hongmiao Hu
- Subjects
Untranslated region ,Multidisciplinary ,biology ,Chemistry ,food and beverages ,Repressor ,Locus (genetics) ,biology.organism_classification ,Cell biology ,chemistry.chemical_compound ,Arabidopsis ,biology.protein ,Binding site ,PRC2 ,Gene ,DNA - Abstract
Arabidopsis TEMPRANILLO 1 (TEM1) is a transcriptional repressor that participates in multiple flowering pathways and negatively regulates the juvenile-to-adult transition and the flowering transition. To understand the molecular basis for the site-specific regulation of FLOWERING LOCUS T (FT) by TEM1, we determined the structures of the two plant-specific DNA-binding domains in TEM1, AP2 and B3, in complex with their target DNA sequences from the FT gene 5'-untranslated region (5'-UTR), revealing the molecular basis for TEM1 specificity for its DNA targets. In vitro binding assays revealed that the combination of the AP2 and B3 binding sites greatly enhanced the overall binding of TEM1 to the FT 5'-UTR, indicating TEM1 combinatorically recognizes the FT gene 5'-UTR. We further showed that TEM1 recruits the Polycomb repressive complex 2 (PRC2) to the FT 5'-UTR. The simultaneous binding of the TEM1 AP2 and B3 domains to FT is necessary for deposition of H3K27me3 at the FT 5'-UTR and for the flowering repressor function of TEM1. Overall, our data suggest that the combinatorial recognition of FT 5'-UTR by TEM1 ensures H3K27me3 deposition to precisely regulate the floral transition.
- Published
- 2021
29. Binding of guide piRNA triggers methylation of the unstructured N-terminal region of Aub leading to assembly of the piRNA amplification complex
- Author
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Ravi Sachidanandam, Alexei A. Aravin, Jiamu Du, Hongmiao Hu, Sisi Li, Katalin Fejes Tóth, Xiawei Huang, Dinshaw J. Patel, Fan Zou, and Alexandre Webster
- Subjects
Male ,Models, Molecular ,0301 basic medicine ,Transposable element ,Protein-Arginine N-Methyltransferases ,endocrine system ,Science ,Protein domain ,General Physics and Astronomy ,Piwi-interacting RNA ,Biology ,Methylation ,Article ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,0302 clinical medicine ,Protein Domains ,Peptide Initiation Factors ,Gene silencing ,Animals ,Drosophila Proteins ,RNA, Small Interfering ,Psychological repression ,X-ray crystallography ,Methylosome ,Multidisciplinary ,urogenital system ,Protein arginine methyltransferase 5 ,General Chemistry ,Cell biology ,030104 developmental biology ,Argonaute Proteins ,Piwi RNAs ,Drosophila ,Female ,Carrier Proteins ,Protein Processing, Post-Translational ,030217 neurology & neurosurgery ,Biogenesis - Abstract
PIWI proteins use guide piRNAs to repress selfish genomic elements, protecting the genomic integrity of gametes and ensuring the fertility of animal species. Efficient transposon repression depends on amplification of piRNA guides in the ping-pong cycle, which in Drosophila entails tight cooperation between two PIWI proteins, Aub and Ago3. Here we show that post-translational modification, symmetric dimethylarginine (sDMA), of Aub is essential for piRNA biogenesis, transposon silencing and fertility. Methylation is triggered by loading of a piRNA guide into Aub, which exposes its unstructured N-terminal region to the PRMT5 methylosome complex. Thus, sDMA modification is a signal that Aub is loaded with piRNA guide. Amplification of piRNA in the ping-pong cycle requires assembly of a tertiary complex scaffolded by Krimper, which simultaneously binds the N-terminal regions of Aub and Ago3. To promote generation of new piRNA, Krimper uses its two Tudor domains to bind Aub and Ago3 in opposite modification and piRNA-loading states. Our results reveal that post-translational modifications in unstructured regions of PIWI proteins and their binding by Tudor domains that are capable of discriminating between modification states is essential for piRNA biogenesis and silencing., PIWI protein contains arginine rich motifs that are post-translationally modified to symmetrically methylated arginine (sDMA) residues. Here the authors show that piRNA loading into Aub triggers sDMA modification which is recognized by Krimper to promote formation of Krimper-Aub-Ago3 complex for piRNA amplification in Drosophila.
- Published
- 2021
30. Author Correction: Making a 6mA demethylase
- Author
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Jiamu Du and Sisi Li
- Subjects
Cell Biology ,Molecular Biology - Published
- 2022
31. Embryonic resetting of the parental vernalized state by two B3 domain transcription factors in Arabidopsis
- Author
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Zeng Tao, Hongmiao Hu, Yuehui He, Jiamu Du, Xiao Luo, and Bei Jia
- Subjects
0106 biological sciences ,0301 basic medicine ,Regulation of gene expression ,biology ,Arabidopsis Proteins ,fungi ,Arabidopsis ,food and beverages ,Plant Science ,Vernalization ,biology.organism_classification ,01 natural sciences ,Chromatin ,Cell biology ,03 medical and health sciences ,030104 developmental biology ,Gene Expression Regulation, Plant ,Seeds ,Fus3 ,Flowering Locus C ,B3 domain ,Transcription factor ,Transcription Factors ,010606 plant biology & botany - Abstract
Some overwintering plants acquire competence to flower, after experiencing prolonged cold in winter, through a process termed vernalization. In the crucifer plant Arabidopsis thaliana, prolonged cold induces chromatin-mediated silencing of the potent floral repressor FLOWERING LOCUS C (FLC) by Polycomb proteins. This vernalized state is epigenetically maintained or ‘memorized’ in warm rendering plants competent to flower in spring, but is reset in the next generation. Here, we show that in early embryogenesis, two homologous B3 domain transcription factors LEAFY COTYLEDON 2 (LEC2) and FUSCA3 (FUS3) compete against two repressive B3-containing epigenome readers and Polycomb partners known as VAL1 and VAL2 for the cis-regulatory cold memory element (CME) of FLC to disrupt Polycomb silencing. Consistently, crystal structures of B3–CME complexes show that B3FUS3, B3LEC2 and B3VAL1 employ a nearly identical binding interface for CME. We further found that LEC2 and FUS3 recruit the scaffold protein FRIGIDA in association with active chromatin modifiers to establish an active chromatin state at FLC, which results in resetting of the silenced FLC to active and erasing the epigenetic parental memory of winter cold in early embryos. Following embryo development, LEC2 and FUS3 are developmentally silenced throughout post-embryonic stages, enabling VALs to bind to the CME again at seedling stages at which plants experience winter cold. Our findings illustrate how overwintering crucifer annuals or biennials in temperate climates employ a subfamily of B3 domain proteins to switch on, off and on again the expression of a key flowering gene in the embryo-to-plant-to-embryo cycle, and thus to synchronize growth and development with seasonal temperature changes in their life cycles. Two B3 domain transcription factors are important for the resetting of the vernalized state in the embryos of Arabidopsis by competing against repressive Polycomb partners and recruiting the scaffold protein FRIGIDA to establish an activate chromatin state at FLC.
- Published
- 2019
32. Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin
- Author
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Kai Tang, P. Zhu, W.A. Tao, Heng Zhang, Yuhui Jiang, H. Wan, F. Wu, Ray A. Bressan, Xin-Jian He, Xingang Wang, Jian-Kang Zhu, Zhusheng Yang, Xiaofan Du, Cui-Jun Zhang, Jiamu Du, Li Pan, and Jianying Luo
- Subjects
0106 biological sciences ,0301 basic medicine ,Heterochromatin ,Science ,Arabidopsis ,General Physics and Astronomy ,01 natural sciences ,DNA-binding protein ,General Biochemistry, Genetics and Molecular Biology ,Article ,Protein Structure, Secondary ,03 medical and health sciences ,Epigenetics ,Amino Acid Sequence ,Gene Silencing ,lcsh:Science ,Regulation of gene expression ,Multidisciplinary ,biology ,Chemistry ,Arabidopsis Proteins ,Lysine ,General Chemistry ,Methylation ,DNA Methylation ,Chromatin ,Cell biology ,030104 developmental biology ,Histone ,Genetic Loci ,DNA methylation ,biology.protein ,DNA Transposable Elements ,lcsh:Q ,Peptides ,010606 plant biology & botany ,Protein Binding - Abstract
Heterochromatin is a tightly packed form of chromatin that is associated with DNA methylation and histone 3 lysine 9 methylation (H3K9me). Here, we identify an H3K9me2-binding protein, Agenet domain (AGD)-containing p1 (AGDP1), in Arabidopsis thaliana. Here we find that AGDP1 can specifically recognize the H3K9me2 mark by its three pairs of tandem AGDs. We determine the crystal structure of the Agenet domain 1 and 2 cassette (AGD12) of Raphanus sativus AGDP1 in complex with an H3K9me2 peptide. In the complex, the histone peptide adopts a unique helical conformation. AGD12 specifically recognizes the H3K4me0 and H3K9me2 marks by hydrogen bonding and hydrophobic interactions. In addition, we find that AGDP1 is required for transcriptional silencing, non-CG DNA methylation, and H3K9 dimethylation at some loci. ChIP-seq data show that AGDP1 preferentially occupies long transposons and is associated with heterochromatin marks. Our findings suggest that, as a heterochromatin-binding protein, AGDP1 links H3K9me2 to DNA methylation in heterochromatin regions., DNA methylation and H3K9 dimethylation are two linked epigenetic marks of silenced chromatin in plants that depend on the activity of CMT3/2 and SUVH4/5/6. Here the authors identify AGDP1 as an H3K9me2-binding protein required for heterochromatic non-CG DNA methylation, H3K9 dimethylation, and transcriptional silencing.
- Published
- 2018
33. A H3K9me2-Binding Protein AGDP3 Limits DNA Methylation and Transcriptional Gene Silencing in Arabidopsis
- Author
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Jian-Kang Zhu, Xi Y, Li Peng, Luo J, Ming Lei, Y. Wang, Du X, X. J. Zhou, Qiantao Zheng, Yi Zhong, Satheesh, M. Wei, Jiamu Du, Kai Tang, Wen-Feng Nie, An G, Yang Z, and Liu R
- Subjects
chemistry.chemical_compound ,Histone ,DNA demethylation ,biology ,Chemistry ,DNA glycosylase ,Acetylation ,DNA methylation ,biology.protein ,Repressor ,Demethylase ,DNA ,Cell biology - Abstract
DNA methylation is critical for tuning gene expression to prevent potentially deleterious gene-silencing. The Arabidopsis DNA glycosylase/lyase REPRESSOR OF SILENCING 1 (ROS1) initiates active DNA demethylation and is required for the prevention of DNA hypermethylation at thousands of genomic loci. However, the mechanism recruiting ROS1 to specific loci is not well understood. Here, we report the discovery of Arabidopsis AGENET Domain Containing Protein 3 (AGDP3) as a cellular factor required for ROS1-mediated DNA demethylation, and targets ROS1 to specific loci. We found that AGDP3 could bind to the H3K9me2 mark by its AGD12 cassette. The crystal structure of the AGDP3 AGD12 in complex with an H3K9me2 peptide reveals the molecular basis for the specific recognition, that the dimethylated H3K9 and unmodified H3K4 are specifically anchored into two different surface pockets. Interestingly, a histidine residue located in the methylysine binding aromatic cage enables AGDP3 pH-dependent H3K9me2 binding capacity. Considering the intracellular pH correlates with the histone acetylation status, our results provide the molecular mechanism for the regulation of ROS1 DNA demethylase by the gene silencing H3K9me2 mark and the potential crosstalk with active histone acetylation mark.
- Published
- 2021
34. Recognition of H3K9me1 by maize RNA-directed DNA methylation factor SHH2
- Author
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Rui Liu, Xuan Du, Fengtong Yuan, Jinyan Luo, Yuhua Wang, Xuelin Zhou, Bei Jia, Heng Zhang, Jiamu Du, and Suhui Lv
- Subjects
0106 biological sciences ,0301 basic medicine ,Regulator ,Plant Science ,De novo DNA methylation ,01 natural sciences ,Biochemistry ,Zea mays ,General Biochemistry, Genetics and Molecular Biology ,Epigenesis, Genetic ,03 medical and health sciences ,Epigenetics ,RNA-Directed DNA Methylation ,Plant Proteins ,biology ,Chemistry ,DNA Methylation ,Cell biology ,DNA-Binding Proteins ,030104 developmental biology ,Histone ,RNA, Plant ,DNA methylation ,biology.protein ,Homeobox ,010606 plant biology & botany - Abstract
RNA-directed DNA methylation (RdDM) is a plant-specific de novo DNA methylation pathway, which has extensive cross-talk with histone modifications. Here, we report that the maize RdDM regulator SAWADEE HOMEODOMAIN HOMOLOG 2 (SHH2) is an H3K9me1 reader. Our structural studies reveal that H3K9me1 recognition is achieved by recognition of the methyl group via a classic aromatic cage and hydrogen-bonding and salt-bridge interactions with the free protons of the mono-methyllysine. The di- and tri-methylation states disrupt the polar interactions, decreasing the binding affinity. Our study reveals a mono-methyllysine recognition mechanism which potentially links RdDM to H3K9me1 in maize.
- Published
- 2021
35. A novel protein complex that regulates active DNA demethylation in Arabidopsis
- Author
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Qingfeng Niu, Xiansong Xiong, Rosa Lozano-Durán, Pei Huang, Yuhua Wang, Xueqiang Lin, Huan Huang, Pan Liu, Jian-Kang Zhu, Wen-Feng Nie, Guochen Qin, Jiamu Du, Zhaobo Lang, and Yuwei Jiang
- Subjects
0106 biological sciences ,0301 basic medicine ,Protein domain ,Arabidopsis ,Plant Science ,01 natural sciences ,Biochemistry ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,chemistry.chemical_compound ,Gene Expression Regulation, Plant ,Proto-Oncogene Proteins ,Promoter Regions, Genetic ,biology ,Arabidopsis Proteins ,Binding protein ,Nuclear Proteins ,biology.organism_classification ,Cell biology ,DNA Demethylation ,030104 developmental biology ,DNA demethylation ,chemistry ,DNA glycosylase ,DNA methylation ,Homeobox ,DNA ,010606 plant biology & botany - Abstract
Active DNA demethylation is critical for altering DNA methylation patterns and regulating gene expression. The 5-methylcytosine DNA glycosylase/lyase ROS1 initiates a base-excision repair pathway for active DNA demethylation and is required for the prevention of DNA hypermethylation at 1 000s of genomic regions in Arabidopsis. How ROS1 is regulated and targeted to specific genomic regions is not well understood. Here, we report the discovery of an Arabidopsis protein complex that contains ROS1, regulates ROS1 gene expression, and likely targets the ROS1 protein to specific genomic regions. ROS1 physically interacts with a WD40 domain protein (RWD40), which in turn interacts with a methyl-DNA binding protein (RMB1) as well as with a zinc finger and homeobox domain protein (RHD1). RMB1 binds to DNA that is methylated in any sequence context, and this binding is necessary for its function in vivo. Loss-of-function mutations in RWD40, RMB1, or RHD1 cause DNA hypermethylation at several tested genomic regions independently of the known ROS1 regulator IDM1. Because the hypermethylated genomic regions include the DNA methylation monitoring sequence in the ROS1 promoter, plants mutated in RWD40, RMB1, or RHD1 show increased ROS1 expression. Importantly, ROS1 binding to the ROS1 promoter requires RWD40, RMB1, and RHD1, suggesting that this complex dictates ROS1 targeting to this locus. Our results demonstrate that ROS1 forms a protein complex with RWD40, RMB1, and RHD1, and that this novel complex regulates active DNA demethylation at several endogenous loci in Arabidopsis.
- Published
- 2020
36. A novel histone H3K4me1-specific binding protein is required for siRNA accumulation and DNA methylation at a subset of loci targeted by RNA-directed DNA methylation
- Author
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Qingfeng Niu, Zhe Song, Kai Tang, Lixian Chen, Ting Ban, Zhongxin Guo, Chanhong Kim, Heng Zhang, Cheng-Guo Duan, Huiming Zhang, Jian-Kang Zhu, Jiamu Du, and Zhaobo Lang
- Abstract
In plants, RNA-directed DNA methylation (RdDM) is a well-known de novo DNA methylation pathway that involves two plant-specific RNA polymerases, Pol IV and Pol V. In this study, we discovered and characterized a new RdDM factor, RDM15. Through DNA methylome and genome wide siRNA analyses, we show that RDM15 is required for RdDM-dependent DNA methylation and siRNA accumulation at a subset of RdDM target loci. We show that RDM15 contributes to Pol V-dependent downstream siRNA accumulation, and interacts with NRPE3B, a subunit specific to Pol V. We also show that the C-terminal tudor domain of RDM15 specifically recognizes the histone 3 lysine 4 monomethylation (H3K4me1) mark. Structure analysis of RDM15 in complex with the H3K4me1 peptide showed that the RDM15 tudor domain specifically recognizes the monomethyllysine through an aromatic cage and a specific hydrogen bonding network; this chemical feature-based recognition mechanism differs from all previously reported lower methyllysine recognition mechanisms. RDM15 and H3K4me1 have similar genome-wide distribution patterns at RDM15-dependent RdDM target loci, establishing a link between H3K4me1 and RDM15-mediated RdDM in vivo. In summary, we have identified and characterized a histone H3K4me1-specific binding protein as a new RdDM component, and our structural analysis of RDM15 revealed a new type of chemical feature-based lower methyllysine recognition mechanism.
- Published
- 2020
37. Coupling of H3K27me3 recognition with transcriptional repression through the BAH-PHD-CPL2 complex inArabidopsis
- Author
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Yuhua Wang, Cheng-Guo Duan, Guiping Zhang, Li Peng, Jiamu Du, Si-Si Xie, Yi-Zhe Zhang, Jian-Kang Zhu, Chunxiang Chen, Lingrui Zhang, Jianlong Yuan, and Jing Jiang
- Subjects
biology ,Chemistry ,RNA polymerase II ,macromolecular substances ,Argonaute ,biology.organism_classification ,Cell biology ,RNA silencing ,Histone ,Transcription (biology) ,Arabidopsis ,biology.protein ,Gene silencing ,BAH domain - Abstract
SUMMARYHistone 3 Lys 27 trimethylation (H3K27me3)-mediated epigenetic silencing plays a critical role in multiple biological processes. However, the H3K27me3 recognition and transcriptional repression mechanisms are only partially understood. Here, we report a new mechanism for H3K27me3 recognition and transcriptional repression. Our structural and biochemical data showed that the BAH domain protein AIPP3 and the PHD proteins AIPP2 and PAIPP2 cooperate to read H3K27me3 and unmodified H3K4 histone marks, respectively, inArabidopsis. The BAH-PHD bivalent histone reader complex silences a substantial subset of H3K27me3-enriched loci, including a number of development and stress response-related genes such as the RNA silencing effector geneARGONAUTE 5(AGO5) and We found that the BAH-PHD module associates with CPL2, a plant-specific Pol II carboxyl terminal domain (CTD) phosphatase, to form the BAH-PHD-CPL2 complex (BPC) for transcriptional repression. The BPC complex represses transcription through CPL2-mediated CTD dephosphorylation, thereby causing inhibition of Pol II release from the transcriptional start site. Our work reveals a mechanism coupling H3K27me3 recognition with transcriptional repression through the alteration of Pol II phosphorylation states, thereby contributing to our understanding of the mechanism of H3K27me3-dependent silencing.
- Published
- 2020
38. Structural insights into the multivalent binding of the Arabidopsis FLOWERING LOCUS T promoter by the CO-NF-Y master transcription factor complex
- Author
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Lixian Chen, Hongmiao Hu, Changshi Wang, Yuehui He, Jiamu Du, Yue Liu, Xinchen Lv, Rui Liu, Zhe Wu, Xiaolin Zeng, Fan Zhang, Xuelin Zhou, and Chanhong Kim
- Subjects
0106 biological sciences ,0301 basic medicine ,Protein domain ,Arabidopsis ,Transcription factor complex ,Plant Science ,Crystallography, X-Ray ,01 natural sciences ,03 medical and health sciences ,chemistry.chemical_compound ,Protein Domains ,Gene Expression Regulation, Plant ,Arabidopsis thaliana ,Binding site ,Promoter Regions, Genetic ,Gene ,Transcription factor ,Binding Sites ,biology ,Arabidopsis Proteins ,food and beverages ,Cell Biology ,biology.organism_classification ,Cell biology ,DNA-Binding Proteins ,030104 developmental biology ,chemistry ,Multiprotein Complexes ,Trans-Activators ,Florigen ,010606 plant biology & botany ,Transcription Factors - Abstract
Flowering plants sense various environmental and endogenous signals to trigger the floral transition and start the reproductive growth cycle. CONSTANS (CO) is a master transcription factor in the photoperiod floral pathway that integrates upstream signals and activates the florigen gene FLOWERING LOCUS T (FT). Here, we performed comprehensive structural and biochemical analyses to study the molecular mechanism underlying the regulation of FT by CO in Arabidopsis thaliana. We show that the four previously characterized cis-elements in the FT promoter proximal region, CORE1, CORE2, P1, and P2, are all direct CO binding sites. Structural analysis of CO in complex with NUCLEAR FACTOR-YB/YC (NF–YB/YC) and the CORE2 or CORE1 elements revealed the molecular basis for the specific recognition of the shared TGTG motifs. Biochemical analysis suggested that CO might form a homomultimeric assembly via its N-terminal B-Box domain and simultaneously occupy multiple cis-elements within the FT promoter. We suggest that this multivalent binding gives the CO–NF–Y complex high affinity and specificity for FT promoter binding. Overall, our data provide a detailed molecular model for the regulation of FT by the master transcription factor complex CO–NF–Y during the floral transition.
- Published
- 2020
39. Coupling of H3K27me3 recognition with transcriptional repression through the BAH-PHD-CPL2 complex in Arabidopsis
- Author
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Jianlong Yuan, Guiping Zhang, Jing Jiang, Lingrui Zhang, Yi-Zhe Zhang, Jian-Kang Zhu, Li Peng, Cheng-Guo Duan, Si-Si Xie, Chunxiang Chen, Yuhua Wang, and Jiamu Du
- Subjects
Models, Molecular ,Time Factors ,Plant molecular biology ,Protein Conformation ,Science ,Transcriptional regulatory elements ,Arabidopsis ,General Physics and Astronomy ,RNA polymerase II ,macromolecular substances ,Flowers ,Methylation ,General Biochemistry, Genetics and Molecular Biology ,Article ,Epigenesis, Genetic ,Histones ,03 medical and health sciences ,0302 clinical medicine ,Transcription (biology) ,Gene Expression Regulation, Plant ,Histone post-translational modifications ,Phosphoprotein Phosphatases ,Gene silencing ,BAH domain ,030304 developmental biology ,Regulation of gene expression ,0303 health sciences ,Multidisciplinary ,biology ,Chemistry ,Arabidopsis Proteins ,Lysine ,Gene Expression Regulation, Developmental ,General Chemistry ,Argonaute ,Cell biology ,Histone Code ,RNA silencing ,Histone ,Multiprotein Complexes ,biology.protein ,030217 neurology & neurosurgery - Abstract
Histone 3 Lys 27 trimethylation (H3K27me3)-mediated epigenetic silencing plays a critical role in multiple biological processes. However, the H3K27me3 recognition and transcriptional repression mechanisms are only partially understood. Here, we report a mechanism for H3K27me3 recognition and transcriptional repression. Our structural and biochemical data showed that the BAH domain protein AIPP3 and the PHD proteins AIPP2 and PAIPP2 cooperate to read H3K27me3 and unmodified H3K4 histone marks, respectively, in Arabidopsis. The BAH-PHD bivalent histone reader complex silences a substantial subset of H3K27me3-enriched loci, including a number of development and stress response-related genes such as the RNA silencing effector gene ARGONAUTE 5 (AGO5). We found that the BAH-PHD module associates with CPL2, a plant-specific Pol II carboxyl terminal domain (CTD) phosphatase, to form the BAH-PHD-CPL2 complex (BPC) for transcriptional repression. The BPC complex represses transcription through CPL2-mediated CTD dephosphorylation, thereby causing inhibition of Pol II release from the transcriptional start site. Our work reveals a mechanism coupling H3K27me3 recognition with transcriptional repression through the alteration of Pol II phosphorylation states, thereby contributing to our understanding of the mechanism of H3K27me3-dependent silencing., Histone 3 Lys 27 trimethylation (H3K27me3) mediates epigenetic silencing of gene expression. Here, Zhang et al. show that in Arabidopsis, the BAH-domain H3K27me3-reader protein AIPP3 forms a complex with PHD proteins and CPL2, a plant-specific Pol II phosphatase, to inhibit Pol II activity by dephosphorylation.
- Published
- 2020
40. A novel protein complex that regulates active DNA demethylation in Arabidopsis
- Author
-
Jian-Kang Zhu, Huan Huang, Xiansong Xiong, Qingfeng Niu, Xueqiang Lin, Guochen Qin, Zhaobo Lang, Pan Liu, Pei Huang, Wen-Feng Nie, Jiamu Du, Yuhua Wang, Yuwei Jiang, and Rosa Lozano-Durán
- Subjects
chemistry.chemical_compound ,DNA demethylation ,biology ,Chemistry ,DNA glycosylase ,Binding protein ,Arabidopsis ,DNA methylation ,Protein domain ,Homeobox ,biology.organism_classification ,DNA ,Cell biology - Abstract
SUMMARYActive DNA demethylation is critical for altering DNA methylation patterns and regulating gene expression. The 5-methylcytosine DNA glycosylase/lyase ROS1 initiates a base excision repair pathway for active DNA demethylation and is required for the prevention of DNA hypermethylation at thousands of genomic regions in Arabidopsis. How ROS1 is regulated and targeted to specific genomic regions is not well understood. Here, we report the discovery of an Arabidopsis protein complex that contains ROS1, regulates ROS1 gene expression, and likely targets the ROS1 protein to specific genomic regions. ROS1 physically interacts with a WD40 domain protein (RWD40), which in turn interacts with a methyl-DNA binding protein (RMB1) as well as with a zinc finger and homeobox domain protein (RHD1). RMB1 binds to DNA that is methylated in any sequence context, and this binding is necessary for its function in vivo.Loss-of-function mutations in RWD40, RMB1, or RHD1 cause DNA hypermethylation at several tested genomic regions independently of the known ROS1 regulator IDM1. Because the hypermethylated genomic regions include the DNA methylation monitoring sequence in the ROS1 promoter, plants mutated in RWD40, RMB1, or RHD1 show increased ROS1 expression. Importantly, ROS1 binding to the ROS1 promoter requires RWD40, RMB1, and RHD1, suggesting that this complex dictates ROS1 targeting to this locus. Our results demonstrate that ROS1 forms a protein complex with RWD40, RMB1, and RHD1, and that this novel complex regulates active DNA demethylation at several endogenous loci in Arabidopsis.
- Published
- 2020
41. EBS is a bivalent histone reader that regulates floral phase transition in Arabidopsis
- Author
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Ray N. Scheid, Jiamu Du, Lloyd M. Smith, Shuiming Qian, John M. Denu, Xinchen Lv, Zhilin Yang, Xuehua Zhong, Xiongming Du, Xiangsong Chen, Mark Scalf, Rui Liu, Lei Lu, and Boersma
- Subjects
0301 basic medicine ,biology ,Repressor ,macromolecular substances ,biology.organism_classification ,Chromatin ,Cell biology ,03 medical and health sciences ,030104 developmental biology ,Histone ,Arabidopsis ,Genetics ,biology.protein ,Transcriptional regulation ,H3K4me3 ,PRC2 ,Bivalent chromatin - Abstract
The ability of cells to perceive and translate versatile cues into differential chromatin and transcriptional states is critical for many biological processes1-5. In plants, timely transition to a flowering state is crucial for successful reproduction6-9. EARLY BOLTING IN SHORT DAY (EBS) is a negative transcriptional regulator that prevents premature flowering in Arabidopsis thaliana10,11. We found that EBS contains bivalent bromo-adjacent homology (BAH)-plant homeodomain (PHD) reader modules that bind H3K27me3 and H3K4me3, respectively. We observed co-enrichment of a subset of EBS-associated genes with H3K4me3, H3K27me3, and Polycomb repressor complex 2 (PRC2). Notably, EBS adopted an autoinhibition mode to mediate its switch in binding preference between H3K27me3 and H3K4me3. This binding balance was critical because disruption of either EBS-H3K27me3 or EBS-H3K4me3 interaction induced early floral transition. Our results identify a bivalent chromatin reader capable of recognizing two antagonistic histone marks, and we propose a distinct mechanism of interaction between active and repressive chromatin states.
- Published
- 2018
42. Dual recognition of H3K4me3 and H3K27me3 by a plant histone reader SHL
- Author
-
Xinchen Lv, Ray N. Scheid, Jiamu Du, Rui Liu, Shuiming Qian, Xuehua Zhong, Melissa D. Boersma, Li Lu, Wei Chen, John M. Denu, and Zhenlin Yang
- Subjects
0301 basic medicine ,Science ,Arabidopsis ,General Physics and Astronomy ,macromolecular substances ,Biology ,Methylation ,General Biochemistry, Genetics and Molecular Biology ,Article ,Histones ,03 medical and health sciences ,Gene Expression Regulation, Plant ,Histone code ,Epigenetics ,lcsh:Science ,Psychological repression ,Regulation of gene expression ,Homeodomain Proteins ,Multidisciplinary ,Models, Genetic ,Arabidopsis Proteins ,food and beverages ,General Chemistry ,Chromatin ,Cell biology ,Histone Code ,030104 developmental biology ,Histone ,biology.protein ,H3K4me3 ,Homeobox ,lcsh:Q - Abstract
The ability of a cell to dynamically switch its chromatin between different functional states constitutes a key mechanism regulating gene expression. Histone mark “readers” display distinct binding specificity to different histone modifications and play critical roles in regulating chromatin states. Here, we show a plant-specific histone reader SHORT LIFE (SHL) capable of recognizing both H3K27me3 and H3K4me3 via its bromo-adjacent homology (BAH) and plant homeodomain (PHD) domains, respectively. Detailed biochemical and structural studies suggest a binding mechanism that is mutually exclusive for either H3K4me3 or H3K27me3. Furthermore, we show a genome-wide co-localization of SHL with H3K27me3 and H3K4me3, and that BAH-H3K27me3 and PHD-H3K4me3 interactions are important for SHL-mediated floral repression. Together, our study establishes BAH-PHD cassette as a dual histone methyl-lysine binding module that is distinct from others in recognizing both active and repressive histone marks., Histone mark reader proteins bind to particular histone modifications and regulate chromatin state. Here, Qian et al. show that the SHORT LIFE reader has a unique ability to recognize both activating and repressive histone marks and that these interactions enable SHORT LIFE to repress flowering in plants.
- Published
- 2018
43. Erratum for: Multiplex CRISPR-Cas9 editing of DNA methyltransferases in rice uncovers a class of non-CG methylation specific for GC-rich regions
- Author
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Daoheng Hu, Yiming Yu, Chun Wang, Yanping Long, Yue Liu, Li Feng, Dongdong Lu, Bo Liu, Jinbu Jia, Rui Xia, Jiamu Du, Xuehua Zhong, Lei Gong, Kejian Wang, and Jixian Zhai
- Subjects
Errata ,Cell Biology ,Plant Science - Published
- 2021
44. Combining chemical and genetic approaches to increase drought resistance in plants
- Author
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Chunzhao Zhao, Jian-Kang Zhu, Wenwu Wu, Min-Jie Cao, Yulu Zhang, Jiamu Du, Wenlong Wang, Xue Liu, Ai Zeng, Tong Si, X. Edward Zhou, Huan Huang, H. Eric Xu, and Fuxing Wang
- Subjects
0106 biological sciences ,0301 basic medicine ,Agonist ,medicine.drug_class ,Transgene ,Science ,Arabidopsis ,General Physics and Astronomy ,Genetically modified crops ,Pyruvate dehydrogenase phosphatase ,Biology ,01 natural sciences ,Article ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,chemistry.chemical_compound ,Gene Expression Regulation, Plant ,Botany ,Escherichia coli ,medicine ,Receptor ,lcsh:Science ,Abscisic acid ,Multidisciplinary ,Molecular Structure ,Arabidopsis Proteins ,organic chemicals ,fungi ,Water ,food and beverages ,Fluorine ,General Chemistry ,Plants, Genetically Modified ,biology.organism_classification ,Droughts ,Cell biology ,Genetically modified organism ,Protein Phosphatase 2C ,030104 developmental biology ,chemistry ,lcsh:Q ,Soybeans ,Abscisic Acid ,010606 plant biology & botany - Abstract
Drought stress is a major threat to crop production, but effective methods to mitigate the adverse effects of drought are not available. Here, we report that adding fluorine atoms in the benzyl ring of the abscisic acid (ABA) receptor agonist AM1 optimizes its binding to ABA receptors by increasing the number of hydrogen bonds between the compound and the surrounding amino acid residues in the receptor ligand-binding pocket. The new chemicals, known as AMFs, have long-lasting effects in promoting stomatal closure and inducing the expression of stress-responsive genes. Application of AMFs or transgenic overexpression of the receptor PYL2 in Arabidopsis and soybean plants confers increased drought resistance. The greatest increase in drought resistance is achieved when AMFs are applied to the PYL2-overexpression transgenic plants. Our results demonstrate that the combining of potent chemicals with transgenic overexpression of an ABA receptor is very effective in helping plants combat drought stress., Plants respond to abiotic stress via the phytohormone ABA. Here, Cao et al. report a series of new ABA receptor agonists, named AMFs, which have higher receptor-binding affinities and show that, when employed in tandem with ABA receptor overexpression, can significantly increase drought resistance
- Published
- 2017
45. The Arabidopsis H3K27me3 demethylase JUMONJI 13 is a temperature and photoperiod dependent flowering repressor
- Author
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Huimin Ren, Xinye Liu, Xiaomei Chen, Xiekui Cui, Bing Zhou, Qi Qiu, Jiamu Du, Daye Sun, Weiwei Qi, Xiaofeng Cao, Zhenlin Yang, Sisi Li, Hongmiao Hu, and Shuzhi Zheng
- Subjects
Models, Molecular ,Protein Conformation, alpha-Helical ,0301 basic medicine ,Jumonji Domain-Containing Histone Demethylases ,Light ,Mutant ,Arabidopsis ,Gene Expression ,General Physics and Astronomy ,02 engineering and technology ,Crystallography, X-Ray ,Substrate Specificity ,Histones ,Protein structure ,Gene Expression Regulation, Plant ,Gene expression ,Cloning, Molecular ,lcsh:Science ,Regulation of gene expression ,photoperiodism ,Multidisciplinary ,biology ,Chemistry ,Temperature ,Gene Expression Regulation, Developmental ,food and beverages ,021001 nanoscience & nanotechnology ,Recombinant Proteins ,Cell biology ,0210 nano-technology ,Hydrophobic and Hydrophilic Interactions ,Protein Binding ,Science ,Photoperiod ,Repressor ,Flowers ,macromolecular substances ,Article ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,Tobacco ,Protein Interaction Domains and Motifs ,Amino Acid Sequence ,Binding Sites ,Arabidopsis Proteins ,fungi ,Hydrogen Bonding ,General Chemistry ,biology.organism_classification ,030104 developmental biology ,Agrobacterium tumefaciens ,Mutation ,biology.protein ,Demethylase ,Protein Conformation, beta-Strand ,lcsh:Q ,Peptides - Abstract
In plants, flowering time is controlled by environmental signals such as day-length and temperature, which regulate the floral pathway integrators, including FLOWERING LOCUS T (FT), by genetic and epigenetic mechanisms. Here, we identify an H3K27me3 demethylase, JUMONJI 13 (JMJ13), which regulates flowering time in Arabidopsis. Structural characterization of the JMJ13 catalytic domain in complex with its substrate peptide reveals that H3K27me3 is specifically recognized through hydrogen bonding and hydrophobic interactions. Under short-day conditions, the jmj13 mutant flowers early and has increased FT expression at high temperatures, but not at low temperatures. In contrast, jmj13 flowers early in long-day conditions regardless of temperature. Long-day condition and higher temperature induce the expression of JMJ13 and increase accumulation of JMJ13. Together, our data suggest that the H3K27me3 demethylase JMJ13 acts as a temperature- and photoperiod-dependent flowering repressor., Jumonji domain-containing histone demethylases regulate flowering in plants. Here Zheng et al. show that Arabidopsis JMJ13 is an H3K27me3 demethylase that recognizes H3K27me3 via hydrogen bonding and hydrophobic interactions and affects both photoperiod and temperature-dependent flowering responses.
- Published
- 2019
46. A DNA methylation reader complex that enhances gene transcription
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Wanlu Liu, Shima Rayatpisheh, Somsakul Pop Wongpalee, William D. Barshop, Robert M. Vaughan, Steven E. Jacobsen, Jiamu Du, James A. Wohlschlegel, Linda Yen, Wei Chen, C. Jake Harris, Evan M. Cornett, Javier Gallego-Bartolomé, Martin Groth, Zhenhui Zhong, X.Y. Li, Marion Scheibe, Zonghua Wang, Yan Xue, Falk Butter, and Scott B. Rothbart
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Freedom ,0106 biological sciences ,0301 basic medicine ,Transcription, Genetic ,General Science & Technology ,1.1 Normal biological development and functioning ,Arabidopsis ,Biology ,DNAJ Protein ,01 natural sciences ,Article ,03 medical and health sciences ,chemistry.chemical_compound ,Genetic ,Protein Domains ,Gene Expression Regulation, Plant ,Transcription (biology) ,Underpinning research ,Gene expression ,Genetics ,Gene ,Regulation of gene expression ,Multidisciplinary ,Arabidopsis Proteins ,Methylation ,Methyltransferases ,Histone-Lysine N-Methyltransferase ,Plant ,DNA Methylation ,HSP40 Heat-Shock Proteins ,Cell biology ,030104 developmental biology ,chemistry ,Gene Expression Regulation ,DNA methylation ,CpG Islands ,Generic health relevance ,Transcription ,DNA ,010606 plant biology & botany - Abstract
DNA methylation promotes transcription DNA methylation generally represses transcription, but in some instances, it has also been implicated in transcription activation. Harris et al. identified a protein complex in Arabidopsis that is recruited to chromatin by DNA methylation. This complex specifically activated the transcription of genes that are already mildly transcribed but had no effect on transcriptionally silent genes such as transposable elements. The complex thereby counteracts the repression effect caused by transposon insertion in neighboring genes while leaving transposons silent. Thus, by balancing both repressive and activating transcriptional effects, DNA methylation can act to fine-tune gene expression. Science , this issue p. 1182
- Published
- 2018
47. Resistance protein Pit interacts with the GEF OsSPK1 to activate OsRac1 and trigger rice immunity
- Author
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Jiamu Du, Yuying Li, Kazuya Ishikawa, Qiong A. Wang, Shingo Nagawa, Li Tan, Kazumi Uno, Ken-ichi Kosami, Yoji Kawano, and Ko Shimamoto
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0301 basic medicine ,Multidisciplinary ,Architecture domain ,Chemistry ,Activator (genetics) ,Oryza ,NLR Proteins ,Cell biology ,03 medical and health sciences ,Magnaporthe ,030104 developmental biology ,Immune system ,PNAS Plus ,Gene Expression Regulation, Plant ,Small GTPase ,Guanine nucleotide exchange factor ,Effector-triggered immunity ,Receptor ,Plant Diseases ,Plant Proteins - Abstract
Resistance (R) genes encode intracellular nucleotide-binding/leucine-rich repeat-containing (NLR) family proteins that serve as critical plant immune receptors to induce effector-triggered immunity (ETI). NLR proteins possess a tripartite domain architecture consisting of an N-terminal variable region, a central nucleotide-binding domain, and a C-terminal leucine-rich repeat. N-terminal coiled-coil (CC) or Toll-interleukin 1 receptor (TIR) domains of R proteins appear to serve as platforms to trigger immune responses, because overexpression of the CC or TIR domain of some R proteins is sufficient to induce an immune response. Because direct downstream signaling molecules of R proteins remain obscure, the molecular mechanisms by which R proteins regulate downstream signaling are largely unknown. We reported previously that a rice R protein named Pit triggers ETI through a small GTPase, OsRac1, although how Pit activates OsRac1 is unclear. Here, we identified OsSPK1, a DOCK family guanine nucleotide exchange factor, as an interactor of Pit and activator for OsRac1. OsSPK1 contributes to signaling by two disease-resistance genes, Pit and Pia, against the rice blast fungus Magnaporthe oryzae and facilitates OsRac1 activation in vitro and in vivo. The CC domain of Pit is required for its binding to OsSPK1, OsRac1 activation, and the induction of cell death. Overall, we conclude that OsSPK1 is a direct and key signaling target of Pit-mediated immunity. Our results shed light on how R proteins trigger ETI through direct downstream molecules.
- Published
- 2018
48. Structure and function of the bacterial decapping enzyme NudC
- Author
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Katharina Höfer, Dinshaw J. Patel, Florian Abele, Jiamu Du, Sisi Li, Andres Jäschke, Jasmin Schlotthauer, Julia Grawenhoff, and Jens Frindert
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Models, Molecular ,0301 basic medicine ,chemistry.chemical_classification ,RNA capping ,biology ,Protein Conformation ,RNA ,Cell Biology ,Crystallography, X-Ray ,Nudix hydrolase ,Article ,Cofactor ,03 medical and health sciences ,030104 developmental biology ,Protein structure ,chemistry ,Biochemistry ,Hydrolase ,Biocatalysis ,Escherichia coli ,biology.protein ,Nucleotide ,NAD+ kinase ,Pyrophosphatases ,Molecular Biology - Abstract
RNA capping and decapping are thought to be distinctive features of eukaryotes. The redox cofactor NAD was recently discovered to be attached to small regulatory RNAs in bacteria in a cap-like manner, and Nudix hydrolase NudC was found to act as a NAD-decapping enzyme in vitro and in vivo. Here, crystal structures of Escherichia coli NudC in complex with substrate NAD and with cleavage product NMN reveal the catalytic residues lining the binding pocket and principles underlying molecular recognition of substrate and product. Biochemical mutation analysis identifies the conserved Nudix motif as the catalytic center of the enzyme, which needs to be homodimeric, as the catalytic pocket is composed of amino acids from both monomers. NudC is single-strand specific and has a purine preference for the 5'-terminal nucleotide. The enzyme strongly prefers NAD-linked RNA (NAD-RNA) over NAD and binds to a diverse set of cellular RNAs in an unspecific manner.
- Published
- 2016
49. Structural Basis for the Unique Multivalent Readout of Unmodified H3 Tail by Arabidopsis ORC1b BAH-PHD Cassette
- Author
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Rui Liu, Steven E. Jacobsen, Sisi Li, Or Gozani, Zhenlin Yang, Xuan Du, Jiamu Du, Alex W. Wilkinson, and Dinshaw J. Patel
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Models, Molecular ,0301 basic medicine ,DNA Replication ,DNA replication initiation ,education ,Protein domain ,Arabidopsis ,Biophysics ,Cell Cycle Proteins ,Biology ,Article ,Epigenesis, Genetic ,Histones ,03 medical and health sciences ,Genetic ,Protein Domains ,Models ,Structural Biology ,Information and Computing Sciences ,Genetics ,ORC1 ,Molecular Biology ,BAH domain ,Binding Sites ,Arabidopsis Proteins ,DNA replication ,Molecular ,Biological Sciences ,biology.organism_classification ,Cell biology ,030104 developmental biology ,PHD finger ,Chemical Sciences ,Origin recognition complex ,Peptides ,Epigenesis ,Protein Binding - Abstract
DNA replication initiation relies on the formation of the origin recognition complex (ORC). The plant ORC subunit 1 (ORC1) protein possesses a conserved N-terminal BAH domain with an embedded plant-specific PHD finger, whose function may be potentially regulated by an epigenetic mechanism. Here, we report structural and biochemical studies on the Arabidopsis thaliana ORC1b BAH-PHD cassette which specifically recognizes the unmodified H3 tail. The crystal structure of ORC1b BAH-PHD cassette in complex with an H3(1-15) peptide reveals a strict requirement for the unmodified state of R2, T3, and K4 on the H3 tail and a novel multivalent BAH and PHD readout mode for H3 peptide recognition. Such recognition may contribute to epigenetic regulation of the initiation of DNA replication.
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- 2016
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50. Mechanistic insights into plant SUVH family H3K9 methyltransferases and their binding to context-biased non-CG DNA methylation
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Zhenhui Zhong, Jiamu Du, Rui Liu, C.J. Harris, Zonghua Wang, Baoqian Jia, Steven E. Jacobsen, Sisi Li, Xuezhen Li, and Wei Chen
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0301 basic medicine ,Models, Molecular ,Methyltransferase ,Protein Conformation ,1.1 Normal biological development and functioning ,Arabidopsis ,Genetically Modified ,plant ,Crystallography, X-Ray ,Methylation ,H3K9me2 ,Histones ,03 medical and health sciences ,chemistry.chemical_compound ,Models ,Underpinning research ,Genetics ,SUVH6 ,Regulation of gene expression ,Cofactor binding ,Multidisciplinary ,Crystallography ,DNA methylation ,biology ,Base Sequence ,Chemistry ,Arabidopsis Proteins ,histone methyltransferase ,Lysine ,Human Genome ,Molecular ,DNA ,Histone-Lysine N-Methyltransferase ,Plants ,DNA Methylation ,Plants, Genetically Modified ,030104 developmental biology ,Histone ,PNAS Plus ,Histone methyltransferase ,biology.protein ,X-Ray ,Nucleic Acid Conformation ,Generic health relevance ,Protein Binding - Abstract
DNA methylation functions in gene silencing and the maintenance of genome integrity. In plants, non-CG DNA methylation is linked through a self-reinforcing loop with histone 3 lysine 9 dimethylation (H3K9me2). The plant-specific SUPPRESSOR OF VARIEGATION 3–9 HOMOLOG (SUVH) family H3K9 methyltransferases (MTases) bind to DNA methylation marks and catalyze H3K9 methylation. Here, we analyzed the structure and function of Arabidopsis thaliana SUVH6 to understand how this class of enzyme maintains methylation patterns in the genome. We reveal that SUVH6 has a distinct 5-methyl-dC (5mC) base-flipping mechanism involving a thumb loop element. Autoinhibition of H3 substrate entry is regulated by a SET domain loop, and a conformational transition in the post-SET domain upon cofactor binding may control catalysis. In vitro DNA binding and in vivo ChIP-seq data reveal that the different SUVH family H3K9 MTases have distinct DNA binding preferences, targeting H3K9 methylation to sites with different methylated DNA sequences, explaining the context biased non-CG DNA methylation in plants.
- Published
- 2018
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