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Mechanism studies of the activation of DNA methyltransferase DNMT1 triggered by histone H3 ubiquitination,revealed by multi-scale molecular dynamics simulations

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Science China(Life Sciences) 2023年第2期66卷 313-323页

作者： Jixue Sun Fei Liu Longxiao Yuan Ning-Ning Pang Bing Zhu Na Yang State key laboratory of Medicinal Chemical Biology College of Pharmacy and Key Laboratory of Medical Data Analysis and Statistical Research of TianjinNankai UniversityTianjin 300353China national laboratory of biomacromolecules CAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing 100101China

DNMT1 is a DNA methyltransferase that catalyzes and maintains methylation in CpG dinucleotides.It blocks the entrance of DNA into the catalytic pocket via the replication foci targeting sequence(RFTS)domain.Recent studies have shown that an H3-tail-conjugated two-mono-ubiquitin mark(H3Ub2)activates DNMT1 by binding to the RFTS domain.However,the activation mechanism of DNMT1 remains unclear.In this work,we combine various sampling methods of extensive simulations,including conventional molecular dynamics,Gaussian-accelerated molecular dynamics,and coarse-grained molecular dynamics,to elucidate the activation mechanism of DNMT1.Geometric and energy analyses show that binding of H3Ub2 to the RFTS domain of DNMT1 results in the bending of theα4-helix in the RFTS domain at approximately 30°–35°,and the RFTS domain rotates~20°anti-clockwise and moves~3?away from the target recognition domain(TRD).The hydrogen-bonding network at the RFTSTRD interface is significantly disrupted,implying that the RFTS domain is dissociated from the catalytic core,which contributes to activating the auto-inhibited conformation of DNMT1.These results provide structural and dynamic evidence for the role of H3Ub2 in regulating the catalytic activity of DNMT1.

关键词： DNA methyltransferase conformational change molecular dynamics simulation activation molecular mechanism

Mechanism and design of allosteric activators of SIRT1

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Protein & Cell 2023年第5期14卷 387-392页

作者： Fei Liu Ningning Pang Rui-Ming Xu Na Yang State key laboratory of Medicinal Chemical Biology College of Pharmacy and Key Laboratory of Medical Data Analysis and Statistical Research of TianjinNankai UniversityTianjin 300353China national laboratory of biomacromolecules CAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing 100101China

Dear Editor,The sirtuin family Nicotinamide adenine dinucleotide-dependent deacetylases have important roles in many biological processes(Milne and Denu,2008).SIRT1 is a mammalian homolog of yeast Sir2,which is the founding member of the sirtuin family.Many SIRT1 substrates have been reported,including histones,p53,FOXOs,and PGC1α(Hsu et al.,2013).Stimulating the activity of SIRT1 has been shown to be an attractive therapeutic strategy for various physiological and pathological conditions such as aging,metabolic disorders,inflammation,and neurodegeneration(Guarente,2011).Several small molecules have been identified or developed as potential sirtuinactivating compounds(STACs).Most notably,resveratrol,a natural STAC,was shown to activate the SIRT1-catalyzed deacetylation of the Fluor de Lys(FDL)peptide,which is a p53 peptide fused to a 7-amino-4-methylcoumarin(AMC)fluorophore at the C-terminus(Table S1;Howitz et al.,2003).However,the activation of deacetylation of the p53 peptide is dependent on the presence of the AMC fluorophore(Borra et al.,2005;Wu et al.,2013).

关键词： SIRT1 PGC1α

RID1 sets rice heading date by balancing its binding with SLR1 and SDG722

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Journal of Integrative Plant Biology 2022年第1期64卷 149-165页

作者： Shuo Zhang Li Deng Rui Cheng Jie Hu Chang-Yin Wu national key laboratory of Crop Genetic Improvement and national Center of Plant Gene Research(Wuhan) Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China national laboratory of biomacromolecules CAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing 100101China University of the Chinese Academy of Sciences Beijing 100049China

Rice(Oryza sativa) is a major crop that feeds billions of people, and its yield is strongly influenced by flowering time(heading date). Loss of RICE INDETERMINATE1(RID1) function causes plants not to flower;thus, RID1 is considered a master switch among flowering-related genes. However, it remains unclear whether other proteins function together with RID1 to regulate rice floral transition.Here, we revealed that the chromatin accessibilityand H3 K9 ac, H3 K4 me3, and H3 K36 me3 levels at Heading date 3 a(Hd3 a) and RICE FLOWERING LOCUS T1(RFT1) loci were significantly reduced in rid1 mutants. Notably, RID1 interacted with SET DOMAIN GROUP PROTEIN 722(SDG722), a methyltransferase. We determined that SDG722 affects the global level of H3 K4 me2/3 and H3 K36 me2/3, and promotes flowering primarily through the Early heading date1-Hd3 a/RFT1 pathway. We further established that rice DELLA protein SLENDER RICE1(SLR1) interacted with RID1 to inhibit its transactivation activity, that SLR1 suppresses rice flowering, and that messenger RNA and protein levels of SLR1 gradually decrease with plant growth. Furthermore, SLR1 competed with SDG722 for interaction with RID1. Overall, our results establish that interplay between RID1, SLR1, and SDG722 feeds into rice flowering-time control.

关键词： heading date histone modification rice RID1 SDG722 SLR1

Isolation and proteomic study of fish liver lipid droplets

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Biophysics Reports 2023年第3期9卷 120-133页

作者： Yuwei Sun Jian Heng Feng Liu Shuyan Zhang Pingsheng Liu national laboratory of biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences University of Chinese Academy of Sciences State key laboratory of Membrane Biology Institute of Zoology Chinese Academy of Sciences Institute of Stem Cell and Regeneration Chinese Academy of Sciences

Lipid droplets(LDs) are a neutral lipid storage organelle that is conserved in almost all species. Excessive storage of neutral lipids in LDs is directly associated with many metabolic syndromes. Zebrafish is a better model animal for the study of LD biology due to its transparent embryonic stage compared to other organisms. However, the study of LDs in fish has been difficult due to the lack of specific LD marker proteins and the limitation of purification technology. In this paper, the purification and proteomic analysis of liver LDs of fish including zebrafish and Carassius auratus were performed for the first time. 259 and 267 proteins were identified respectively. Besides most of the identified proteins were reported in previous LD proteomes of mammals, indicating the similarity between mammal and fish LDs. We also identified many unique proteins of liver LDs in fish that are involved in the regulation of LD dynamics. Through morphological and biochemical analysis, we found that the marker protein Plin2 of zebrafish LD was located on LDs in Huh7 cells. These results will facilitate further study of LDs in fish and liver metabolic diseases using fish as a model animal.

关键词： Lipid droplet Fish Liver Proteomics Plin2

The patterns and participants of parental histone recycling during DNA replication in Saccharomyces cerevisiae

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Science China(Life Sciences) 2023年第7期66卷 1600-1614页

作者： Zhongqing Shan Yan Zhang Jiachen Bu Huizhi Li Zhuqiang Zhang Jun Xiong Bing Zhu national laboratory of biomacromolecules CAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing100101China College of Life Sciences University of Chinese Academy of SciencesBeijing100049China

Epigenetic information carried by histone modifications not only reflects the state of gene expression,but also participates in the maintenance of chromatin states and the regulation of gene expression.Recycling of parental histones to daughter chromatin after DNA replication is vital to mitotic inheritance of epigenetic information and the maintenance of cell identity,because the locus-specific modifications of the parental histones need to be maintained.To assess the precision of parental histone recycling,we developed a synthetic local label-chasing system in budding yeast Saccharomyces cerevisiae.Using this system,we observed that parental histone H3 can be recycled to their original position,thereby recovering their position information after DNA replication at all tested loci,including heterochromatin boundary,non-transcribed region,and actively transcribed regions.Moreover,the recycling rate appears to be affected by local chromatin environment.We surveyed a number of potential regulatory factors and observed that histone H3-H4 chaperon Asf1 contributed to parental histone recycling,while the eukaryotic replisome-associated components Mcm2 and Dpb3 displayed compounding effects in this process.In addition,the FACT complex also plays a role in the recycling of parental histones and helps to stabilize the nucleosomes.

关键词： epigenetic inheritance parental histone recycling Asf1 Mcm2 Dpb3 FACT

Cryogenic superresolution correlative light and electron microscopy of vitreous sections

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Biophysics Reports 2022年第4期8卷 193-204页

作者： Buyun Tian Maoge Zhou Fengping Feng Xiaojun Xu Pei Wang Huiqin Luan Wei Ji Yanhong Xue Tao Xu national laboratory of biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences University of Chinese Academy of Sciences national Research Center for Rehabilitation Technical Aids

Fluorescence microscopy and electron microscopy complement each other as the former provides labelling and localisation of specific molecules and target structures while the latter possesses excellent revolving power of fine structure in context. These two techniques can combine as correlative light and electron microscopy(CLEM) to reveal the organisation of materials within the cell. Frozen hydrated sections allow microscopic observations of cellular components in situ in a near-native state and are compatible with superresolution fluorescence microscopy and electron tomography if sufficient hardware and software support is available and a well-designed protocol is followed. The development of superresolution fluorescence microscopy greatly increases the precision of fluorescence annotation of electron tomograms. Here, we provide detailed instructions on how to perform cryogenic superresolution CLEM on vitreous sections. From fluorescence-labelled cells to high pressure freezing, cryoultramicrotomy, cryogenic single-molecule localisation microscopy, cryogenic electron tomography and image registration, electron tomograms with features of interest highlighted by superresolution fluorescence signals are expected to be obtained.

关键词： Cryogenic Superresolution Fluorescence microscopy Electron microscopy Correlative light and electron microscopy (CLEM) Electron tomography

Design and biosynthesis of functional protein nanostructures

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Science China(Life Sciences) 2020年第8期63卷 1142-1158页

作者： Feng Li Dianbing Wang Juan Zhou Dong Men Xian-En Zhang State key laboratory of Virology Wuhan Institute of VirologyCenter for Biosafety Mega-ScienceChinese Academy of SciencesWuhan 430071China national laboratory of biomacromolecules CAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing 100101China

Proteins are one of the major classes of biomolecules that execute biological functions for maintenance of life.Various kinds of nanostructures self-assembled from proteins have been created in nature over millions of years of evolution,including protein nanowires,layers and nanocages.These protein nanostructures can be reconstructed and equipped with desired new functions.Learning from and manipulating the self-assembly of protein nanostructures not only help to deepen our understanding of the nature of life but also offer new routes to fabricate novel nanomaterials for diverse applications.This review summarizes the recent research progress in this field,focusing on the characteristics,functionalization strategies,and applications of protein nanostructures.

关键词： protein nanostructures protein nanowires S-layer protein nanocages self-assembly biosynthesis functionalization

染色质复制过程中新核小体组装的机制揭示（英文）

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Science Bulletin 2023年第24期 3091-3093页

作者：杨娜郁珍瑜 State key laboratory of Medicinal Chemical Biology College of Pharmacy Nankai University national laboratory of biomacromolecules and key laboratory of Epigenetic Regulation and Intervention Institute of Biophysics Chinese Academy of Sciences

Eukaryotic cell division duplicates the chromosomes in the parental cell and equally segregates sister chromatids into daughter cells. This process involves the replication of chromosomal DNA and packaging the replicated DNA in nucleosomes, which consist of ～147 base pairs(bp) of DNA wrapped around an octamer of histones H2A, H2B, H3, and H4 [1]. The passage of the replication fork disrupts the structure of the nucleosome it encounters,

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No longer ‘blob-ology': Cryo-EM is getting into molecular details

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Science China(Life Sciences) 2015年第11期58卷 1154-1156页

作者： ZHU HongTao ZHU Ping national laboratory of biomacromolecules Institute of Biophysics Chinese Academy of Sciences

The structural information of functionally important macromolecular assemblies is a key to molecular biology and is of great interest to structural biologists.Cryo-electron microscopy(cryo-EM),particularly the single ... 详细信息

关键词：分子生物学冷冻电镜透射电子显微镜单颗粒分析斑点结构信息 X射线晶体学生物学家