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Deng Z, Ai H, Sun M, Tong Z, Du Y, Qu Q, Zhang L, Xu Z, Tao S, Shi Q, Li JB, Pan M, Liu L. Mechanistic insights into nucleosomal H2B monoubiquitylation mediated by yeast Bre1-Rad6 and its human homolog RNF20/RNF40-hRAD6A. Mol Cell 2023; 83:3080-3094.e14. [PMID: 37633270 DOI: 10.1016/j.molcel.2023.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/27/2023] [Accepted: 08/02/2023] [Indexed: 08/28/2023]
Abstract
Histone H2B monoubiquitylation plays essential roles in chromatin-based transcriptional processes. A RING-type E3 ligase (yeast Bre1 or human RNF20/RNF40) and an E2 ubiquitin-conjugating enzyme (yeast Rad6 or human hRAD6A), together, precisely deposit ubiquitin on H2B K123 in yeast or K120 in humans. Here, we developed a chemical trapping strategy and successfully captured the transient structures of Bre1- or RNF20/RNF40-mediated ubiquitin transfer from Rad6 or hRAD6A to nucleosomal H2B. Our structures show that Bre1 and RNF40 directly bind nucleosomal DNA, exhibiting a conserved E3/E2/nucleosome interaction pattern from yeast to humans for H2B monoubiquitylation. We also find an uncanonical non-hydrophobic contact in the Bre1 RING-Rad6 interface, which positions Rad6 directly above the target H2B lysine residue. Our study provides mechanistic insights into the site-specific monoubiquitylation of H2B, reveals a critical role of nucleosomal DNA in mediating E3 ligase recognition, and provides a framework for understanding the cancer-driving mutations of RNF20/RNF40.
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Affiliation(s)
- Zhiheng Deng
- Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Huasong Ai
- Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China; Institute of Translational Medicine, National Center for Translational Medicine (Shanghai), School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Maoshen Sun
- Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Zebin Tong
- Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yunxiang Du
- Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Qian Qu
- Institute of Translational Medicine, National Center for Translational Medicine (Shanghai), School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Liying Zhang
- Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Ziyu Xu
- Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Shixian Tao
- Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Qiang Shi
- Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Jia-Bin Li
- College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China
| | - Man Pan
- Institute of Translational Medicine, National Center for Translational Medicine (Shanghai), School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lei Liu
- Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China.
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Qin P, Ye J, Gong X, Yan X, Lin M, Lin T, Liu T, Li H, Wang X, Zhu Y, Li X, Liu Y, Li Y, Ling Y, Zhang X, Fang F. Quantitative proteomics analysis to assess protein expression levels in the ovaries of pubescent goats. BMC Genomics 2022; 23:507. [PMID: 35831802 PMCID: PMC9281040 DOI: 10.1186/s12864-022-08699-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/13/2022] [Indexed: 11/30/2022] Open
Abstract
Background Changes in the abundance of ovarian proteins play a key role in the regulation of reproduction. However, to date, no studies have investigated such changes in pubescent goats. Herein we applied isobaric tags for relative and absolute quantitation (iTRAQ) and liquid chromatography–tandem mass spectrometry to analyze the expression levels of ovarian proteins in pre-pubertal (n = 3) and pubertal (n = 3) goats. Results Overall, 7,550 proteins were recognized; 301 (176 up- and 125 downregulated) were identified as differentially abundant proteins (DAPs). Five DAPs were randomly selected for expression level validation by Western blotting; the results of Western blotting and iTRAQ analysis were consistent. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis indicated that DAPs were enriched in olfactory transduction, glutathione metabolism, and calcium signaling pathways. Besides, gene ontology functional enrichment analysis revealed that several DAPs enriched in biological processes were associated with cellular process, biological regulation, metabolic process, and response to stimulus. Protein–protein interaction network showed that proteins interacting with CDK1, HSPA1A, and UCK2 were the most abundant. Conclusions We identified 301 DAPs, which were enriched in olfactory transduction, glutathione metabolism, and calcium signaling pathways, suggesting the involvement of these processes in the onset of puberty. Further studies are warranted to more comprehensively explore the function of the identified DAPs and aforementioned signaling pathways to gain novel, deeper insights into the mechanisms underlying the onset of puberty. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08699-y.
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Affiliation(s)
- Ping Qin
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui, China.,Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Jing Ye
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui, China.,Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Xinbao Gong
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui, China.,Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Xu Yan
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui, China.,Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Maosen Lin
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui, China.,Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Tao Lin
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui, China.,Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Tong Liu
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui, China.,Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Hailing Li
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui, China.,Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Xiujuan Wang
- Animal Husbandry Development Center, Huoqiu Animal Health Supervision Institute, Huoqiu County, Auditorium Road, Luan, 237400, Anhui, China
| | - Yanyun Zhu
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui, China
| | - Xiaoqian Li
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui, China
| | - Ya Liu
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui, China.,Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Yunsheng Li
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui, China.,Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Yinghui Ling
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Xiaorong Zhang
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui, China.,Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Fugui Fang
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui, China. .,Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China.
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Chu GC, Zhao R, Wu X, Shi J, Li YM. One-Pot Synthesis of a Bis-Thio-Acetone Linked Ubiquitinated Histones Using 1,3-Dibromoacetone. J Org Chem 2020; 85:15631-15637. [PMID: 33191736 DOI: 10.1021/acs.joc.0c01851] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Histone ubiquitination affects the structure and function of nucleosomes. Here, we reported a one-pot synthesis of ubiquitinated histone analogues using 1,3-dibromoacetone (DBA) as the cross-linking reagent. The key step is that under the acidic borate buffer, the DBA linker can be efficiently installed to the Cys of the recombinant Ub mutant, followed by the coupling between the Ub-DBA with histones at physiological pH. The process requires a single HPLC step or orthogonal affinity tag purification to obtain ubiquitinated histone at about 24-38 mg/L expression.
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Affiliation(s)
- Guo-Chao Chu
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui 230009, China.,Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Rui Zhao
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Xiangwei Wu
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Jing Shi
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Yi-Ming Li
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui 230009, China
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Aparicio Pelaz D, Yerkesh Z, Kirchgäßner S, Mahler H, Kharchenko V, Azhibek D, Jaremko M, Mootz HD, Jaremko Ł, Schwarzer D, Fischle W. Examining histone modification crosstalk using immobilized libraries established from ligation-ready nucleosomes. Chem Sci 2020; 11:9218-9225. [PMID: 34123170 PMCID: PMC8163371 DOI: 10.1039/d0sc03407j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Chromatin signaling relies on a plethora of posttranslational modifications (PTM) of the histone proteins which package the long DNA molecules of our cells in reoccurring units of nucleosomes. Determining the biological function and molecular working mechanisms of different patterns of histone PTMs requires access to various chromatin substrates of defined modification status. Traditionally, these are achieved by individual reconstitution of single nucleosomes or arrays of nucleosomes in conjunction with modified histones produced by means of chemical biology. Here, we report an alternative strategy for establishing a library of differentially modified nucleosomes that bypasses the need for many individual syntheses, purification and assembly reactions by installing modified histone tails on ligation-ready, immobilized nucleosomes reconstituted in a single batch. Using the ligation-ready nucleosome strategy with sortase-mediated ligation for histone H3 and intein splicing for histone H2A, we generated libraries of up to 280 individually modified nucleosomes in 96-well plate format. Screening these libraries for the effects of patterns of PTMs onto the recruitment of a well-known chromatin factor, HP1 revealed a previously unknown long-range cross-talk between two modifications. H3S28 phosphorylation enhances recruitment of the HP1 protein to the H3K9 methylated H3-tail only in nucleosomal context. Detailed structural analysis by NMR measurements implies negative charges at position 28 to increase nucleosomal H3-tail dynamics and flexibility. Our work shows that ligation-ready nucleosomes enable unprecedented access to the ample space and complexity of histone modification patterns for the discovery and dissection of chromatin regulatory principles. 280 different patterns of histone modifications were installed in preassembled nucleosomes using PTS and SML enabling screening of readout crosstalk.![]()
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Affiliation(s)
- Diego Aparicio Pelaz
- Interfaculty Institute of Biochemistry, University of Tübingen Auf der Morgenstelle 34 D-72076 Tübingen Germany
| | - Zhadyra Yerkesh
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology Thuwal 23955 Saudi Arabia
| | - Sören Kirchgäßner
- Interfaculty Institute of Biochemistry, University of Tübingen Auf der Morgenstelle 34 D-72076 Tübingen Germany
| | - Henriette Mahler
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry 37077 Göttingen Germany
| | - Vladlena Kharchenko
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology Thuwal 23955 Saudi Arabia
| | - Dulat Azhibek
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology Thuwal 23955 Saudi Arabia
| | - Mariusz Jaremko
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology Thuwal 23955 Saudi Arabia
| | - Henning D Mootz
- Institute of Biochemistry, University of Muenster Corrensstr. 36 48149 Münster Germany
| | - Łukasz Jaremko
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology Thuwal 23955 Saudi Arabia
| | - Dirk Schwarzer
- Interfaculty Institute of Biochemistry, University of Tübingen Auf der Morgenstelle 34 D-72076 Tübingen Germany
| | - Wolfgang Fischle
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology Thuwal 23955 Saudi Arabia .,Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry 37077 Göttingen Germany
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