1
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Weyh M, Jokisch ML, Nguyen TA, Fottner M, Lang K. Deciphering functional roles of protein succinylation and glutarylation using genetic code expansion. Nat Chem 2024; 16:913-921. [PMID: 38531969 PMCID: PMC11164685 DOI: 10.1038/s41557-024-01500-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 03/01/2024] [Indexed: 03/28/2024]
Abstract
Post-translational modifications (PTMs) dynamically regulate cellular processes. Lysine undergoes a range of acylations, including malonylation, succinylation (SucK) and glutarylation (GluK). These PTMs increase the size of the lysine side chain and reverse its charge from +1 to -1 under physiological conditions, probably impacting protein structure and function. To understand the functional roles of these PTMs, homogeneously modified proteins are required for biochemical studies. While the site-specific encoding of PTMs and their mimics via genetic code expansion has facilitated the characterization of the functional roles of many PTMs, negatively charged lysine acylations have defied this approach. Here we describe site-specific incorporation of SucK and GluK into proteins via temporarily masking their negative charge through thioester derivatives. We prepare succinylated and glutarylated bacterial and mammalian target proteins, including non-refoldable multidomain proteins. This allows us to study how succinylation and glutarylation impact enzymatic activity of metabolic enzymes and regulate protein-DNA and protein-protein interactions in biological processes from replication to ubiquitin signalling.
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Affiliation(s)
- Maria Weyh
- Laboratory for Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Marie-Lena Jokisch
- Laboratory for Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Tuan-Anh Nguyen
- Department of Chemistry, Laboratory for Synthetic Biochemistry, Technical University of Munich Institute for Advanced Study, Garching, Germany
- CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | - Maximilian Fottner
- Laboratory for Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland.
| | - Kathrin Lang
- Laboratory for Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland.
- Department of Chemistry, Laboratory for Synthetic Biochemistry, Technical University of Munich Institute for Advanced Study, Garching, Germany.
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2
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Kubatzky KF, Gao Y, Yu D. Post-translational modulation of cell signalling through protein succinylation. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2023; 4:1260-1285. [PMID: 38213532 PMCID: PMC10776603 DOI: 10.37349/etat.2023.00196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 08/22/2023] [Indexed: 01/13/2024] Open
Abstract
Cells need to adapt their activities to extra- and intracellular signalling cues. To translate a received extracellular signal, cells have specific receptors that transmit the signal to downstream proteins so that it can reach the nucleus to initiate or repress gene transcription. Post-translational modifications (PTMs) of proteins are reversible or irreversible chemical modifications that help to further modulate protein activity. The most commonly observed PTMs are the phosphorylation of serine, threonine, and tyrosine residues, followed by acetylation, glycosylation, and amidation. In addition to PTMs that involve the modification of a certain amino acid (phosphorylation, hydrophobic groups for membrane localisation, or chemical groups like acylation), or the conjugation of peptides (SUMOylation, NEDDylation), structural changes such as the formation of disulphide bridge, protein cleavage or splicing can also be classified as PTMs. Recently, it was discovered that metabolites from the tricarboxylic acid (TCA) cycle are not only intermediates that support cellular metabolism but can also modify lysine residues. This has been shown for acetate, succinate, and lactate, among others. Due to the importance of mitochondria for the overall fitness of organisms, the regulatory function of such PTMs is critical for protection from aging, neurodegeneration, or cardiovascular disease. Cancer cells and activated immune cells display a phenotype of accelerated metabolic activity known as the Warburg effect. This metabolic state is characterised by enhanced glycolysis, the use of the pentose phosphate pathway as well as a disruption of the TCA cycle, ultimately causing the accumulation of metabolites like citrate, succinate, and malate. Succinate can then serve as a signalling molecule by directly interacting with proteins, by binding to its G protein-coupled receptor 91 (GPR91) and by post-translationally modifying proteins through succinylation of lysine residues, respectively. This review is focus on the process of protein succinylation and its importance in health and disease.
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Affiliation(s)
- Katharina F. Kubatzky
- Department of Infectious Diseases, Medical Faculty Heidelberg, Medical Microbiology and Hygiene, Heidelberg University, 69120 Heidelberg, Germany
- Department of Infectious Diseases, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Yue Gao
- Department of Infectious Diseases, Medical Faculty Heidelberg, Medical Microbiology and Hygiene, Heidelberg University, 69120 Heidelberg, Germany
- Department of Infectious Diseases, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Dayoung Yu
- Department of Infectious Diseases, Medical Faculty Heidelberg, Medical Microbiology and Hygiene, Heidelberg University, 69120 Heidelberg, Germany
- Department of Infectious Diseases, University Hospital Heidelberg, 69120 Heidelberg, Germany
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3
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Liu Z, Wang R, Wang Y, Duan Y, Zhan H. Targeting succinylation-mediated metabolic reprogramming as a potential approach for cancer therapy. Biomed Pharmacother 2023; 168:115713. [PMID: 37852104 DOI: 10.1016/j.biopha.2023.115713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/08/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023] Open
Abstract
Metabolic reprogramming is a common hallmark of cancers and involves alterations in many metabolic pathways during tumor initiation and progression. However, the cancer-specific modulation of metabolic reprogramming requires further elucidation. Succinylation, a newly identified protein posttranslational modification (PTM), participates in many cellular processes by transferring a succinyl group to a residue of the target protein, which is related to various pathological disorders including cancers. In recent years, there has been a gradual increase in the number of studies on the regulation of tumors by protein succinylation. Notably, accumulating evidence suggests that succinylation can mediate cancer cell metabolism by altering the structure or activity of metabolism-related proteins and plays vital roles in metabolic reprogramming. Furthermore, some antitumor drugs have been linked to succinylation-mediated tumor-associated metabolism. To better elucidate lysine succinylation mediated tumor metabolic reprogramming, this review mainly summarizes recent studies on the regulation and effects of protein succinylation in tumors, focusing on the metabolic regulation of tumorigenesis and development, which will provide new directions for cancer diagnosis as well as possible therapeutic targets.
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Affiliation(s)
- Zhenya Liu
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong 250012, China
| | - Runxian Wang
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong 250012, China
| | - Yunshan Wang
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250012, China
| | - Yangmiao Duan
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Cell Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China.
| | - Hanxiang Zhan
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong 250012, China.
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4
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You H, Li S, Chen Y, Lin J, Wang Z, Dennis M, Li C, Yang D. Global proteome and lysine succinylation analyses provide insights into the secondary metabolism in Salvia miltiorrhiza. J Proteomics 2023; 288:104959. [PMID: 37478968 DOI: 10.1016/j.jprot.2023.104959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/10/2023] [Accepted: 07/01/2023] [Indexed: 07/23/2023]
Abstract
Danshen, belongs to the Lamiaceae family, and its scientific name is Salvia miltiorrhiza Bunge. It is a valuable medicinal plant to prevent and treat cardiovascular and cerebrovascular diseases. Lysine succinylation, a widespread modification found in various organisms, plays a critical role in regulating secondary metabolism in plants. The hairy roots of Salvia miltiorrhiza were subject to proteomic analysis to identify lysine succinylation sites using affinity purification and HPLC-MS/MS in this investigation. Our findings reveal 566 lysine succinylation sites in 348 protein sequences. We observed 110 succinylated proteins related to secondary metabolism, totaling 210 modification sites. Our analysis identified 53 types of enzymes among the succinylated proteins, including phenylalanine ammonia-lyase (PAL) and aldehyde dehydrogenase (ALDH). PAL, a crucial enzyme involved in the biosynthesis of rosmarinic acid and flavonoids, displayed succinylation at two sites. ALDH, which participates in the phenylpropane metabolic pathway, was succinylated at 8 eight sites. These observations suggest that lysine succinylation may play a vital role in regulating the production of secondary metabolites in Salvia miltiorrhiza. Our study may provide valuable insights for further investigation on plant succinylation, specifically as a reference point. SIGNIFICANCE: Salvia miltiorrhiza Bunge is a valuable medicinal plant that prevents and treats cardiovascular and cerebrovascular diseases. Lysine succinylation plays a critical role in regulating secondary metabolism in plants. The hairy roots of Salvia miltiorrhiza were subject to proteomic analysis to identify lysine succinylation sites using affinity purification and HPLC-MS/MS in this investigation. These observations suggest that lysine succinylation may act as a vital role in regulating the production of secondary metabolites in Salvia miltiorrhiza. Our study may provide valuable insights for further investigation on succinylation in plants, specifically as a reference point.
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Affiliation(s)
- Huaqian You
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Binjiang District, Hangzhou 310053, Zhejiang, China; College of Life Sciences and Medicine, Key Laboratory of Plant Secondary Metabolism and Regulation in Zhejiang Province, Zhejiang Sci-Tech University, 928 Second Avenue, Xiasha Higher Education Zone, Hangzhou 310018, Zhejiang, China
| | - Shiqing Li
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Binjiang District, Hangzhou 310053, Zhejiang, China
| | - Yiwen Chen
- College of Life Sciences and Medicine, Key Laboratory of Plant Secondary Metabolism and Regulation in Zhejiang Province, Zhejiang Sci-Tech University, 928 Second Avenue, Xiasha Higher Education Zone, Hangzhou 310018, Zhejiang, China
| | - Junjie Lin
- College of Life Sciences and Medicine, Key Laboratory of Plant Secondary Metabolism and Regulation in Zhejiang Province, Zhejiang Sci-Tech University, 928 Second Avenue, Xiasha Higher Education Zone, Hangzhou 310018, Zhejiang, China
| | - Zixuan Wang
- College of Life Sciences and Medicine, Key Laboratory of Plant Secondary Metabolism and Regulation in Zhejiang Province, Zhejiang Sci-Tech University, 928 Second Avenue, Xiasha Higher Education Zone, Hangzhou 310018, Zhejiang, China
| | - Mans Dennis
- Faculty of Medical Sciences, Anton de Kom University of Suriname, Paramaribo, Suriname
| | - Changyu Li
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Binjiang District, Hangzhou 310053, Zhejiang, China
| | - Dongfeng Yang
- College of Life Sciences and Medicine, Key Laboratory of Plant Secondary Metabolism and Regulation in Zhejiang Province, Zhejiang Sci-Tech University, 928 Second Avenue, Xiasha Higher Education Zone, Hangzhou 310018, Zhejiang, China.
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5
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Li S, Zhou Y, Xu Y, Ran S, Hou M, Li Q, Zhong X, Zhong F. The analysis of lysine succinylation modification reveals the mechanism of oxybenzone damaging of pakchoi ( Brassica rapa L. ssp. chinensis). FRONTIERS IN PLANT SCIENCE 2022; 13:1001935. [PMID: 36570927 PMCID: PMC9772522 DOI: 10.3389/fpls.2022.1001935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
Oxybenzone (OBZ), one of a broad spectrum of ultraviolet (UV) absorbents, has been proven to be harmful to both plants and animals, while omics analysis of big data at the molecular level is still lacking. Lysine succinylation (Ksuc) is an important posttranslational modification of proteins that plays a crucial role in regulating the metabolic network in organisms under stress. Here, we report the changes in intracellular Ksuc modification in plants under OBZ stress. A total of 1276 succinylated sites on 507 proteins were identified. Among these sites, 181 modified proteins were hypersulfinylated/succinylated in OBZ-stressed pakchoi leaves. Differentially succinylated proteins (DSPs) are distributed mainly in the chloroplast, cytoplasm, and mitochondria and are distributed mainly in primary metabolic pathways, such as reactive oxygen species (ROS) scavenging, stress resistance, energy generation and transfer, photosynthetic carbon fixation, glycolysis, and the tricarboxylic acid (TCA) cycle. Comprehensive analysis shows that Ksuc mainly changes the carbon flow distribution, enhances the activity of the antioxidant system, affects the biosynthesis of amino acids, and increases the modification of histones. The results of this study first showed the profiling of the Kusc map under OBZ treatment and proposed the adaptive mechanism of pakchoi in response to pollutants and other abiotic stresses at the posttranslational level, which revealed the importance of Ksuc in the regulation of various life activities and provides a reference dataset for future research on molecular function.
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Affiliation(s)
- Shuhao Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fu’zhou, China
| | - Yuqi Zhou
- College of Horticulture, Fujian Agriculture and Forestry University, Fu’zhou, China
| | - Yang Xu
- College of Horticulture, Fujian Agriculture and Forestry University, Fu’zhou, China
| | - Shengxiang Ran
- College of Horticulture, Fujian Agriculture and Forestry University, Fu’zhou, China
| | - Maomao Hou
- College of Horticulture, Fujian Agriculture and Forestry University, Fu’zhou, China
| | - Qingming Li
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Cheng’du, China
| | - Xin Zhong
- Institute of Marine Science and Technology, Shandong University, Qing’dao, China
| | - Fenglin Zhong
- College of Horticulture, Fujian Agriculture and Forestry University, Fu’zhou, China
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6
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Afonso CF, Marques MC, António JPM, Cordeiro C, Gois PMP, Cal PMSD, Bernardes GJL. Cysteine-Assisted Click-Chemistry for Proximity-Driven, Site-Specific Acetylation of Histones. Angew Chem Int Ed Engl 2022; 61:e202208543. [PMID: 36124857 PMCID: PMC9828500 DOI: 10.1002/anie.202208543] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Indexed: 01/12/2023]
Abstract
Post-translational modifications of histones are essential in the regulation of chromatin structure and function. Among these modifications, lysine acetylation is one of the most established. Earlier studies relied on the use of chromatin containing heterogeneous mixtures of histones acetylated at multiple sites. Differentiating the individual contribution of single acetylation events towards chromatin regulation is thus of great relevance. However, it is difficult to access homogeneous samples of histones, with a single acetylation, in sufficient quantities for such studies. By engineering histone H3 with a cysteine in proximity of the lysine of interest, we demonstrate that conjugation with maleimide-DBCO followed by a strain-promoted alkyne-azide cycloaddition reaction results in the acetylation of a single lysine in a controlled, site-specific manner. The chemical precision offered by our click-to-acetylate approach will facilitate access to and the study of acetylated histones.
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Affiliation(s)
- Cláudia F. Afonso
- Instituto de Medicina Molecular João Lobo AntunesFaculdade de MedicinaUniversidade de LisboaAvenida Professor Egas Moniz1649-028LisboaPortugal
| | - Marta C. Marques
- Instituto de Medicina Molecular João Lobo AntunesFaculdade de MedicinaUniversidade de LisboaAvenida Professor Egas Moniz1649-028LisboaPortugal
| | - João P. M. António
- Research Institute for Medicines (iMed.ULisboa)Faculdade de FarmáciaUniversidade de LisboaAv. Prof. Gama Pinto1649-003LisboaPortugal
| | - Carlos Cordeiro
- Laboratório de FT-ICR e Espectrometria de Massa EstruturalFaculdade de CiênciasUniversidade de LisboaCampo Grande1749-016LisboaPortugal
| | - Pedro M. P. Gois
- Research Institute for Medicines (iMed.ULisboa)Faculdade de FarmáciaUniversidade de LisboaAv. Prof. Gama Pinto1649-003LisboaPortugal
| | - Pedro M. S. D. Cal
- Instituto de Medicina Molecular João Lobo AntunesFaculdade de MedicinaUniversidade de LisboaAvenida Professor Egas Moniz1649-028LisboaPortugal
| | - Gonçalo J. L. Bernardes
- Instituto de Medicina Molecular João Lobo AntunesFaculdade de MedicinaUniversidade de LisboaAvenida Professor Egas Moniz1649-028LisboaPortugal,Yusuf Hamied Department of ChemistryUniversity of CambridgeLensfield RoadCB2 1EWCambridgeUK
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7
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Ting CY, Kolbeck PT, Colombo R, Chakiath C, Rice M, Marelli M, Christie RJ. Cyclopentadiene as a Multifunctional Reagent for Normal- and Inverse-Electron Demand Diels-Alder Bioconjugation. Bioconjug Chem 2022; 33:1609-1619. [PMID: 35943835 DOI: 10.1021/acs.bioconjchem.2c00222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Optimizing the Diels-Alder (DA) reaction for aqueous coupling has resulted in practical methods to link molecules such as drugs and diagnostic agents to proteins. Both normal electron demand (NED) and inverse electron demand (IED) DA coupling schemes have been employed, but neither mechanism entails a common multipurpose reactive group. This report focuses on expanding the bioconjugation toolbox for cyclopentadiene through the identification of reactive groups that couple through NED or IED mechanisms in aqueous solution. Dienophiles and tetrazine derivatives were screened for reactivity and selectivity toward antibodies bearing cyclopentadiene amino acids to yield bioconjugates. Twelve NED dienophiles and four tetrazine-based IED substrates were identified as capable of practical biocoupling. Furthermore, tetrazine ligation to cyclopentadiene occurred at a rate of 3.3 ± 0.5 M-1 s-1 and was capable of bioorthogonal transformations, as evidenced by the selective protein labeling in serum. Finally, an antibody-drug conjugate (ADC)-bearing monomethyl auristatin E was prepared via tetrazine conjugation to cyclopentadiene. The resulting ADC was stable and demonstrated potent activity in vitro. These findings expand the utility of cyclopentadiene as a tool to couple entities to proteins via dual DA addition mechanisms.
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Affiliation(s)
- Cheng-Yueh Ting
- AstraZeneca R&D, Biologics Engineering, Gaithersburg, Maryland 20878, United States
| | - Paul T Kolbeck
- AstraZeneca R&D, Biologics Engineering, Gaithersburg, Maryland 20878, United States
| | - Raffaele Colombo
- AstraZeneca R&D, Biologics Engineering, Gaithersburg, Maryland 20878, United States
| | - Chacko Chakiath
- AstraZeneca R&D, Biologics Engineering, Gaithersburg, Maryland 20878, United States
| | - Megan Rice
- AstraZeneca R&D, Biologics Engineering, Gaithersburg, Maryland 20878, United States
| | - Marcello Marelli
- AstraZeneca R&D, Biologics Engineering, Gaithersburg, Maryland 20878, United States
| | - R James Christie
- AstraZeneca R&D, Biologics Engineering, Gaithersburg, Maryland 20878, United States
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8
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Wu D, Zhang Y, Tang Z, Chen X, Ling X, Li L, Cao W, Zheng W, Wu J, Tang H, Liu X, Luo X, Liu T. Creation of a Yeast Strain with Co‐Translationally Acylated Nucleosomes. Angew Chem Int Ed Engl 2022; 61:e202205570. [DOI: 10.1002/anie.202205570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Dan Wu
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center Department of Molecular and Cellular, Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Yunfeng Zhang
- Center for Synthetic Biochemistry Institute of Synthetic Biology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Zhiheng Tang
- Department of Microbiology School of Basic Medical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Xiaoxu Chen
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center Department of Molecular and Cellular, Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Xinyu Ling
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center Department of Molecular and Cellular, Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Longtu Li
- Key Laboratory of Protein and Plant Gene Research School of Life Sciences and Peking-Tsinghua Center for Life Science Peking University Beijing 100871 China
| | - Wenbing Cao
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center Department of Molecular and Cellular, Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Wei Zheng
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center Department of Molecular and Cellular, Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Jiale Wu
- Key Laboratory of Protein and Plant Gene Research School of Life Sciences and Peking-Tsinghua Center for Life Science Peking University Beijing 100871 China
| | - Hongting Tang
- Center for Synthetic Biochemistry Institute of Synthetic Biology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Xiaoyun Liu
- Department of Microbiology School of Basic Medical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Xiaozhou Luo
- Center for Synthetic Biochemistry Institute of Synthetic Biology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
- CAS Key Laboratory of Quantitative Engineering Biology Institute of Synthetic Biology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Tao Liu
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center Department of Molecular and Cellular, Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
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9
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Posttranslational Chemical Mutagenesis Methods to Insert Posttranslational Modifications into Recombinant Proteins. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27144389. [PMID: 35889261 PMCID: PMC9316245 DOI: 10.3390/molecules27144389] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 06/27/2022] [Accepted: 07/06/2022] [Indexed: 11/17/2022]
Abstract
Posttranslational modifications (PTMs) dramatically expand the functional diversity of the proteome. The precise addition and removal of PTMs appears to modulate protein structure and function and control key regulatory processes in living systems. Deciphering how particular PTMs affect protein activity is a current frontier in biology and medicine. The large number of PTMs which can appear in several distinct positions, states, and combinations makes preparing such complex analogs using conventional biological and chemical tools challenging. Strategies to access homogeneous and precisely modified proteins with desired PTMs at selected sites and in feasible quantities are critical to interpreting their molecular code. Here, we summarize recent advances in posttranslational chemical mutagenesis and late-stage functionalization chemistry to transfer novel PTM mimicry into recombinant proteins with emphasis on novel transformations.
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10
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Wu D, Zhang Y, Tang Z, Chen X, Ling X, Li L, Cao W, Zheng W, Wu J, Tang H, Liu X, Luo X, Liu T. Creation of a Yeast Strain with Co‐Translationally Acylated Nucleosomes. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Dan Wu
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center Department of Molecular and Cellular, Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Yunfeng Zhang
- Center for Synthetic Biochemistry Institute of Synthetic Biology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Zhiheng Tang
- Department of Microbiology School of Basic Medical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Xiaoxu Chen
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center Department of Molecular and Cellular, Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Xinyu Ling
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center Department of Molecular and Cellular, Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Longtu Li
- Key Laboratory of Protein and Plant Gene Research School of Life Sciences and Peking-Tsinghua Center for Life Science Peking University Beijing 100871 China
| | - Wenbing Cao
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center Department of Molecular and Cellular, Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Wei Zheng
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center Department of Molecular and Cellular, Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Jiale Wu
- Key Laboratory of Protein and Plant Gene Research School of Life Sciences and Peking-Tsinghua Center for Life Science Peking University Beijing 100871 China
| | - Hongting Tang
- Center for Synthetic Biochemistry Institute of Synthetic Biology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Xiaoyun Liu
- Department of Microbiology School of Basic Medical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Xiaozhou Luo
- Center for Synthetic Biochemistry Institute of Synthetic Biology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
- CAS Key Laboratory of Quantitative Engineering Biology Institute of Synthetic Biology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Tao Liu
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center Department of Molecular and Cellular, Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
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11
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Toyobe M, Yakushiji F. Synthetic modifications of histones and their functional evaluation. Chem Asian J 2022; 17:e202200197. [PMID: 35489041 DOI: 10.1002/asia.202200197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/22/2022] [Indexed: 11/07/2022]
Abstract
Post-transrational modifications (PTMs) of histones play a key role in epigenetic regulation. Unraveling the roles of each epigenetic mark can provide new insights into their biological mechanisms. On the other hand, it is generally difficult to prepare homogeneously-modified histones/nucleosomes to investigate their specific functions. Therefore, synthetic approaches to acquire precisely mimicked histones/nucleosomes are in great demand, and further development of this research field is anticipated. In this review, synthetic strategies to modify histones/nucleosomes, including cysteine modifications, transformations of dehydroalanine residues and lysine acylation using a catalyst system, are cited. In addition, the functional evaluation of synthetically modified histones/nucleosomes is described.
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Affiliation(s)
- Moe Toyobe
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Fumika Yakushiji
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
- Global Station for Biosurfaces and Drug Discovery, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
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12
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Etier A, Dumetz F, Chéreau S, Ponts N. Post-Translational Modifications of Histones Are Versatile Regulators of Fungal Development and Secondary Metabolism. Toxins (Basel) 2022; 14:toxins14050317. [PMID: 35622565 PMCID: PMC9145779 DOI: 10.3390/toxins14050317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/16/2022] [Accepted: 04/25/2022] [Indexed: 02/04/2023] Open
Abstract
Chromatin structure is a major regulator of DNA-associated processes, such as transcription, DNA repair, and replication. Histone post-translational modifications, or PTMs, play a key role on chromatin dynamics. PTMs are involved in a wide range of biological processes in eukaryotes, including fungal species. Their deposition/removal and their underlying functions have been extensively investigated in yeasts but much less in other fungi. Nonetheless, the major role of histone PTMs in regulating primary and secondary metabolisms of filamentous fungi, including human and plant pathogens, has been pinpointed. In this review, an overview of major identified PTMs and their respective functions in fungi is provided, with a focus on filamentous fungi when knowledge is available. To date, most of these studies investigated histone acetylations and methylations, but the development of new methodologies and technologies increasingly allows the wider exploration of other PTMs, such as phosphorylation, ubiquitylation, sumoylation, and acylation. Considering the increasing number of known PTMs and the full range of their possible interactions, investigations of the subsequent Histone Code, i.e., the biological consequence of the combinatorial language of all histone PTMs, from a functional point of view, are exponentially complex. Better knowledge about histone PTMs would make it possible to efficiently fight plant or human contamination, avoid the production of toxic secondary metabolites, or optimize the industrial biosynthesis of certain beneficial compounds.
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13
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Jing Y, Li X, Liu Z, Li XD. Roles of Negatively Charged Histone Lysine Acylations in Regulating Nucleosome Structure and Dynamics. Front Mol Biosci 2022; 9:899013. [PMID: 35547393 PMCID: PMC9081332 DOI: 10.3389/fmolb.2022.899013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 04/06/2022] [Indexed: 01/08/2023] Open
Abstract
The nucleosome, the basic repeating unit of chromatin, is a dynamic structure that consists of DNA and histones. Insights derived from biochemical and biophysical approaches have revealed that histones posttranslational modifications (PTMs) are key regulators of nucleosome structure and dynamics. Mounting evidence suggests that the newly identified negatively charged histone lysine acylations play significant roles in altering nucleosome and chromatin dynamics, subsequently affecting downstream DNA-templated processes including gene transcription and DNA damage repair. Here, we present an overview of the dynamic changes of nucleosome and chromatin structures in response to negatively charged histone lysine acylations, including lysine malonylation, lysine succinylation, and lysine glutarylation.
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Affiliation(s)
- Yihang Jing
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory (SZBL), Shenzhen, China
- *Correspondence: Xiang David Li, ; Yihang Jing,
| | - Xin Li
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory (SZBL), Shenzhen, China
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Zheng Liu
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Xiang David Li
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory (SZBL), Shenzhen, China
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
- *Correspondence: Xiang David Li, ; Yihang Jing,
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14
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Shi X, Zhai Z, Chen Y, Li J, Nordenskiöld L. Recent Advances in Investigating Functional Dynamics of Chromatin. Front Genet 2022; 13:870640. [PMID: 35450211 PMCID: PMC9017861 DOI: 10.3389/fgene.2022.870640] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/11/2022] [Indexed: 11/26/2022] Open
Abstract
Dynamics spanning the picosecond-minute time domain and the atomic-subcellular spatial window have been observed for chromatin in vitro and in vivo. The condensed organization of chromatin in eukaryotic cells prevents regulatory factors from accessing genomic DNA, which requires dynamic stabilization and destabilization of structure to initiate downstream DNA activities. Those processes are achieved through altering conformational and dynamic properties of nucleosomes and nucleosome–protein complexes, of which delineating the atomistic pictures is essential to understand the mechanisms of chromatin regulation. In this review, we summarize recent progress in determining chromatin dynamics and their modulations by a number of factors including post-translational modifications (PTMs), incorporation of histone variants, and binding of effector proteins. We focus on experimental observations obtained using high-resolution techniques, primarily including nuclear magnetic resonance (NMR) spectroscopy, Förster (or fluorescence) resonance energy transfer (FRET) microscopy, and molecular dynamics (MD) simulations, and discuss the elucidated dynamics in the context of functional response and relevance.
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Affiliation(s)
- Xiangyan Shi
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen, China
| | - Ziwei Zhai
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen, China
| | - Yinglu Chen
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen, China
| | - Jindi Li
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen, China
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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15
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Song H, Shen R, Liu X, Yang X, Xie K, Guo Z, Wang D. Histone post-translational modification and the DNA damage response. Genes Dis 2022. [DOI: 10.1016/j.gendis.2022.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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16
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Qin YP, Yu HB, Yuan SY, Yang Z, Ren F, Wang Q, Li F, Ren JH, Cheng ST, Zhou YJ, He X, Zhou HZ, Zhang Y, Tan M, Yang ML, Zhang DP, Wen X, Dong ML, Zhang H, Liu J, Li ZH, Chen Y, Huang AL, Chen WX, Chen J. KAT2A Promotes Hepatitis B Virus Transcription and Replication Through Epigenetic Regulation of cccDNA Minichromosome. Front Microbiol 2022; 12:795388. [PMID: 35140694 PMCID: PMC8818952 DOI: 10.3389/fmicb.2021.795388] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/13/2021] [Indexed: 01/05/2023] Open
Abstract
Hepatitis B virus (HBV) infection remains a major health problem worldwide. Sufficient maintenance of the HBV covalently closed circular DNA (cccDNA), which serves as a template for HBV transcription, is responsible for the failure of antiviral therapies. While accumulating evidence suggests that cccDNA transcription is regulated by epigenetic machinery, particularly the acetylation and methylation of cccDNA-bound histone 3 (H3) and histone 4 (H4), the potential contributions of histone succinylation and related host factors remain obscured. Here, by screening a series of succinyltransferases and desuccinylases, we identified KAT2A as an important host factor of HBV transcription and replication. By using HBV-infected cells and mouse models with HBV infection, KAT2A was found to affect the transcriptional activity of cccDNA but did not affect cccDNA production. Mechanism studies showed that KAT2A is mainly located in the nucleus and could bind to cccDNA through interaction with HBV core protein (HBc). Moreover, we confirmed histone H3K79 succinylation (H3K79succ) as a histone modification on cccDNA minichromosome by using the cccDNA ChIP-Seq approach. Importantly, KAT2A silencing specifically reduced the level of cccDNA-bound succinylated H3K79. In conclusion, KAT2A promotes HBV transcription and replication through epigenetic machinery, and our findings may provide new insight into the treatment of HBV infection.
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Affiliation(s)
- Yi-Ping Qin
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Hai-Bo Yu
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Si-Yu Yuan
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Zhen Yang
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Fang Ren
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Qing Wang
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Fan Li
- Department of Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ji-Hua Ren
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Sheng-Tao Cheng
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Yu-Jiao Zhou
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Xin He
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Hong-Zhong Zhou
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Yuan Zhang
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Ming Tan
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Min-Li Yang
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Da-Peng Zhang
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Xu Wen
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Mei-Ling Dong
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Hui Zhang
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Jing Liu
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Zhi-Hong Li
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Yao Chen
- Department of Medical Examination Centre, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ai-Long Huang
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Wei-Xian Chen
- Department of Clinical Laboratory, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Juan Chen
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
- *Correspondence: Juan Chen,
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17
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Neumann-Staubitz P, Lammers M, Neumann H. Genetic Code Expansion Tools to Study Lysine Acylation. Adv Biol (Weinh) 2021; 5:e2100926. [PMID: 34713630 DOI: 10.1002/adbi.202100926] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 12/17/2022]
Abstract
Lysine acylation is a ubiquitous protein modification that controls various aspects of protein function, such as the activity, localization, and stability of enzymes. Mass spectrometric identification of lysine acylations has witnessed tremendous improvements in sensitivity over the last decade, facilitating the discovery of thousands of lysine acylation sites in proteins involved in all essential cellular functions across organisms of all domains of life. However, the vast majority of currently known acylation sites are of unknown function. Semi-synthetic methods for installing lysine derivatives are ideally suited for in vitro experiments, while genetic code expansion (GCE) allows the installation and study of such lysine modifications, especially their dynamic properties, in vivo. An overview of the current state of the art is provided, and its potential is illustrated with case studies from recent literature. These include the application of engineered enzymes and GCE to install lysine modifications or photoactivatable crosslinker amino acids. Their use in the context of central metabolism, bacterial and viral pathogenicity, the cytoskeleton and chromatin dynamics, is investigated.
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Affiliation(s)
- Petra Neumann-Staubitz
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Stephanstrasse 7, 64295, Darmstadt, Germany
| | - Michael Lammers
- Institute for Biochemistry, Department Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Heinz Neumann
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Stephanstrasse 7, 64295, Darmstadt, Germany
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18
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Li X, Li XD. Integrative Chemical Biology Approaches to Deciphering the Histone Code: A Problem-Driven Journey. Acc Chem Res 2021; 54:3734-3747. [PMID: 34553920 DOI: 10.1021/acs.accounts.1c00463] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The hereditary blueprint of a eukaryotic cell is encoded in its genomic DNA that is tightly compacted into chromatin together with histone proteins. The basic repeating units of chromatin fibers are nucleosomes, in which approximately 1.7 turns of DNA wrap around a proteinaceous octamer consisting of two copies of histones H2A, H2B, H3, and H4. Histones are extensively decorated by a variety of posttranslational modifications (PTMs, e.g., methylation, acetylation, ubiquitylation, phosphorylation, etc.), serving as one of the cellular mechanisms that regulates DNA-templated processes, including but not limited to gene transcription, DNA replication, and DNA damage repair. Most of the histone PTMs exist in dynamic fluctuations, and their on and off states are exquisitely regulated by enzymes known as "writers" and "erasers", respectively. When installed at certain sites, histone PTMs can change the local physicochemical environment and thereby directly influence the nucleosome and chromatin structures. Alternatively, histone PTMs can recruit effectors (or "readers") to signal the downstream events. A "histone code" hypothesis has been proposed in which the combinatory actions of different histone PTMs orchestrate the epigenetic landscape of cells, modulating the activity of the underlying DNA and maintaining the genome stability between generations. Accumulating evidence also suggests that malfunctions of histone PTMs are associated with the pathogenesis of human diseases, such as cancer. It is therefore important to fully decipher the histone code, namely, to dissect the regulatory mechanisms and biological functions of histone PTMs.Owing to the advances in state-of-the-art mass spectrometry, dozens of novel histone modifications have been archived during the past decade. However, most of these newly identified histone PTMs remain poorly explored. To unravel the roles played by these PTMs in histone code, key questions that have driven our study are (i) how to detect the novel histone PTMs; (ii) how to identify the enzymes that catalyze the addition (writers) and removal (erasers) of the histone PTMs along with the regulating mechanisms; (iii) what is the biological significance of the histone PTMs and how do they function, by affecting the nucleosome and chromatin dynamics or by recruiting readers; and (iv) how to develop chemical probes to interrogate the histone PTMs or even serve as potential leads for the drug discovery campaigns to treat diseases caused by abnormalities in the regulation of histone PTMs.This Account focuses on our efforts in developing and applying chemical tools and methods to answer the above questions. Specifically, we review the detection of negatively charged histone acylations by developing and applying chemical reporters; preparing homogeneous nucleosomes carrying negatively charged acylations by protein chemistry approaches and the in vitro biophysical analyses of the effects of the acylations on nucleosome structures; investigating the negatively charged acylations' influence on chromatin dynamics in vivo using yeast genetic approaches; identifying and characterizing protein-protein interactions (PPIs) mediated by histone PTMs in different biological contexts (i.e., to identify the readers and erasers) by establishing a chemical proteomics platform that is enabled by photo-cross-linking chemistry and quantitative proteomics strategies; and manipulating PTM-mediated PPIs by the structure-guided design of inhibitors. We also discuss possible future directions in our journey to fully decipher the histone code.
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Affiliation(s)
- Xin Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, 999077 China
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, 999077 China
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19
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Jing Y, Liu Z, Li XD. Protocol for the preparation of site-specific succinylated histone mimics to investigate the impact on nucleosome dynamics. STAR Protoc 2021; 2:100604. [PMID: 34189470 PMCID: PMC8215284 DOI: 10.1016/j.xpro.2021.100604] [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] [Indexed: 11/23/2022] Open
Abstract
Lysine succinylation is a recently discovered posttranslational modification that plays critical roles in metabolism, epigenetic signaling, and human diseases. To investigate the effects of site-specific histone lysine succinylation on nucleosome dynamics requires the generation of homogeneously modified histones, which is a significant challenge. Here, we report a protocol for the rapid site-specific installation of a succinyl lysine analog onto histone. We then use a Förster resonance energy transfer approach to characterize the impact on nucleosome dynamics. For complete details on the use and execution of this protocol, please refer to Jing et al. (2018). Strategy for site-specific installation of a succinyl-lysine analog into histones Strategy is generally applicable to all histones and other acid-resistant proteins A FRET-based biophysical assay reveals that H2BK34succ destabilizes nucleosomes
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Affiliation(s)
- Yihang Jing
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Zheng Liu
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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20
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Succinylation of Polyallylamine: Influence on Biological Efficacy and the Formation of Electrospun Fibers. Polymers (Basel) 2021; 13:polym13172840. [PMID: 34502880 PMCID: PMC8433649 DOI: 10.3390/polym13172840] [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: 07/23/2021] [Revised: 08/17/2021] [Accepted: 08/21/2021] [Indexed: 11/17/2022] Open
Abstract
Succinylation of proteins is a commonly encountered reaction in biology and introduces negatively charged carboxylates on previously basic primary amine groups of amino acid residues. In analogy, this work investigates the succinylation of primary amines of the synthetic polyelectrolyte polyallylamine (PAA). It investigates the influence of the degree of succinylation on the cytotoxicity and antibacterial activity of the resulting polymers. Succinylation was performed in water with varying amounts of succinic anhydride and at different pH values. The PAA derivatives were analyzed in detail with respect to molecular structure using nuclear magnetic resonance and infrared absorbance spectroscopy. Polyelectrolyte and potentiometric charge titrations were used to elucidate charge ratios between primary amines and carboxylates in the polymers. The obtained materials were then evaluated with respect to their minimum inhibitory concentration against Staphylococcus aureus and Pseudomonas aeruginosa. The biocompatibility was assessed using mouse L929 fibroblasts. The degree of succinylation decreased cytotoxicity but more significantly reduced antibacterial efficacy, demonstrating the sensitivity of the fibroblast cells against this type of ampholytic polyelectrolytes. The obtained polymers were finally electrospun into microfiber webs in combination with neutral water-soluble polyvinyl alcohol. The resulting non-woven could have the potential to be used as wound dressing materials or coatings.
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21
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Blasl AT, Schulze S, Qin C, Graf LG, Vogt R, Lammers M. Post-translational lysine ac(et)ylation in health, ageing and disease. Biol Chem 2021; 403:151-194. [PMID: 34433238 DOI: 10.1515/hsz-2021-0139] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 06/18/2021] [Indexed: 12/13/2022]
Abstract
The acetylation/acylation (ac(et)ylation) of lysine side chains is a dynamic post-translational modification (PTM) regulating fundamental cellular processes with implications on the organisms' ageing process: metabolism, transcription, translation, cell proliferation, regulation of the cytoskeleton and DNA damage repair. First identified to occur on histones, later studies revealed the presence of lysine ac(et)ylation in organisms of all kingdoms of life, in proteins covering all essential cellular processes. A remarkable finding showed that the NAD+-dependent sirtuin deacetylase Sir2 has an impact on replicative lifespan in Saccharomyces cerevisiae suggesting that lysine acetylation has a direct role in the ageing process. Later studies identified sirtuins as mediators for beneficial effects of caloric/dietary restriction on the organisms' health- or lifespan. However, the molecular mechanisms underlying these effects are only incompletely understood. Progress in mass-spectrometry, structural biology, synthetic and semi-synthetic biology deepened our understanding of this PTM. This review summarizes recent developments in the research field. It shows how lysine ac(et)ylation regulates protein function, how it is regulated enzymatically and non-enzymatically, how a dysfunction in this post-translational machinery contributes to disease development. A focus is set on sirtuins and lysine acyltransferases as these are direct sensors and mediators of the cellular metabolic state. Finally, this review highlights technological advances to study lysine ac(et)ylation.
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Affiliation(s)
- Anna-Theresa Blasl
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
| | - Sabrina Schulze
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
| | - Chuan Qin
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
| | - Leonie G Graf
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
| | - Robert Vogt
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
| | - Michael Lammers
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
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22
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Jing Y, Tian G, Qin X, Liu Z, Li XD. Lysine succinylation on non-histone chromosomal protein HMG-17 (HMGN2) regulates nucleosomal DNA accessibility by disrupting the HMGN2-nucleosome association. RSC Chem Biol 2021; 2:1257-1262. [PMID: 34458839 PMCID: PMC8341127 DOI: 10.1039/d1cb00070e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/25/2021] [Indexed: 02/01/2023] Open
Abstract
Lysine succinylation (Ksucc) is a novel posttranslational modification that frequently occurs on chromatin proteins including histones and non-histone proteins. Histone Ksucc affects nucleosome dynamics by increasing the DNA unwrapping rate and accessibility. However, very little is known about the regulation and functions of Ksucc located on non-histone chromosomal proteins. Here, we site-specifically installed a succinyl lysine analogue (Kcsucc) onto the non-histone chromosomal protein HMG-17 (HMGN2) to mimic the natural succinylated protein. We found that the incorporation of Kcsucc into HMGN2 at the K30 site (HMGN2Kc30succ), which is located within the nucleosome-binding domain (NBD), leads to significantly decreased HMGN2 binding to the mononucleosome. HMGN2Kc30succ also increased the nucleosomal DNA accessibility by promoting nucleosomal DNA unwrapping in the entry/exit region. This study reveals a novel mechanism of non-histone protein succinylation on altering chromatin recruitment, which can further affect nucleosome and chromatin dynamics. Succinylated HMGN2, prepared by a ‘thiol–ene reaction’, disrupted the association of HMGN2 with the nucleosome and increased nucleosomal DNA accessibility.![]()
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Affiliation(s)
- Yihang Jing
- Department of Chemistry, The University of Hong Kong Pokfulam Road Hong Kong China
| | - Gaofei Tian
- Department of Chemistry, The University of Hong Kong Pokfulam Road Hong Kong China
| | - Xiaoyu Qin
- Department of Chemistry, The University of Hong Kong Pokfulam Road Hong Kong China
| | - Zheng Liu
- Department of Chemistry, The University of Hong Kong Pokfulam Road Hong Kong China
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong Pokfulam Road Hong Kong China
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23
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Nitsch S, Zorro Shahidian L, Schneider R. Histone acylations and chromatin dynamics: concepts, challenges, and links to metabolism. EMBO Rep 2021; 22:e52774. [PMID: 34159701 PMCID: PMC8406397 DOI: 10.15252/embr.202152774] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/08/2021] [Accepted: 05/31/2021] [Indexed: 01/17/2023] Open
Abstract
In eukaryotic cells, DNA is tightly packed with the help of histone proteins into chromatin. Chromatin architecture can be modified by various post-translational modifications of histone proteins. For almost 60 years now, studies on histone lysine acetylation have unraveled the contribution of this acylation to an open chromatin state with increased DNA accessibility, permissive for gene expression. Additional complexity emerged from the discovery of other types of histone lysine acylations. The acyl group donors are products of cellular metabolism, and distinct histone acylations can link the metabolic state of a cell with chromatin architecture and contribute to cellular adaptation through changes in gene expression. Currently, various technical challenges limit our full understanding of the actual impact of most histone acylations on chromatin dynamics and of their biological relevance. In this review, we summarize the state of the art and provide an overview of approaches to overcome these challenges. We further discuss the concept of subnuclear metabolic niches that could regulate local CoA availability and thus couple cellular metabolisms with the epigenome.
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Affiliation(s)
- Sandra Nitsch
- Institute of Functional Epigenetics (IFE)Helmholtz Zentrum MünchenNeuherbergGermany
| | - Lara Zorro Shahidian
- Institute of Functional Epigenetics (IFE)Helmholtz Zentrum MünchenNeuherbergGermany
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC)University of CantabriaSantanderSpain
| | - Robert Schneider
- Institute of Functional Epigenetics (IFE)Helmholtz Zentrum MünchenNeuherbergGermany
- German Center for Diabetes Research (DZD)NeuherbergGermany
- Faculty of BiologyLudwig‐Maximilians Universität MünchenPlanegg‐MartinsriedGermany
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24
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Liu J, Shangguan Y, Tang D, Dai Y. Histone succinylation and its function on the nucleosome. J Cell Mol Med 2021; 25:7101-7109. [PMID: 34160884 PMCID: PMC8335665 DOI: 10.1111/jcmm.16676] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/01/2021] [Accepted: 05/05/2021] [Indexed: 02/06/2023] Open
Abstract
Protein post‐translational modifications (PTMs) of histones are ubiquitous regulatory mechanisms involved in many biological processes, including replication, transcription, DNA damage repair and ontogenesis. Recently, many short‐chain acylation histone modifications have been identified by mass spectrometry (MS). Lysine succinylation (Ksuc or Ksucc) is a newly identified histone PTM that changes the chemical environment of histones and is similar to other acylation modifications; lysine succinylation appears to accumulate at transcriptional start sites and to correlate with gene expression. Although numerous studies are ongoing, there is a lack of reviews on the Ksuc of histones. Here, we review lysine succinylation sites on histones, including the chemical characteristics and the mechanism by which lysine succinylation influences nucleosomal structure, chromatin dynamics and several diseases and then discuss lysine succinylation regulation to identify theoretical and experimental proof of Ksuc on histones and in diseases to inspire further research into histone lysine succinylation as a target of disease treatment in the future.
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Affiliation(s)
- Jiayi Liu
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The First Affiliated Hospital(Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China.,School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Yu Shangguan
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The First Affiliated Hospital(Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China.,Guangxi Key Laboratory of Metabolic Disease Research, Central Laboratory of Guilin, 924st Hospital, Guilin, China
| | - Donge Tang
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The First Affiliated Hospital(Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China.,School of Medicine, Southern University of Science and Technology, Shenzhen, China.,Guangxi Key Laboratory of Metabolic Disease Research, Central Laboratory of Guilin, 924st Hospital, Guilin, China
| | - Yong Dai
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The First Affiliated Hospital(Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China.,School of Medicine, Southern University of Science and Technology, Shenzhen, China.,Guangxi Key Laboratory of Metabolic Disease Research, Central Laboratory of Guilin, 924st Hospital, Guilin, China
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25
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A tri-functional amino acid enables mapping of binding sites for posttranslational-modification-mediated protein-protein interactions. Mol Cell 2021; 81:2669-2681.e9. [PMID: 33894155 DOI: 10.1016/j.molcel.2021.04.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 03/01/2021] [Accepted: 03/31/2021] [Indexed: 12/16/2022]
Abstract
Posttranslational modification (PTM), through the recruitment of effector proteins (i.e., "readers") that signal downstream events, plays key roles in regulating a variety of cellular processes. To understand how a PTM is recognized, it is necessary to find its readers and, importantly, the location of the binding pockets responsible for PTM recognition. Although various methods have been developed to identify PTM readers, it remains a challenge to directly map the PTM-binding regions, especially for intrinsically disordered domains. Here, we demonstrate a photo-crosslinkable, clickable, and cleavable tri-functional amino acid, ADdis-Cys, that when coupled with mass spectrometry (ADdis-Cys-MS) can not only identify PTM readers from complex proteomes but also simultaneously map their PTM-recognition modules. Using ADdis-Cys-MS, we successfully identify the binding sites of several reader-PTM interactions, among which we discover human C1QBP as a histone chaperone. This robust method should find wide applications in examining other histone or non-histone PTM-mediated protein-protein interactions.
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26
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Figlia G, Willnow P, Teleman AA. Metabolites Regulate Cell Signaling and Growth via Covalent Modification of Proteins. Dev Cell 2021; 54:156-170. [PMID: 32693055 DOI: 10.1016/j.devcel.2020.06.036] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/15/2020] [Accepted: 06/28/2020] [Indexed: 02/07/2023]
Abstract
Metabolites affect cell growth in two different ways. First, they serve as building blocks for biomass accumulation. Second, metabolites regulate the activity of growth-relevant signaling pathways. They do so in part by covalently attaching to proteins, thereby generating post-translational modifications (PTMs) that affect protein function, the focus of this Perspective. Recent advances in mass spectrometry have revealed a wide variety of such metabolites, including lipids, amino acids, Coenzyme-A, acetate, malonate, and lactate to name a few. An active area of research is to understand which modifications affect protein function and how they do so. In many cases, the cellular levels of these metabolites affect the stoichiometry of the corresponding PTMs, providing a direct link between cell metabolism and the control of cell signaling, transcription, and cell growth.
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Affiliation(s)
- Gianluca Figlia
- German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg 69120, Germany; Heidelberg University, Heidelberg, Baden-Württemberg 69120, Germany
| | - Philipp Willnow
- German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg 69120, Germany; Heidelberg University, Heidelberg, Baden-Württemberg 69120, Germany
| | - Aurelio A Teleman
- German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg 69120, Germany; Heidelberg University, Heidelberg, Baden-Württemberg 69120, Germany.
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27
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Yao T, Przybyla JJ, Yeh P, Woodard AM, Nilsson HJ, Brandsen BM, Silverman SK. DNAzymes for amine and peptide lysine acylation. Org Biomol Chem 2021; 19:171-181. [PMID: 33150349 PMCID: PMC7790989 DOI: 10.1039/d0ob02015j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNAzymes were previously identified by in vitro selection for a variety of chemical reactions, including several biologically relevant peptide modifications. However, finding DNAzymes for peptide lysine acylation is a substantial challenge. By using suitably reactive aryl ester acyl donors as the electrophiles, here we used in vitro selection to identify DNAzymes that acylate amines, including lysine side chains of DNA-anchored peptides. Some of the DNAzymes can transfer a small glutaryl group to an amino group. These results expand the scope of DNAzyme catalysis and suggest the future broader applicability of DNAzymes for sequence-selective lysine acylation of peptide and protein substrates.
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Affiliation(s)
- Tianjiong Yao
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA.
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28
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Jing Y, Ding D, Tian G, Kwan KCJ, Liu Z, Ishibashi T, Li XD. Semisynthesis of site-specifically succinylated histone reveals that succinylation regulates nucleosome unwrapping rate and DNA accessibility. Nucleic Acids Res 2020; 48:9538-9549. [PMID: 32766790 PMCID: PMC7515725 DOI: 10.1093/nar/gkaa663] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/22/2020] [Accepted: 07/29/2020] [Indexed: 01/06/2023] Open
Abstract
Posttranslational modifications (PTMs) of histones represent a crucial regulatory mechanism of nucleosome and chromatin dynamics in various of DNA-based cellular processes, such as replication, transcription and DNA damage repair. Lysine succinylation (Ksucc) is a newly identified histone PTM, but its regulation and function in chromatin remain poorly understood. Here, we utilized an expressed protein ligation (EPL) strategy to synthesize histone H4 with site-specific succinylation at K77 residue (H4K77succ), an evolutionarily conserved succinylation site at the nucleosomal DNA-histone interface. We then assembled mononucleosomes with the semisynthetic H4K77succ in vitro. We demonstrated that this succinylation impacts nucleosome dynamics and promotes DNA unwrapping from the histone surface, which allows proteins such as transcription factors to rapidly access buried regions of the nucleosomal DNA. In budding yeast, a lysine-to-glutamic acid mutation, which mimics Ksucc, at the H4K77 site reduced nucleosome stability and led to defects in DNA damage repair and telomere silencing in vivo. Our findings revealed this uncharacterized histone modification has important roles in nucleosome and chromatin dynamics.
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Affiliation(s)
- Yihang Jing
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Dongbo Ding
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Gaofei Tian
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Ka Chun Jonathan Kwan
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Zheng Liu
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Toyotaka Ishibashi
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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29
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TCA cycle signalling and the evolution of eukaryotes. Curr Opin Biotechnol 2020; 68:72-88. [PMID: 33137653 DOI: 10.1016/j.copbio.2020.09.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/15/2020] [Accepted: 09/21/2020] [Indexed: 12/19/2022]
Abstract
A major question remaining in the field of evolutionary biology is how prokaryotic organisms made the leap to complex eukaryotic life. The prevailing theory depicts the origin of eukaryotic cell complexity as emerging from the symbiosis between an α-proteobacterium, the ancestor of present-day mitochondria, and an archaeal host (endosymbiont theory). A primary contribution of mitochondria to eukaryogenesis has been attributed to the mitochondrial genome, which enabled the successful internalisation of bioenergetic membranes and facilitated remarkable genome expansion. It has also been postulated that a key contribution of the archaeal host during eukaryogenesis was in providing 'archaeal histones' that would enable compaction and regulation of an expanded genome. Yet, how the communication between the host and the symbiont evolved is unclear. Here, we propose an evolutionary concept in which mitochondrial TCA cycle signalling was also a crucial player during eukaryogenesis enabling the dynamic control of an expanded genome via regulation of DNA and histone modifications. Furthermore, we discuss how TCA cycle remodelling is a common evolutionary strategy invoked by eukaryotic organisms to coordinate stress responses and gene expression programmes, with a particular focus on the TCA cycle-derived metabolite itaconate.
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30
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Beyer JN, Raniszewski NR, Burslem GM. Advances and Opportunities in Epigenetic Chemical Biology. Chembiochem 2020; 22:17-42. [PMID: 32786101 DOI: 10.1002/cbic.202000459] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/10/2020] [Indexed: 12/13/2022]
Abstract
The study of epigenetics has greatly benefited from the development and application of various chemical biology approaches. In this review, we highlight the key targets for modulation and recent methods developed to enact such modulation. We discuss various chemical biology techniques to study DNA methylation and the post-translational modification of histones as well as their effect on gene expression. Additionally, we address the wealth of protein synthesis approaches to yield histones and nucleosomes bearing epigenetic modifications. Throughout, we highlight targets that present opportunities for the chemical biology community, as well as exciting new approaches that will provide additional insight into the roles of epigenetic marks.
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Affiliation(s)
- Jenna N Beyer
- Department of Biochemistry and Biophysics Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA
| | - Nicole R Raniszewski
- Department of Biochemistry and Biophysics Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA
| | - George M Burslem
- Department of Biochemistry and Biophysics Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA.,Department of Cancer Biology and Epigenetics Institute Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA
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31
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Wang ZA, Cole PA. The Chemical Biology of Reversible Lysine Post-translational Modifications. Cell Chem Biol 2020; 27:953-969. [PMID: 32698016 PMCID: PMC7487139 DOI: 10.1016/j.chembiol.2020.07.002] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/09/2020] [Accepted: 07/01/2020] [Indexed: 12/31/2022]
Abstract
Lysine (Lys) residues in proteins undergo a wide range of reversible post-translational modifications (PTMs), which can regulate enzyme activities, chromatin structure, protein-protein interactions, protein stability, and cellular localization. Here we discuss the "writers," "erasers," and "readers" of some of the common protein Lys PTMs and summarize examples of their major biological impacts. We also review chemical biology approaches, from small-molecule probes to protein chemistry technologies, that have helped to delineate Lys PTM functions and show promise for a diverse set of biomedical applications.
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Affiliation(s)
- Zhipeng A Wang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 77 Avenue Louis Pasteur NRB, Boston, MA 02115, USA
| | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 77 Avenue Louis Pasteur NRB, Boston, MA 02115, USA.
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32
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Wang M, Chang Q, Yang H, Liu Y, Wang C, Hu F, Wei H, Li R. Elevated lysine crotonylation and succinylation in the brains of BTBR mice. Int J Dev Neurosci 2019; 76:61-64. [PMID: 31255717 DOI: 10.1016/j.ijdevneu.2019.06.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 06/22/2019] [Accepted: 06/26/2019] [Indexed: 10/26/2022] Open
Abstract
The BTBR T + Itpr3tf/J (BTBR) mouse has developmental disorders in the central nervous system and many aberrant neuroanatomical structures. However, identification of the pathological mechanisms underlying these abnormal neuroanatomical structures in the brains of BTBR mice is still lacking. Posttranslational modifications (PTMs) are known to be involved in the regulation of diverse cellular processes, and evidence shows that some types of PTMs are associated with the development of the central nervous system. In this study, we detected four novel PTMs in the cerebral cortex of BTBR mice as compared to C57BL/6 J (B6) mice using western blotting. Results revealed that lysine crotonylation and succinylation were elevated in the cerebral cortex of BTBR mice compared to levels in B6 mice. We speculate that elevated profiles of lysine crotonylation and succinylation may be involved in mechanisms related to neuroanatomical abnormalities in cerebral cortex of BTBR mice.
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Affiliation(s)
- Min Wang
- Department of Neurology, Shanxi Provincial People's Hospital, Affiliate of Shanxi Medical University, Taiyuan, China
| | - Qiaoqiao Chang
- Department of Neurology, Shanxi Provincial People's Hospital, Affiliate of Shanxi Medical University, Taiyuan, China
| | - Hua Yang
- Department of Neurology, Shanxi Provincial People's Hospital, Affiliate of Shanxi Medical University, Taiyuan, China
| | - Yongfeng Liu
- Department of Neurology, Shanxi Provincial People's Hospital, Affiliate of Shanxi Medical University, Taiyuan, China
| | - Chunfang Wang
- Shanxi Key Laboratory of Animal and Animal Model of Human Diseases, Taiyuan, China
| | - Fengyun Hu
- Department of Neurology, Shanxi Provincial People's Hospital, Affiliate of Shanxi Medical University, Taiyuan, China
| | - Hongen Wei
- Department of Neurology, Shanxi Provincial People's Hospital, Affiliate of Shanxi Medical University, Taiyuan, China
| | - Rongshan Li
- Nephrology Division, Shanxi Provincial People's Hospital, Affiliate of Shanxi Medical University, Taiyuan, China
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33
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Linking chromatin composition and structural dynamics at the nucleosome level. Curr Opin Struct Biol 2019; 56:46-55. [DOI: 10.1016/j.sbi.2018.11.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 11/15/2018] [Accepted: 11/15/2018] [Indexed: 01/31/2023]
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34
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Wu L, Gong T, Zhou X, Zeng J, Huang R, Wu Y, Li Y. Global analysis of lysine succinylome in the periodontal pathogen Porphyromonas gingivalis. Mol Oral Microbiol 2019; 34:74-83. [PMID: 30672658 DOI: 10.1111/omi.12255] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 12/22/2018] [Accepted: 01/21/2019] [Indexed: 02/05/2023]
Abstract
The gram-negative anaerobe Porphyromonas gingivalis is not only a keystone periodontal pathogen but also an emerging systemic pathogen. Although the newly discovered protein post-translational modification (PTM), lysine succinylation (Ksuc), appears to play an important role in modulating metabolic processes in bacteria, this PTM has not been investigated in P gingivalis. In this study, we used a highly sensitive proteomics approach combining affinity enrichment with high-resolution liquid chromatography coupled with tandem mass spectrometry to examine Ksuc in P gingivalis. In total, 345 Ksuc sites in 233 proteins were identified and determined to be involved in a variety of cellular processes. In the region surrounding Ksuc sites, lysine residues were drastically overrepresented and sequence motifs with succinyl-lysine flanked by a lysine at the +3 or +6 positions appear to be unique to this pathogen. Additionally, our results suggest a crosstalk between Ksuc and glycosylation, but the overlap between Ksuc and acetylation in P gingivalis is quite different from that observed in other organisms. Notably, Ksuc was observed in proteins associated with established virulence factors, including gingipains, fimbriae, RagB, and PorR. Moreover, products of the factors necessary for P gingivalis in vitro survival (18.5%) were found to be succinylated at lysine sites and the same was observed in products of fitness factors for P gingivalis survival in both abscess and epithelial cell colonization environments (12%). Collectively, these results suggest that Ksuc may be a new mechanism in modulating the virulence, adaptation, and fitness of P gingivalis.
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Affiliation(s)
- Leng Wu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China.,Department of Stomatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Tao Gong
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Jumei Zeng
- Department of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ruijie Huang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Yafei Wu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
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35
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Chu GC, Pan M, Li J, Liu S, Zuo C, Tong ZB, Bai JS, Gong Q, Ai H, Fan J, Meng X, Huang YC, Shi J, Deng H, Tian C, Li YM, Liu L. Cysteine-Aminoethylation-Assisted Chemical Ubiquitination of Recombinant Histones. J Am Chem Soc 2019; 141:3654-3663. [PMID: 30758956 DOI: 10.1021/jacs.8b13213] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Histone ubiquitination affects the structure and function of nucleosomes through tightly regulated dynamic reversible processes. The efficient preparation of ubiquitinated histones and their analogs is important for biochemical and biophysical studies on histone ubiquitination. Here, we report the CAACU (cysteine-aminoethylation assisted chemical ubiquitination) strategy for the efficient synthesis of ubiquitinated histone analogs. The key step in the CAACU strategy is the installation of an N-alkylated 2-bromoethylamine derivative into a recombinant histone through cysteine aminoethylation, followed by native chemical ligation assisted by Seitz's auxiliary to produce mono- and diubiquitin (Ub) and small ubiquitin-like modifier (SUMO) modified histone analogs. This approach enables the rapid production of modified histones from recombinant proteins at about 1.5-6 mg/L expression. The thioether-containing isopeptide bonds in the products are chemically stable and bear only one atomic substitution in the structure, compared to their native counterparts. The ubiquitinated histone analogs prepared by CAACU can be readily reconstituted into nucleosomes and selectively recognized by relevant interacting proteins. The thioether-containing isopeptide bonds can also be recognized and hydrolyzed by deubiquitinases (DUBs). Cryo-electron microscopy (cryo-EM) of the nucleosome containing H2BKC34Ub indicated that the obtained CAACU histones were of good quality for structural studies. Collectively, this work exemplifies the utility of the CAACU strategy for the simple and efficient production of homogeneous ubiquitinated and SUMOylated histones for biochemical and biophysical studies.
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Affiliation(s)
- Guo-Chao Chu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry , Tsinghua University , Beijing 100084 , China.,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 230009 , China
| | - Man Pan
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry , Tsinghua University , Beijing 100084 , China
| | | | | | - Chong Zuo
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry , Tsinghua University , Beijing 100084 , China.,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 230009 , China
| | - Ze-Bin Tong
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry , Tsinghua University , Beijing 100084 , China.,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 230009 , China
| | - Jing-Si Bai
- 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 230009 , China
| | | | - Huasong Ai
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry , Tsinghua University , Beijing 100084 , China
| | | | - Xianbin Meng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences , Tsinghua University , Beijing 100084 , China
| | - Yi-Chao Huang
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry , Tsinghua University , Beijing 100084 , China
| | | | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences , Tsinghua University , Beijing 100084 , 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 230009 , China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry , Tsinghua University , Beijing 100084 , China
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36
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Hasan MM, Khatun MS, Kurata H. Large-Scale Assessment of Bioinformatics Tools for Lysine Succinylation Sites. Cells 2019; 8:cells8020095. [PMID: 30696115 PMCID: PMC6406724 DOI: 10.3390/cells8020095] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 01/24/2019] [Accepted: 01/24/2019] [Indexed: 12/19/2022] Open
Abstract
Lysine succinylation is a form of posttranslational modification of the proteins that play an essential functional role in every aspect of cell metabolism in both prokaryotes and eukaryotes. Aside from experimental identification of succinylation sites, there has been an intense effort geared towards the development of sequence-based prediction through machine learning, due to its promising and essential properties of being highly accurate, robust and cost-effective. In spite of these advantages, there are several problems that are in need of attention in the design and development of succinylation site predictors. Notwithstanding of many studies on the employment of machine learning approaches, few articles have examined this bioinformatics field in a systematic manner. Thus, we review the advancements regarding the current state-of-the-art prediction models, datasets, and online resources and illustrate the challenges and limitations to present a useful guideline for developing powerful succinylation site prediction tools.
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Affiliation(s)
- Md Mehedi Hasan
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680⁻4 Kawazu, Iizuka, Fukuoka 820-8502, Japan.
| | - Mst Shamima Khatun
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680⁻4 Kawazu, Iizuka, Fukuoka 820-8502, Japan.
| | - Hiroyuki Kurata
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680⁻4 Kawazu, Iizuka, Fukuoka 820-8502, Japan.
- Biomedical Informatics R&D Center, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan.
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37
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Structural insights into the molecular mechanism underlying Sirt5-catalyzed desuccinylation of histone peptides. Biochem J 2019; 476:211-223. [PMID: 30523058 DOI: 10.1042/bcj20180745] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/27/2018] [Accepted: 12/05/2018] [Indexed: 12/16/2022]
Abstract
Histone modification is a ubiquitous regulatory mechanism involved in a variety of biological processes, including gene expression, DNA damage repair, cell differentiation, and ontogenesis. Succinylation sites on histones have been identified and may have functional consequences. Here, we demonstrate that human sirtuin 5 (Sirt5) catalyzes the sequence-selective desuccinylation of numerous histone succinyl sites. Structural studies of Sirt5 in complex with four succinyl peptides indicate an essential role for the conserved main chain hydrogen bonds formed by the succinyl lysine (0), +1, and +3 sites for substrate-enzyme recognition. Furthermore, biochemical assays reveal that the proline residue at the +1 site of the histone succinylation substrate is unfavorable for Sirt5 interaction. Our findings illustrate the molecular mechanism underlying the sequence-selective desuccinylase activity of Sirt5 and provide insights for further studies of the biological functions associated with histone succinylation and Sirt5.
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38
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Affiliation(s)
- Seiji SAKAMOTO
- Graduate School of Engineering, Department of Synthetic Chemistry and Biological Chemistry, Kyoto University
| | - Itaru HAMACHI
- Graduate School of Engineering, Department of Synthetic Chemistry and Biological Chemistry, Kyoto University
- ERATO Innovative Molecular Technology for Neuroscience Project, Japan Science and Technology Agency (JST)
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Bhat S, Hwang Y, Gibson MD, Morgan MT, Taverna SD, Zhao Y, Wolberger C, Poirier MG, Cole PA. Hydrazide Mimics for Protein Lysine Acylation To Assess Nucleosome Dynamics and Deubiquitinase Action. J Am Chem Soc 2018; 140:9478-9485. [PMID: 29991262 PMCID: PMC6070418 DOI: 10.1021/jacs.8b03572] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A range of acyl-lysine (acyl-Lys) modifications on histones and other proteins have been mapped over the past decade but for most, their functional and structural significance remains poorly characterized. One limitation in the study of acyl-Lys containing proteins is the challenge of producing them or their mimics in site-specifically modified forms. We describe a cysteine alkylation-based method to install hydrazide mimics of acyl-Lys post-translational modifications (PTMs) on proteins. We have applied this method to install mimics of acetyl-Lys, 2-hydroxyisobutyryl-Lys, and ubiquityl-Lys that could be recognized selectively by relevant acyl-Lys modification antibodies. The acyl-Lys modified histone H3 proteins were reconstituted into nucleosomes to study nucleosome dynamics and stability as a function of modification type and site. We also installed a ubiquityl-Lys mimic in histone H2B and generated a diubiquitin analog, both of which could be cleaved by deubiquitinating enzymes. Nucleosomes containing the H2B ubiquityl-Lys mimic were used to study the SAGA deubiquitinating module's molecular recognition. These results suggest that acyl-Lys mimics offer a relatively simple and promising strategy to study the role of acyl-Lys modifications in the function, structure, and regulation of proteins and protein complexes.
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Affiliation(s)
- Shridhar Bhat
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Yousang Hwang
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Matthew D. Gibson
- Department of Physics, Ohio State University, Columbus, Ohio 43210, USA
| | - Michael T. Morgan
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Sean D. Taverna
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Yingming Zhao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | | | - Philip A. Cole
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Division of Genetics, Brigham and Women’s Hospital; Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 77 Ave Louis Pasteur, HMS New Research Building, Boston, Massachusetts 02115, USA
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Peptide-based approaches to identify and characterize proteins that recognize histone post-translational modifications. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2018.05.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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