1
|
Seath CP, Burton AJ, Sun X, Lee G, Kleiner RE, MacMillan DWC, Muir TW. Tracking chromatin state changes using nanoscale photo-proximity labelling. Nature 2023; 616:574-580. [PMID: 37020029 PMCID: PMC10408239 DOI: 10.1038/s41586-023-05914-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/02/2023] [Indexed: 04/07/2023]
Abstract
Interactions between biomolecules underlie all cellular processes and ultimately control cell fate. Perturbation of native interactions through mutation, changes in expression levels or external stimuli leads to altered cellular physiology and can result in either disease or therapeutic effects1,2. Mapping these interactions and determining how they respond to stimulus is the genesis of many drug development efforts, leading to new therapeutic targets and improvements in human health1. However, in the complex environment of the nucleus, it is challenging to determine protein-protein interactions owing to low abundance, transient or multivalent binding and a lack of technologies that are able to interrogate these interactions without disrupting the protein-binding surface under study3. Here, we describe a method for the traceless incorporation of iridium-photosensitizers into the nuclear micro-environment using engineered split inteins. These Ir-catalysts can activate diazirine warheads through Dexter energy transfer to form reactive carbenes within an approximately 10 nm radius, cross-linking with proteins in the immediate micro-environment (a process termed µMap) for analysis using quantitative chemoproteomics4. We show that this nanoscale proximity-labelling method can reveal the critical changes in interactomes in the presence of cancer-associated mutations, as well as treatment with small-molecule inhibitors. µMap improves our fundamental understanding of nuclear protein-protein interactions and, in doing so, is expected to have a significant effect on the field of epigenetic drug discovery in both academia and industry.
Collapse
Affiliation(s)
- Ciaran P Seath
- Merck Center for Catalysis at Princeton University, Princeton, NJ, USA
- Department of Chemistry, Princeton University, Princeton, NJ, USA
- Department of Chemistry, Scripps-UF, Jupiter, FL, USA
| | - Antony J Burton
- Department of Chemistry, Princeton University, Princeton, NJ, USA
- Discovery Biology, Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Waltham, MA, USA
| | - Xuemeng Sun
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Gihoon Lee
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Ralph E Kleiner
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - David W C MacMillan
- Merck Center for Catalysis at Princeton University, Princeton, NJ, USA.
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
| | - Tom W Muir
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
| |
Collapse
|
2
|
The critical importance of epigenetics in autoimmune-related skin diseases. Front Med 2023; 17:43-57. [PMID: 36811762 DOI: 10.1007/s11684-022-0980-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 12/05/2022] [Indexed: 02/24/2023]
Abstract
Autoimmune-related skin diseases are a group of disorders with diverse etiology and pathophysiology involved in autoimmunity. Genetics and environmental factors may contribute to the development of these autoimmune disorders. Although the etiology and pathogenesis of these disorders are poorly understood, environmental variables that induce aberrant epigenetic regulations may provide some insights. Epigenetics is the study of heritable mechanisms that regulate gene expression without changing DNA sequences. The most important epigenetic mechanisms are DNA methylation, histone modification, and noncoding RNAs. In this review, we discuss the most recent findings regarding the function of epigenetic mechanisms in autoimmune-related skin disorders, including systemic lupus erythematosus, bullous skin diseases, psoriasis, and systemic sclerosis. These findings will expand our understanding and highlight the possible clinical applications of precision epigenetics approaches.
Collapse
|
3
|
Guo AD, Chen XH. Genetically Encoded Noncanonical Amino Acids in Proteins to Investigate Lysine Benzoylation. Methods Mol Biol 2023; 2676:131-146. [PMID: 37277629 DOI: 10.1007/978-1-0716-3251-2_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Posttranslational modifications (PTMs) of lysine residues are major regulators of gene expression, protein-protein interactions, and protein localization and degradation. Histone lysine benzoylation is a recently identified epigenetic marker associated with active transcription, which has physiological relevance distinct from histone acetylation and can be regulated by debenzoylation of sirtuin 2 (SIRT2). Herein, we provide a protocol for the incorporation of benzoyllysine and fluorinated benzoyllysine into full-length histone proteins, which further serve as benzoylated histone probes with NMR or fluorescence signal for investigating the dynamics of SIRT2-mediated debenzoylation.
Collapse
Affiliation(s)
- An-Di Guo
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Xiao-Hua Chen
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
| |
Collapse
|
4
|
Zhang Z, Lin J, Liu Z, Tian G, Li XM, Jing Y, Li X, Li XD. Photo-Cross-Linking To Delineate Epigenetic Interactome. J Am Chem Soc 2022; 144:20979-20997. [DOI: 10.1021/jacs.2c06135] [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)
- Zhuoyuan Zhang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Jianwei Lin
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Zheng Liu
- 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
| | - Xiao-Meng Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yihang Jing
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Xin Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| |
Collapse
|
5
|
Histone Modifications in Neurological Disorders. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1382:95-107. [DOI: 10.1007/978-3-031-05460-0_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
6
|
Tian H, Yang J, Guo AD, Ran Y, Yang YZ, Yang B, Huang R, Liu H, Chen XH. Genetically Encoded Benzoyllysines Serve as Versatile Probes for Interrogating Histone Benzoylation and Interactions in Living Cells. ACS Chem Biol 2021; 16:2560-2569. [PMID: 34618427 DOI: 10.1021/acschembio.1c00614] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Histone posttranslational modifications (PTMs) are vital epigenetic regulators in many fundamental cell signaling pathways and diverse biological processes. Histone lysine benzoylation is a recently identified epigenetic mark associated with active transcription; however, it remains to be explored. Herein, we first report the genetic encoding of benzoyllysine and fluorinated benzoyllysines into full-length histone proteins in a site-specific manner in live cells, based on our rationally designed synthetase and fine-integrated fluorine element into benzoyllysines. The incorporated unnatural amino acids integrating unique features were demonstrated as versatile probes for investigating histone benzoylation under biological environments, conferring multiplex signals such as 19F NMR spectra with chemical clarity and fluorescence signals for benzoylation. Moreover, the site specifically incorporated lysine benzoylation within native full-length histone proteins revealed distinct dynamics of debenzoylation in the presence of debenzoylase sirtuin 2 (SIRT2). Our developed strategy for genetic encoding of benzoyllysines offers a general and novel approach to gain insights into interactions of site-specific histone benzoylation modifications with interactomes and molecular mechanisms in physiological settings, which could not be accessible with fragment histone peptides. This versatile chemical tool enables a direct and new avenue to explore benzoylation, interactions, and histone epigenetics, which will provide broad utilities in chemical biology, protein science, and basic biology research.
Collapse
Affiliation(s)
- Hongtao Tian
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road,
Pudong, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiale Yang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road,
Pudong, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - An-Di Guo
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road,
Pudong, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Ran
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Yun-Zhi Yang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road,
Pudong, Shanghai 201203, China
| | - Bing Yang
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Ruimin Huang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road,
Pudong, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haiming Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xiao-Hua Chen
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road,
Pudong, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| |
Collapse
|
7
|
|
8
|
Wan C, Zhang F, Yao H, Li H, Tuan RS. Histone Modifications and Chondrocyte Fate: Regulation and Therapeutic Implications. Front Cell Dev Biol 2021; 9:626708. [PMID: 33937229 PMCID: PMC8085601 DOI: 10.3389/fcell.2021.626708] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 03/17/2021] [Indexed: 12/12/2022] Open
Abstract
The involvement of histone modifications in cartilage development, pathology and regeneration is becoming increasingly evident. Understanding the molecular mechanisms and consequences of histone modification enzymes in cartilage development, homeostasis and pathology provides fundamental and precise perspectives to interpret the biological behavior of chondrocytes during skeletal development and the pathogenesis of various cartilage related diseases. Candidate molecules or drugs that target histone modifying proteins have shown promising therapeutic potential in the treatment of cartilage lesions associated with joint degeneration and other chondropathies. In this review, we summarized the advances in the understanding of histone modifications in the regulation of chondrocyte fate, cartilage development and pathology, particularly the molecular writers, erasers and readers involved. In addition, we have highlighted recent studies on the use of small molecules and drugs to manipulate histone signals to regulate chondrocyte functions or treat cartilage lesions, in particular osteoarthritis (OA), and discussed their potential therapeutic benefits and limitations in preventing articular cartilage degeneration or promoting its repair or regeneration.
Collapse
Affiliation(s)
- Chao Wan
- MOE Key Laboratory for Regenerative Medicine, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.,Institute for Tissue Engineering and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong, China.,MOE Key Laboratory for Regenerative Medicine (Shenzhen Base), School of Biomedical Sciences Core Laboratory, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Fengjie Zhang
- MOE Key Laboratory for Regenerative Medicine, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.,Institute for Tissue Engineering and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong, China.,MOE Key Laboratory for Regenerative Medicine (Shenzhen Base), School of Biomedical Sciences Core Laboratory, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Hanyu Yao
- MOE Key Laboratory for Regenerative Medicine, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.,Institute for Tissue Engineering and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong, China.,MOE Key Laboratory for Regenerative Medicine (Shenzhen Base), School of Biomedical Sciences Core Laboratory, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Rocky S Tuan
- MOE Key Laboratory for Regenerative Medicine, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.,Institute for Tissue Engineering and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong, China.,MOE Key Laboratory for Regenerative Medicine (Shenzhen Base), School of Biomedical Sciences Core Laboratory, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| |
Collapse
|
9
|
Peng Y, Li S, Landsman D, Panchenko AR. Histone tails as signaling antennas of chromatin. Curr Opin Struct Biol 2021; 67:153-160. [PMID: 33279866 PMCID: PMC8096652 DOI: 10.1016/j.sbi.2020.10.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/07/2020] [Accepted: 10/18/2020] [Indexed: 12/19/2022]
Abstract
Histone tails, representing the N-terminal or C-terminal regions flanking the histone core, play essential roles in chromatin signaling networks. Intrinsic disorder of histone tails and their propensity for post-translational modifications allow them to serve as hubs in coordination of epigenetic processes within the nucleosomal context. Deposition of histone variants with distinct histone tail properties further enriches histone tails' repertoire in epigenetic signaling. Given the advances in experimental techniques and in silico modelling, we review the most recent data on histone tails' effects on nucleosome stability and dynamics, their function in regulating chromatin accessibility and folding. Finally, we discuss different molecular mechanisms to understand how histone tails are involved in nucleosome recognition by binding partners and formation of higher-order chromatin structures.
Collapse
Affiliation(s)
- Yunhui Peng
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
| | - Shuxiang Li
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, ON, Canada
| | - David Landsman
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
| | - Anna R Panchenko
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, ON, Canada.
| |
Collapse
|
10
|
Abstract
The innate immune response is a rapid response to pathogens or danger signals. It is precisely activated not only to efficiently eliminate pathogens but also to avoid excessive inflammation and tissue damage. cis-Regulatory element-associated chromatin architecture shaped by epigenetic factors, which we define as the epiregulome, endows innate immune cells with specialized phenotypes and unique functions by establishing cell-specific gene expression patterns, and it also contributes to resolution of the inflammatory response. In this review, we focus on two aspects: (a) how niche signals during lineage commitment or following infection and pathogenic stress program epiregulomes by regulating gene expression levels, enzymatic activities, or gene-specific targeting of chromatin modifiers and (b) how the programed epiregulomes in turn mediate regulation of gene-specific expression, which contributes to controlling the development of innate cells, or the response to infection and inflammation, in a timely manner. We also discuss the effects of innate immunometabolic rewiring on epiregulomes and speculate on several future challenges to be encountered during the exploration of the master regulators of epiregulomes in innate immunity and inflammation.
Collapse
Affiliation(s)
- Qian Zhang
- Department of Immunology, Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China; , .,National Key Laboratory of Medical Immunology, Institute of Immunology, Navy Military Medical University, Shanghai 200433, China
| | - Xuetao Cao
- Department of Immunology, Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China; , .,National Key Laboratory of Medical Immunology, Institute of Immunology, Navy Military Medical University, Shanghai 200433, China.,Laboratory of Immunity and Inflammation, College of Life Sciences, Nankai University, Tianjin 300071, China
| |
Collapse
|
11
|
Zhang M, Zhao J, Lv Y, Wang W, Feng C, Zou W, Su L, Jiao J. Histone Variants and Histone Modifications in Neurogenesis. Trends Cell Biol 2020; 30:869-880. [PMID: 33011018 DOI: 10.1016/j.tcb.2020.09.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 09/02/2020] [Accepted: 09/07/2020] [Indexed: 12/20/2022]
Abstract
During embryonic brain development, neurogenesis requires the orchestration of gene expression to regulate neural stem cell (NSC) fate specification. Epigenetic regulation with specific emphasis on the modes of histone variants and histone post-translational modifications are involved in interactive gene regulation of central nervous system (CNS) development. Here, we provide a broad overview of the regulatory system of histone variants and histone modifications that have been linked to neurogenesis and diseases. We also review the crosstalk between different histone modifications and discuss how the 3D genome affects cell fate dynamics during brain development. Understanding the mechanisms of epigenetic regulation in neurogenesis has shifted the paradigm from single gene regulation to synergistic interactions to ensure healthy embryonic neurogenesis.
Collapse
Affiliation(s)
- Mengtian Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Innovation Academy for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101 Beijing, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinyue Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Innovation Academy for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101 Beijing, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuqing Lv
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Innovation Academy for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101 Beijing, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenwen Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; School of Life Sciences, University of Science and Technology of China, Hefei 230000, China
| | - Chao Feng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenzheng Zou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Innovation Academy for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101 Beijing, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Libo Su
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Innovation Academy for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101 Beijing, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianwei Jiao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Innovation Academy for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101 Beijing, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
12
|
The evolving metabolic landscape of chromatin biology and epigenetics. Nat Rev Genet 2020; 21:737-753. [PMID: 32908249 DOI: 10.1038/s41576-020-0270-8] [Citation(s) in RCA: 241] [Impact Index Per Article: 60.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2020] [Indexed: 12/12/2022]
Abstract
Molecular inputs to chromatin via cellular metabolism are modifiers of the epigenome. These inputs - which include both nutrient availability as a result of diet and growth factor signalling - are implicated in linking the environment to the maintenance of cellular homeostasis and cell identity. Recent studies have demonstrated that these inputs are much broader than had previously been known, encompassing metabolism from a wide variety of sources, including alcohol and microbiotal metabolism. These factors modify DNA and histones and exert specific effects on cell biology, systemic physiology and pathology. In this Review, we discuss the nature of these molecular networks, highlight their role in mediating cellular responses and explore their modifiability through dietary and pharmacological interventions.
Collapse
|
13
|
Meyer K, Selbach M. Peptide-based Interaction Proteomics. Mol Cell Proteomics 2020; 19:1070-1075. [PMID: 32345597 PMCID: PMC7338088 DOI: 10.1074/mcp.r120.002034] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/28/2020] [Indexed: 12/13/2022] Open
Abstract
Protein-protein interactions are often mediated by short linear motifs (SLiMs) that are located in intrinsically disordered regions (IDRs) of proteins. Interactions mediated by SLiMs are notoriously difficult to study, and many functionally relevant interactions likely remain to be uncovered. Recently, pull-downs with synthetic peptides in combination with quantitative mass spectrometry emerged as a powerful screening approach to study protein-protein interactions mediated by SLiMs. Specifically, arrays of synthetic peptides immobilized on cellulose membranes provide a scalable means to identify the interaction partners of many peptides in parallel. In this minireview we briefly highlight the relevance of SLiMs for protein-protein interactions, outline existing screening technologies, discuss unique advantages of peptide-based interaction screens and provide practical suggestions for setting up such peptide-based screens.
Collapse
Affiliation(s)
- Katrina Meyer
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Matthias Selbach
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine, Berlin, Germany; Charité-Universitätsmedizin Berlin, Berlin, Germany.
| |
Collapse
|
14
|
Duman M, Martinez-Moreno M, Jacob C, Tapinos N. Functions of histone modifications and histone modifiers in Schwann cells. Glia 2020; 68:1584-1595. [PMID: 32034929 DOI: 10.1002/glia.23795] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/24/2020] [Accepted: 01/28/2020] [Indexed: 01/25/2023]
Abstract
Schwann cells (SCs) are the main glial cells present in the peripheral nervous system (PNS). Their primary functions are to insulate peripheral axons to protect them from the environment and to enable fast conduction of electric signals along big caliber axons by enwrapping them in a thick myelin sheath rich in lipids. In addition, SCs have the peculiar ability to foster axonal regrowth after a lesion by demyelinating and converting into repair cells that secrete neurotrophic factors and guide axons back to their former target to finally remyelinate regenerated axons. The different steps of SC development and their role in the maintenance of PNS integrity and regeneration after lesion are controlled by various factors among which transcription factors and chromatin-remodeling enzymes hold major functions. In this review, we discussed how histone modifications and histone-modifying enzymes control SC development, maintenance of PNS integrity and response to injury. The functions of histone modifiers as part of chromatin-remodeling complexes are discussed in another review published in the same issue of Glia.
Collapse
Affiliation(s)
- Mert Duman
- Faculty of Biology, Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Margot Martinez-Moreno
- Department of Neurosurgery, Molecular Neuroscience & Neuro-Oncology Laboratory, Brown University, Providence, Rhode Island
| | - Claire Jacob
- Faculty of Biology, Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Nikos Tapinos
- Department of Neurosurgery, Molecular Neuroscience & Neuro-Oncology Laboratory, Brown University, Providence, Rhode Island
| |
Collapse
|
15
|
Transglutaminases, neuronal cell death and neural repair: implications for traumatic brain injury and therapeutics. Curr Opin Neurol 2019; 32:796-801. [DOI: 10.1097/wco.0000000000000753] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
16
|
Bader M. Serotonylation: Serotonin Signaling and Epigenetics. Front Mol Neurosci 2019; 12:288. [PMID: 31824263 PMCID: PMC6881384 DOI: 10.3389/fnmol.2019.00288] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 11/12/2019] [Indexed: 01/01/2023] Open
Abstract
Serotonylation, the covalent linkage of serotonin to proteins has been discovered more than 60 years ago but only recently the mechanisms and first functions have been elucidated. It has been found that transglutaminases (TG) such as TG2 and the blood coagulation factor XIIIa are the enzymes which catalyze the linkage of serotonin and other monoamines to distinct glutamine (Gln) residues of target proteins. The first target proteins, small G-proteins and extracellular matrix constituents, were found in platelets and are pivotally involved in platelet aggregation and the formation of thrombi. The serotonylation of the same proteins is also involved in insulin secretion and in the proliferation of pulmonary vascular smooth muscle cells and thereby in the pathogenesis of pulmonary arterial hypertension (PAH). Recently histones have been described as targets of serotonylation opening the area of transcriptional control to this posttranslational protein modification. Future studies will certainly reveal further target proteins, signaling pathways, cellular processes, and diseases, in which serotonylation or, more general, monoaminylation is important.
Collapse
Affiliation(s)
- Michael Bader
- Max-Delbrück Center for Molecular Medicine, Berlin, Germany.,Institute for Biology, University of Lübeck, Lübeck, Germany.,Charité University Medicine, Berlin, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
| |
Collapse
|