1
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Valsakumar D, Voigt P. Nucleosomal asymmetry: a novel mechanism to regulate nucleosome function. Biochem Soc Trans 2024:BST20230877. [PMID: 38778762 DOI: 10.1042/bst20230877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024]
Abstract
Nucleosomes constitute the fundamental building blocks of chromatin. They are comprised of DNA wrapped around a histone octamer formed of two copies each of the four core histones H2A, H2B, H3, and H4. Nucleosomal histones undergo a plethora of posttranslational modifications that regulate gene expression and other chromatin-templated processes by altering chromatin structure or by recruiting effector proteins. Given their symmetric arrangement, the sister histones within a nucleosome have commonly been considered to be equivalent and to carry the same modifications. However, it is now clear that nucleosomes can exhibit asymmetry, combining differentially modified sister histones or different variants of the same histone within a single nucleosome. Enabled by the development of novel tools that allow generating asymmetrically modified nucleosomes, recent biochemical and cell-based studies have begun to shed light on the origins and functional consequences of nucleosomal asymmetry. These studies indicate that nucleosomal asymmetry represents a novel regulatory mechanism in the establishment and functional readout of chromatin states. Asymmetry expands the combinatorial space available for setting up complex sets of histone marks at individual nucleosomes, regulating multivalent interactions with histone modifiers and readers. The resulting functional consequences of asymmetry regulate transcription, poising of developmental gene expression by bivalent chromatin, and the mechanisms by which oncohistones deregulate chromatin states in cancer. Here, we review recent progress and current challenges in uncovering the mechanisms and biological functions of nucleosomal asymmetry.
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Affiliation(s)
- Devisree Valsakumar
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, U.K
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, U.K
| | - Philipp Voigt
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, U.K
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2
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Khatua P, Tang PK, Ghosh Moulick A, Patel R, Manandhar A, Loverde SM. Sequence Dependence in Nucleosome Dynamics. J Phys Chem B 2024; 128:3090-3101. [PMID: 38530903 DOI: 10.1021/acs.jpcb.3c07363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
The basic packaging unit of eukaryotic chromatin is the nucleosome that contains 145-147 base pair duplex DNA wrapped around an octameric histone protein. While the DNA sequence plays a crucial role in controlling the positioning of the nucleosome, the molecular details behind the interplay between DNA sequence and nucleosome dynamics remain relatively unexplored. This study analyzes this interplay in detail by performing all-atom molecular dynamics simulations of nucleosomes, comparing the human α-satellite palindromic (ASP) and the strong positioning "Widom-601" DNA sequence at time scales of 12 μs. The simulations are performed at salt concentrations 10-20 times higher than physiological salt concentrations to screen the electrostatic interactions and promote unwrapping. These microsecond-long simulations give insight into the molecular-level sequence-dependent events that dictate the pathway of DNA unwrapping. We find that the "ASP" sequence forms a loop around SHL ± 5 for three sets of simulations. Coincident with loop formation is a cooperative increase in contacts with the neighboring N-terminal H2B tail and C-terminal H2A tail and the release of neighboring counterions. We find that the Widom-601 sequence exhibits a strong breathing motion of the nucleic acid ends. Coincident with the breathing motion is the collapse of the full N-terminal H3 tail and formation of an α-helix that interacts with the H3 histone core. We postulate that the dynamics of these histone tails and their modification with post-translational modifications (PTMs) may play a key role in governing this dynamics.
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Affiliation(s)
- Prabir Khatua
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New York 10314, United States
| | - Phu K Tang
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New York 10314, United States
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Abhik Ghosh Moulick
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New York 10314, United States
| | - Rutika Patel
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New York 10314, United States
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Anjela Manandhar
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New York 10314, United States
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Sharon M Loverde
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New York 10314, United States
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
- Ph.D. Program in Physics, The Graduate Center of the City University of New York, New York, New York 10016, United States
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3
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Hananya N, Koren S, Muir TW. Interrogating epigenetic mechanisms with chemically customized chromatin. Nat Rev Genet 2024; 25:255-271. [PMID: 37985791 DOI: 10.1038/s41576-023-00664-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2023] [Indexed: 11/22/2023]
Abstract
Genetic and genomic techniques have proven incredibly powerful for identifying and studying molecular players implicated in the epigenetic regulation of DNA-templated processes such as transcription. However, achieving a mechanistic understanding of how these molecules interact with chromatin to elicit a functional output is non-trivial, owing to the tremendous complexity of the biochemical networks involved. Advances in protein engineering have enabled the reconstitution of 'designer' chromatin containing customized post-translational modification patterns, which, when used in conjunction with sophisticated biochemical and biophysical methods, allow many mechanistic questions to be addressed. In this Review, we discuss how such tools complement established 'omics' techniques to answer fundamental questions on chromatin regulation, focusing on chromatin mark establishment and protein-chromatin interactions.
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Affiliation(s)
- Nir Hananya
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Shany Koren
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Tom W Muir
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
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4
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Shukla S, Murmu S, Mora T, Dhanasekaran K, Roy RP. Unravelling HDAC Selectivity for Erasing Acetyl Mark on Lys-5 of Histone H2B. Chembiochem 2024; 25:e202300875. [PMID: 38251898 DOI: 10.1002/cbic.202300875] [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: 12/31/2023] [Revised: 01/21/2024] [Accepted: 01/21/2024] [Indexed: 01/23/2024]
Abstract
The reversible acetylation of specific Lysine residues of histones plays crucial role in the epigenetic regulation of chromatin activity. Importantly, perturbations of acetylation-deacetylation dynamics have important implications for cancer and neurological disorders. There are 18 human HDACs including sirtuins. The site-selective acetyl eraser specificity of HDACs is poorly defined. Deciphering the site specificity preference of HDACs from a gamut of lysine in histones may be critical for targeted inhibitor development and delineation of regulatory mechanisms associated with chromatin. Here, we have interrogated the propensity of HDACs to erase acetyl mark at Lys-5 of H2B namely, H2BK5Ac engineered by a peptide ligation reaction catalyzed by transpeptidase sortase. HDACs and Sirtuins were individually over-expressed in HEK293 cells and the deacetylation propensity of respective cell lysates was evaluated against H2BK5Ac for initial screening of potential acetyl erasers. This screen indicated HDAC1 as the prime eraser of acetyl mark in H2BK5Ac. The propensity of HDAC1 to erase acetyl mark of H2BK5Ac was further probed using semisynthetic designer nucleosomes with whole cell lysates, recombinant enzyme, and specific inhibitors. Consistent with the above data, siRNA knockdown of HDAC1 and closely related HDAC3 in HEK293 cells prevented the loss of H2BK5 acetylation.
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Affiliation(s)
- Shagun Shukla
- National Institute of Immunology, Delhi, 110067, India
| | - Sumit Murmu
- National Institute of Immunology, Delhi, 110067, India
- Regional Centre for Biotechnology, Faridabad 121001, Haryana, India
| | - Tulasiram Mora
- Regional Centre for Biotechnology, Faridabad 121001, Haryana, India
| | | | - Rajendra P Roy
- National Institute of Immunology, Delhi, 110067, India
- Regional Centre for Biotechnology, Faridabad 121001, Haryana, India
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5
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Weinzapfel EN, Fedder-Semmes KN, Sun ZW, Keogh MC. Beyond the tail: the consequence of context in histone post-translational modification and chromatin research. Biochem J 2024; 481:219-244. [PMID: 38353483 PMCID: PMC10903488 DOI: 10.1042/bcj20230342] [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: 12/30/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/16/2024]
Abstract
The role of histone post-translational modifications (PTMs) in chromatin structure and genome function has been the subject of intense debate for more than 60 years. Though complex, the discourse can be summarized in two distinct - and deceptively simple - questions: What is the function of histone PTMs? And how should they be studied? Decades of research show these queries are intricately linked and far from straightforward. Here we provide a historical perspective, highlighting how the arrival of new technologies shaped discovery and insight. Despite their limitations, the tools available at each period had a profound impact on chromatin research, and provided essential clues that advanced our understanding of histone PTM function. Finally, we discuss recent advances in the application of defined nucleosome substrates, the study of multivalent chromatin interactions, and new technologies driving the next era of histone PTM research.
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Yang M, Hu X, Tang B, Deng F. Exploring the interplay between methylation patterns and non-coding RNAs in non-small cell lung cancer: Implications for pathogenesis and therapeutic targets. Heliyon 2024; 10:e24811. [PMID: 38312618 PMCID: PMC10835372 DOI: 10.1016/j.heliyon.2024.e24811] [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: 11/06/2023] [Revised: 01/10/2024] [Accepted: 01/15/2024] [Indexed: 02/06/2024] Open
Abstract
Lung cancer is a global public health issue, with non-small cell lung cancer (NSCLC) accounting for 80-85 % of cases. With over two million new diagnoses annually, understanding the complex evolution of this disease is crucial. The development of lung cancer involves a complex interplay of genetic, epigenetic, and environmental factors, leading the key oncogenes and tumor suppressor genes to disorder, and activating the cancer related signaling pathway. Non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNA (lncRNAs), and circular RNA (circRNAs) are unique RNA transcripts with diverse biological functions. These ncRNAs are generated through genome transcription and play essential roles in cellular processes. Epigenetic modifications such as DNA methylation, N6-methyladenosine (m6A) modification, and histone methylation have gained significant attention in NSCLC research. The complexity of the interactions among these methylation modifications and ncRNAs contribute to the precise regulation of NSCLC development. This review comprehensively summarizes the associations between ncRNAs and different methylation modifications and discusses their effects on NSCLC. By elucidating these relationships, we aim to advance our understanding of NSCLC pathogenesis and identify potential therapeutic targets for this devastating disease.
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Affiliation(s)
- Mei Yang
- School of Clinical Medicine, Chengdu Medical College, Chengdu, 610500, China
| | - Xue Hu
- School of Basic Medical Science, Chengdu Medical College, Chengdu, 610500, China
| | - Bin Tang
- Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500, China
| | - Fengmei Deng
- School of Basic Medical Science, Chengdu Medical College, Chengdu, 610500, China
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7
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Saumer P, Scheffner M, Marx A, Stengel F. Interactome of intact chromatosome variants with site-specifically ubiquitylated and acetylated linker histone H1.2. Nucleic Acids Res 2024; 52:101-113. [PMID: 37994785 PMCID: PMC10783519 DOI: 10.1093/nar/gkad1113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 10/31/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023] Open
Abstract
Post-translational modifications (PTMs) of histones have fundamental effects on chromatin structure and function. While the impact of PTMs on the function of core histones are increasingly well understood, this is much less the case for modifications of linker histone H1, which is at least in part due to a lack of proper tools. In this work, we establish the assembly of intact chromatosomes containing site-specifically ubiquitylated and acetylated linker histone H1.2 variants obtained by a combination of chemical biology approaches. We then use these complexes in a tailored affinity enrichment mass spectrometry workflow to identify and comprehensively characterize chromatosome-specific cellular interactomes and the impact of site-specific linker histone modifications on a proteome-wide scale. We validate and benchmark our approach by western-blotting and by confirming the involvement of chromatin-bound H1.2 in the recruitment of proteins involved in DNA double-strand break repair using an in vitro ligation assay. We relate our data to previous work and in particular compare it to data on modification-specific interaction partners of free H1. Taken together, our data supports the role of chromatin-bound H1 as a regulatory protein with distinct functions beyond DNA compaction and constitutes an important resource for future investigations of histone epigenetic modifications.
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Affiliation(s)
- Philip Saumer
- Department of Chemistry, University of Konstanz; Universitätsstraße 10, 78464 Konstanz, Germany
- Konstanz Research School Chemical Biology, University of Konstanz; Universitätsstraße 10, 78464 Konstanz, Germany
| | - Martin Scheffner
- Konstanz Research School Chemical Biology, University of Konstanz; Universitätsstraße 10, 78464 Konstanz, Germany
- Department of Biology, University of Konstanz; Universitätsstraße 10, 78464 Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry, University of Konstanz; Universitätsstraße 10, 78464 Konstanz, Germany
- Konstanz Research School Chemical Biology, University of Konstanz; Universitätsstraße 10, 78464 Konstanz, Germany
| | - Florian Stengel
- Konstanz Research School Chemical Biology, University of Konstanz; Universitätsstraße 10, 78464 Konstanz, Germany
- Department of Biology, University of Konstanz; Universitätsstraße 10, 78464 Konstanz, Germany
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8
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Chen Z, Qi Y, Shen J, Chen Z. Histone demethylase KDM6A coordinating with KMT2B regulates self-renewal and chemoresistance of non-small cell lung cancer stem cells. Transl Oncol 2023; 37:101778. [PMID: 37683307 PMCID: PMC10493599 DOI: 10.1016/j.tranon.2023.101778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 08/25/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023] Open
Abstract
BACKGROUND AND AIMS Wnt signaling is essential for the maintenance of cancer stem cells (CSCs), but mutations in the β-catenin and APC genes are less common in non-small cell lung carcinoma (NSCLC). Thus, the mechanism underlying the constitutive activation of Wnt signaling in lung CSCs is still unknown. MATERIALS AND METHODS Gene set enrichment analysis and immunohistochemistry were performed to establish the correlation between KDM6A/KM2B and CSC stemness. Human NSCLC cell lines were genetically manipulated for functional studies. Sphere formation assay and stemness gene expression profiling were examined to investigate the role of KDM6A/KMT2B in lung CSCs. Tumor xenograft assay were used to identify the function of KDM6A/KMT2B on tumorigenicity and tumor recurrence in vivo. Western blot analysis, coimmunoprecipitation and chromatin immunoprecipitation were performed to understand KDM6A/KMT2B mediated epigenetic regulation of Histone 3 lysine 4 methylation (H3K4me) on Wnt signaling pathway. RESULTS We discovered that the expression of Histone demethylase KDM6A and methyltransferase KMT2B correlate with the stemness of CSCs in NSCLC. KDM6A coordinates with KMT2B to activate the Wnt/β-catenin signaling pathway by regulating the H3K4me3 level and promotes the tumorigenicity and maintenance of CSC stemness. Furthermore, KDM6A/ KMT2B overexpression promotes the CSC chemoresistance and tumor recurrence both in vitro and in vivo. Inhibition of KDM6A and KMT2B potently suppress tumor initiation and recurrence in xenografted animal models. CONCLUSION Our findings suggest that KDM6A and KMT2B mediate the constitutive activation of Wnt/β-catenin signaling in lung CSCs, potentially providing a therapeutic target for NSCLC.
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Affiliation(s)
- Zhiwei Chen
- Department of Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yuwen Qi
- Department of Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Shen
- Department of Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Zhen Chen
- Department of Pathology, Shidong hospital, Yangpu District, Shidong hospital affiliated to University of Shanghai for Science and Technology, China.
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9
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Lu-Culligan WJ, Connor LJ, Xie Y, Ekundayo BE, Rose BT, Machyna M, Pintado-Urbanc AP, Zimmer JT, Vock IW, Bhanu NV, King MC, Garcia BA, Bleichert F, Simon MD. Acetyl-methyllysine marks chromatin at active transcription start sites. Nature 2023; 622:173-179. [PMID: 37731000 PMCID: PMC10845139 DOI: 10.1038/s41586-023-06565-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 08/23/2023] [Indexed: 09/22/2023]
Abstract
Lysine residues in histones and other proteins can be modified by post-translational modifications that encode regulatory information1. Lysine acetylation and methylation are especially important for regulating chromatin and gene expression2-4. Pathways involving these post-translational modifications are targets for clinically approved therapeutics to treat human diseases. Lysine methylation and acetylation are generally assumed to be mutually exclusive at the same residue. Here we report cellular lysine residues that are both methylated and acetylated on the same side chain to form Nε-acetyl-Nε-methyllysine (Kacme). We show that Kacme is found on histone H4 (H4Kacme) across a range of species and across mammalian tissues. Kacme is associated with marks of active chromatin, increased transcriptional initiation and is regulated in response to biological signals. H4Kacme can be installed by enzymatic acetylation of monomethyllysine peptides and is resistant to deacetylation by some HDACs in vitro. Kacme can be bound by chromatin proteins that recognize modified lysine residues, as we demonstrate with the crystal structure of acetyllysine-binding protein BRD2 bound to a histone H4Kacme peptide. These results establish Kacme as a cellular post-translational modification with the potential to encode information distinct from methylation and acetylation alone and demonstrate that Kacme has all the hallmarks of a post-translational modification with fundamental importance to chromatin biology.
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Affiliation(s)
- William J Lu-Culligan
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, CT, USA
| | - Leah J Connor
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, CT, USA
| | - Yixuan Xie
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
| | - Babatunde E Ekundayo
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
| | - Brendan T Rose
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, CT, USA
| | - Martin Machyna
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, CT, USA
| | - Andreas P Pintado-Urbanc
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, CT, USA
| | - Joshua T Zimmer
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, CT, USA
| | - Isaac W Vock
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, CT, USA
| | - Natarajan V Bhanu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
| | - Megan C King
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
| | - Franziska Bleichert
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
| | - Matthew D Simon
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA.
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, CT, USA.
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10
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Ratre P, Chauhan P, Bhargava A, Tiwari R, Thareja S, Srivastava RK, Mishra PK. Nano-engineered vitamins as a potential epigenetic modifier against environmental air pollutants. REVIEWS ON ENVIRONMENTAL HEALTH 2023; 38:547-564. [PMID: 35724323 DOI: 10.1515/reveh-2022-0027] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
Air pollution has emerged as a serious threat to human health due to close association with spectrum of chronic ailments including cardiovascular disorders, respiratory diseases, nervous system dysfunctions, diabetes and cancer. Exposure to air-borne pollutants along with poor eating behaviours and inferior dietary quality irreversibly impacts epigenomic landscape, leading to aberrant transcriptional control of gene expression which is central to patho-physiology of non-communicable diseases. It is assumed that nutriepigenomic interventions such as vitamins can control such adverse effects through their immediate action on mitochondrial epigenomic-axis. Importantly, the exhaustive clinical utility of vitamins-interceded epigenetic synchronization is not well characterized. Therefore, improving the current limitations linked to stability and bioavailability issues in vitamin formulations is highly warranted. The present review not only sums up the available data on the role of vitamins as potential epigenetic modifiers but also discusses the importance of nano-engineered vitamins as potential epidrugs for dietary and pharmacological intervention to mitigate the long-term effects of air pollution toxicity.
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Affiliation(s)
- Pooja Ratre
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Prachi Chauhan
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Arpit Bhargava
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Rajnarayan Tiwari
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Suresh Thareja
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, India
| | | | - Pradyumna Kumar Mishra
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India
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11
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Hong ZZ, Yu RR, Zhang X, Webb AM, Burge NL, Poirier MG, Ottesen JJ. Development of Convergent Hybrid Phase Ligation for Efficient and Convenient Total Synthesis of Proteins. Pept Sci (Hoboken) 2023; 115:e24323. [PMID: 37692919 PMCID: PMC10488053 DOI: 10.1002/pep2.24323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/16/2023] [Indexed: 09/12/2023]
Abstract
Simple and efficient total synthesis of homogeneous and chemically modified protein samples remains a significant challenge. Here, we report development of a convergent hybrid phase native chemical ligation (CHP-NCL) strategy for facile preparation of proteins. In this strategy, proteins are split into ~100-residue blocks, and each block is assembled on solid support from synthetically accessible peptide fragments before ligated together into full-length protein in solution. With the new method, we increase the yield of CENP-A synthesis by 2.5-fold compared to the previous hybrid phase ligation approach. We further extend the new strategy to the total chemical synthesis of 212-residue linker histone H1.2 in unmodified, phosphorylated, and citrullinated forms, each from eight peptide segments with only one single purification. We demonstrate that fully synthetic H1.2 replicates the binding interactions of linker histones to intact mononucleosomes, as a proxy for the essential function of linker histones in the formation and regulation of higher order chromatin structure.
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Affiliation(s)
- Ziyong Z. Hong
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, 43210
| | - Ruixuan R. Yu
- Ohio State Biochemistry Graduate Program, The Ohio State University, Columbus, Ohio, 43210
| | - Xiaoyu Zhang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, 43210
| | - Allison M. Webb
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, 43210
| | - Nathaniel L. Burge
- Ohio State Biochemistry Graduate Program, The Ohio State University, Columbus, Ohio, 43210
| | - Michael G. Poirier
- Ohio State Biochemistry Graduate Program, The Ohio State University, Columbus, Ohio, 43210
- Department of Physics, Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio, 43210
| | - Jennifer J. Ottesen
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, 43210
- Ohio State Biochemistry Graduate Program, The Ohio State University, Columbus, Ohio, 43210
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12
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Nickel GA, Diehl KL. Chemical Biology Approaches to Identify and Profile Interactors of Chromatin Modifications. ACS Chem Biol 2023; 18:1014-1026. [PMID: 35238546 PMCID: PMC9440160 DOI: 10.1021/acschembio.1c00794] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In eukaryotes, DNA is packaged with histone proteins in a complex known as chromatin. Both the DNA and histone components of chromatin can be chemically modified in a wide variety of ways, resulting in a complex landscape often referred to as the "epigenetic code". These modifications are recognized by effector proteins that remodel chromatin and modulate transcription, translation, and repair of the underlying DNA. In this Review, we examine the development of methods for characterizing proteins that interact with these histone and DNA modifications. "Mark first" approaches utilize chemical, peptide, nucleosome, or oligonucleotide probes to discover interactors of a specific modification. "Reader first" approaches employ arrays of peptides, nucleosomes, or oligonucleotides to profile the binding preferences of interactors. These complementary strategies have greatly enhanced our understanding of how chromatin modifications effect changes in genomic regulation, bringing us ever closer to deciphering this complex language.
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Affiliation(s)
- Garrison A. Nickel
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, United States
| | - Katharine L. Diehl
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, United States
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13
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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: 16] [Impact Index Per Article: 16.0] [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.
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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.
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14
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Kirchgäßner S, Braun MB, Bartlick N, Koç C, Reinkemeier CD, Lemke EA, Stehle T, Schwarzer D. Synthesis, Biochemical Characterization, and Genetic Encoding of a 1,2,4-Triazole Amino Acid as an Acetyllysine Mimic for Bromodomains of the BET Family. Angew Chem Int Ed Engl 2023; 62:e202215460. [PMID: 36585954 DOI: 10.1002/anie.202215460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/23/2022] [Accepted: 12/29/2022] [Indexed: 01/01/2023]
Abstract
Lysine acetylation is a charge-neutralizing post-translational modification of proteins bound by bromodomains (Brds). A 1,2,4-triazole amino acid (ApmTri) was established as acetyllysine (Kac) mimic recruiting Brds of the BET family in contrast to glutamine commonly used for simulating this modification. Optimization of triazole substituents and side chain spacing allowed BET Brd recruitment to ApmTri-containing peptides with affinities similar to native substrates. Crystal structures of ApmTri-containing peptides in complex with two BET Brds revealed the binding mode which mirrored that of Kac ligands. ApmTri was genetically encoded and recombinant ApmTri-containing proteins co-enriched BRD3(2) from cellular lysates. This interaction was blocked by BET inhibitor JQ1. With genetically encoded ApmTri, biochemistry is now provided with a stable Kac mimic reflecting charge neutralization and Brd recruitment, allowing new investigations into BET proteins in vitro and in vivo.
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Affiliation(s)
- Sören Kirchgäßner
- Interfakultäres Institut für Biochemie, Universität Tübingen, Auf der Morgenstelle 34, 72076, Tübingen, Germany
| | - Michael B Braun
- Interfakultäres Institut für Biochemie, Universität Tübingen, Auf der Morgenstelle 34, 72076, Tübingen, Germany
| | - Natascha Bartlick
- Interfakultäres Institut für Biochemie, Universität Tübingen, Auf der Morgenstelle 34, 72076, Tübingen, Germany
| | - Cengiz Koç
- Interfakultäres Institut für Biochemie, Universität Tübingen, Auf der Morgenstelle 34, 72076, Tübingen, Germany.,Current address: Department of Infection, Immunity & Cardiovascular Disease, University of Sheffield, The Medical School, Beech Hill Rd, Sheffield, S10 2RX, UK
| | - Christopher D Reinkemeier
- Biocenter, Johannes Gutenberg University Mainz, 55128, Mainz, Germany.,Institute of Molecular Biology Mainz, 55128, Mainz, Germany.,Current address: Department of Biosystems Science and Engineering Basel, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Edward A Lemke
- Biocenter, Johannes Gutenberg University Mainz, 55128, Mainz, Germany.,Institute of Molecular Biology Mainz, 55128, Mainz, Germany
| | - Thilo Stehle
- Interfakultäres Institut für Biochemie, Universität Tübingen, Auf der Morgenstelle 34, 72076, Tübingen, Germany
| | - Dirk Schwarzer
- Interfakultäres Institut für Biochemie, Universität Tübingen, Auf der Morgenstelle 34, 72076, Tübingen, Germany
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15
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Balakrishnan D, El Maiss J, Olthuis W, Pascual García C. Miniaturized Control of Acidity in Multiplexed Microreactors. ACS OMEGA 2023; 8:7587-7594. [PMID: 36872992 PMCID: PMC9979314 DOI: 10.1021/acsomega.2c06897] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
The control of acidity drives the assembly of biopolymers that are essential for a wide range of applications. Its miniaturization can increase the speed and the possibilities of combinatorial throughput for their manipulation, similar to the way that the miniaturization of transistors allows logical operations in microelectronics with a high throughput. Here, we present a device containing multiplexed microreactors, each one enabling independent electrochemical control of acidity in ∼2.5 nL volumes, with a large acidity range from pH 3 to 7 and an accuracy of at least 0.4 pH units. The attained pH within each microreactor (with footprints of ∼0.3 mm2 for each spot) was kept constant for long retention times (∼10 min) and over repeated cycles of >100. The acidity is driven by redox proton exchange reactions, which can be driven at different rates influencing the efficiency of the device in order to achieve more charge exchange (larger acidity range) or better reversibility. The achieved performance in acidity control, miniaturization, and the possibility to multiplex paves the way for the control of combinatorial chemistry through pH- and acidity-controlled reactions.
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Affiliation(s)
- Divya Balakrishnan
- Luxembourg
Institute of Science and Technology (LIST), 41 Rue du Brill, L-4422Belvaux, Luxembourg
| | - Janwa El Maiss
- Luxembourg
Institute of Science and Technology (LIST), 41 Rue du Brill, L-4422Belvaux, Luxembourg
| | - Wouter Olthuis
- MESA+
Institute, University of Twente, Drienerlolaan 5, 7522 NBEnschede, Netherlands
| | - César Pascual García
- Luxembourg
Institute of Science and Technology (LIST), 41 Rue du Brill, L-4422Belvaux, Luxembourg
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16
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Isenegger PG, Josephson B, Gaunt B, Davy MJ, Gouverneur V, Baldwin AJ, Davis BG. Posttranslational, site-directed photochemical fluorine editing of protein sidechains to probe residue oxidation state via 19F-nuclear magnetic resonance. Nat Protoc 2023; 18:1543-1562. [PMID: 36806799 DOI: 10.1038/s41596-022-00800-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 11/23/2022] [Indexed: 02/22/2023]
Abstract
The fluorination of amino acid residues represents a near-isosteric alteration with the potential to report on biological pathways, yet the site-directed editing of carbon-hydrogen (C-H) bonds in complex biomolecules to carbon-fluorine (C-F) bonds is challenging, resulting in its limited exploitation. Here, we describe a protocol for the posttranslational and site-directed alteration of native γCH2 to γCF2 in protein sidechains. This alteration allows the installation of difluorinated sidechain analogs of proteinogenic amino acids, in both native and modified states. This chemical editing is robust, mild, fast and highly efficient, exploiting photochemical- and radical-mediated C-C bonds grafted onto easy-to-access cysteine-derived dehydroalanine-containing proteins as starting materials. The heteroaryl-sulfonyl reagent required for generating the key carbon-centered C• radicals that install the sidechain can be synthesized in two to six steps from commercially available precursors. This workflow allows the nonexpert to create fluorinated proteins within 24 h, starting from a corresponding purified cysteine-containing protein precursor, without the need for bespoke biological systems. As an example, we readily introduce three γCF2-containing methionines in all three progressive oxidation states (sulfide, sulfoxide and sulfone) as D-/L- forms into histone eH3.1 at site 4 (a relevant lysine to methionine oncomutation site), and each can be detected by 19F-nuclear magnetic resonance of the γCF2 group, as well as the two diastereomers of the sulfoxide, even when found in a complex protein mixture of all three. The site-directed editing of C-H→C-F enables the use of γCF2 as a highly sensitive, 'zero-size-zero-background' label in protein sidechains, which may be used to probe biological phenomena, protein structures and/or protein-ligand interactions by 19F-based detection methods.
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Affiliation(s)
| | | | - Ben Gaunt
- The Rosalind Franklin Institute, Oxfordshire, UK
| | - Matthew J Davy
- The Rosalind Franklin Institute, Oxfordshire, UK.,Department of Pharmacology, University of Oxford, Oxford, UK
| | | | - Andrew J Baldwin
- Department of Chemistry, University of Oxford, Oxford, UK. .,The Rosalind Franklin Institute, Oxfordshire, UK. .,Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK.
| | - Benjamin G Davis
- Department of Chemistry, University of Oxford, Oxford, UK. .,The Rosalind Franklin Institute, Oxfordshire, UK. .,Department of Pharmacology, University of Oxford, Oxford, UK.
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17
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Raval M, Mishra S, Tiwari AK. Epigenetic regulons in Alzheimer's disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 198:185-247. [DOI: 10.1016/bs.pmbts.2023.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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18
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Kawashima SA, Kanai M. Live Cell Synthetic Histone Acetylation by Chemical Catalyst. Methods Mol Biol 2023; 2519:155-161. [PMID: 36066720 DOI: 10.1007/978-1-0716-2433-3_17] [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] [Indexed: 06/15/2023]
Abstract
Posttranslational modifications (PTMs) of histones, such as lysine acetylation and ubiquitination, regulate chromatin structure and gene expression. In living organisms, histone PTMs are catalyzed by histone-modifying enzymes. Here, we describe an entirely chemical method to introduce histone modifications in living cells without genetic manipulation. The chemical catalyst PEG-LANA-DSSMe activates a thioester acetyl donor, N,S-diacetylcysteamine (NAC-Ac), and promotes regioselective, synthetic histone acetylation at H2BK120 in living cells.
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Affiliation(s)
| | - Motomu Kanai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
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19
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Yang Q, Gao Y, Liu X, Xiao Y, Wu M. A General Method to Edit Histone H3 Modifications on Chromatin Via Sortase-Mediated Metathesis. Angew Chem Int Ed Engl 2022; 61:e202209945. [PMID: 36305862 DOI: 10.1002/anie.202209945] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Indexed: 11/07/2022]
Abstract
The post-translational modifications (PTMs) on the tail of histone H3 control chromatin structure and influence epigenetics and gene expression. The current chemical methods including unnatural amino acid incorporation and protein splicing enable preparations of the histone with diverse PTMs in cellular contexts, but they are not applicable to edit native chromatin. The manipulation of histone-modifying enzymes alter the endogenous histone PTMs but the lack of specificity of most histone-modifying enzymes prevents precise control of specific H3 tail PTM patterns. Here we report a new method to edit the N-tail of histone H3 via sortase mediated metathesis (SMM). The sortase can install desired PTM patterns into histone H3 on nucleosomes in vitro and in cellulo. This study expands the application scope of sortase from ligation to metathesis in live cells using cell-penetrating peptides (CPPs). In addition, it offers a strategy to edit PTMs of cellular histone H3 with potential for the development of precise epigenome editing.
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Affiliation(s)
- Qingyun Yang
- Department of Chemistry, Zhejiang University, 310027, Hangzhou, Zhejiang Province, China.,Department of Chemistry, School of Science, Westlake University, 600 Dunyu Road, 310030, Hangzhou, Zhejiang Province, China.,Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, 310024, Hangzhou, Zhejiang Province, China
| | - Yingxiao Gao
- Department of Chemistry, School of Science, Westlake University, 600 Dunyu Road, 310030, Hangzhou, Zhejiang Province, China.,Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, 310024, Hangzhou, Zhejiang Province, China.,Department of Chemistry, Fudan University, 200438, Shanghai, China
| | - Xia Liu
- Department of Chemistry, School of Science, Westlake University, 600 Dunyu Road, 310030, Hangzhou, Zhejiang Province, China.,Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, 310024, Hangzhou, Zhejiang Province, China
| | - Yihang Xiao
- Department of Chemistry, Zhejiang University, 310027, Hangzhou, Zhejiang Province, China.,Department of Chemistry, School of Science, Westlake University, 600 Dunyu Road, 310030, Hangzhou, Zhejiang Province, China.,Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, 310024, Hangzhou, Zhejiang Province, China
| | - Mingxuan Wu
- Department of Chemistry, School of Science, Westlake University, 600 Dunyu Road, 310030, Hangzhou, Zhejiang Province, China.,Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, 310024, Hangzhou, Zhejiang Province, China.,Westlake Laboratory of Life Sciences and Biomedicine, 310024, Hangzhou, Zhejiang Province, China
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20
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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
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21
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Ai H, Chu GC, Gong Q, Tong ZB, Deng Z, Liu X, Yang F, Xu Z, Li JB, Tian C, Liu L. Chemical Synthesis of Post-Translationally Modified H2AX Reveals Redundancy in Interplay between Histone Phosphorylation, Ubiquitination, and Methylation on the Binding of 53BP1 with Nucleosomes. J Am Chem Soc 2022; 144:18329-18337. [PMID: 36166692 DOI: 10.1021/jacs.2c06156] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The chemical synthesis of homogeneously modified histones is a powerful approach to quantitatively decipher how post-translational modifications (PTMs) modulate epigenetic events. Herein, we describe the expedient syntheses of a selection of phosphorylated and ubiquitinated H2AX proteins in a strategy integrating expressed protein hydrazinolysis and auxiliary-mediated protein ligation. These modified H2AX proteins were then used to discover that although H2AXS139 phosphorylation can enhance the binding of the DNA damage repair factor 53BP1 to either an unmodified nucleosome or that bearing a single H2AXK15ub or H4K20me2 modification, it augments 53BP1's binding only weakly to nucleosomes bearing both H2AXK15ub and H4K20me2. To better understand why such a trivalent additive effect is lacking, we solved the cryo-EM structure (3.38 Å) of the complex of 53BP1 with the H2AXK15ub/S139ph_H4K20me2 nucleosome, which showed that H2AXS139 phosphorylation distorts the interaction interface between ubiquitin and 53BP1's UDR motif. Our study revealed that there is redundancy in the interplay of multiple histone PTMs, which may be useful for controlling the dynamic distribution of effector proteins onto nucleosomes bearing different histone variants and PTMs in a time-dependent fashion, through specific cellular biochemical events.
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Affiliation(s)
- Huasong Ai
- Department of Chemistry, Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Guo-Chao Chu
- Department of Chemistry, Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Qingyue Gong
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Ze-Bin Tong
- Department of Chemistry, Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Zhiheng Deng
- Department of Chemistry, Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Xin Liu
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Fan Yang
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Ziyu Xu
- Department of Chemistry, Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Jia-Bin Li
- College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China
| | - Changlin Tian
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Lei Liu
- Department of Chemistry, Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
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22
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Maas MN, Hintzen JCJ, Mecinović J. Probing lysine posttranslational modifications by unnatural amino acids. Chem Commun (Camb) 2022; 58:7216-7231. [PMID: 35678513 DOI: 10.1039/d2cc00708h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Posttranslational modifications, typically small chemical tags attached on amino acids following protein biosynthesis, have a profound effect on protein structure and function. Numerous chemically and structurally diverse posttranslational modifications, including methylation, acetylation, hydroxylation, and ubiquitination, have been identified and characterised on lysine residues in proteins. In this feature article, we focus on chemical tools that rely on the site-specific incorporation of unnatural amino acids into peptides and proteins to probe posttranslational modifications of lysine. We highlight that simple amino acid mimics enable detailed mechanistic and functional assignment of enzymes that install and remove such modifications, and proteins that specifically recognise lysine posttranslational modifications.
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Affiliation(s)
- Marijn N Maas
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark.
| | - Jordi C J Hintzen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark.
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark.
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23
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Hintzen JCJ, Ma H, Deng H, Witecka A, Andersen SB, Drozak J, Guo H, Qian P, Li H, Mecinović J. Histidine methyltransferase
SETD3
methylates structurally diverse histidine mimics in actin. Protein Sci 2022; 31:e4305. [PMID: 35481649 PMCID: PMC9004244 DOI: 10.1002/pro.4305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/15/2022] [Accepted: 03/18/2022] [Indexed: 01/05/2023]
Abstract
Actin histidine Nτ‐methylation by histidine methyltransferase SETD3 plays an important role in human biology and diseases. Here, we report integrated synthetic, biocatalytic, biostructural, and computational analyses on human SETD3‐catalyzed methylation of actin peptides possessing histidine and its structurally and chemically diverse mimics. Our enzyme assays supported by biostructural analyses demonstrate that SETD3 has a broader substrate scope beyond histidine, including N‐nucleophiles on the aromatic and aliphatic side chains. Quantum mechanical/molecular mechanical molecular dynamics and free‐energy simulations provide insight into binding geometries and the free energy barrier for the enzymatic methyl transfer to histidine mimics, further supporting experimental data that histidine is the superior SETD3 substrate over its analogs. This work demonstrates that human SETD3 has a potential to catalyze efficient methylation of several histidine mimics, overall providing mechanistic, biocatalytic, and functional insight into actin histidine methylation by SETD3. PDB Code(s): 7W28 and 7W29
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Affiliation(s)
- Jordi C. J. Hintzen
- Department of Physics, Chemistry and Pharmacy University of Southern Denmark Odense Denmark
| | - Huida Ma
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua‐Peking Center for Life Sciences Tsinghua University Beijing China
| | - Hao Deng
- Chemistry and Materials Science Faculty Shandong Agricultural University Tai'an Shandong China
| | - Apolonia Witecka
- Department of Metabolic Regulation, Faculty of Biology University of Warsaw Warsaw Poland
| | - Steffen B. Andersen
- Department of Physics, Chemistry and Pharmacy University of Southern Denmark Odense Denmark
| | - Jakub Drozak
- Department of Metabolic Regulation, Faculty of Biology University of Warsaw Warsaw Poland
| | - Hong Guo
- Department of Biochemistry and Cellular and Molecular Biology University of Tennessee Knoxville Tennessee USA
- UT/ORNL Center for Molecular Biophysics Oak Ridge National Laboratory Oak Ridge Tennessee USA
| | - Ping Qian
- Chemistry and Materials Science Faculty Shandong Agricultural University Tai'an Shandong China
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua‐Peking Center for Life Sciences Tsinghua University Beijing China
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy University of Southern Denmark Odense Denmark
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24
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Ren M, Greenberg MM, Zhou C. Participation of Histones in DNA Damage and Repair within Nucleosome Core Particles: Mechanism and Applications. Acc Chem Res 2022; 55:1059-1073. [PMID: 35271268 PMCID: PMC8983524 DOI: 10.1021/acs.accounts.2c00041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
DNA is damaged by various endogenous and exogenous sources, leading to a diverse group of reactive intermediates that yield a complex mixture of products. The initially formed products are often metastable and can react to yield lesions that are more biologically deleterious. Mechanistic studies are frequently carried out on free DNA as the substrate. The observations do not necessarily reflect the reaction environment inside human cells where genomic DNA is condensed as chromatin in the nucleus. Chromatin is made up of monomeric structural units called nucleosomes, which are comprised of DNA wrapped around an octameric core of histone proteins (two copies each of histones H2A, H2B, H3, and H4).This account presents a summary of our work in the past decade on the mechanistic studies of DNA damage and repair in reconstituted nucleosome core particles (NCPs). A series of metastable lesions and reactive intermediates, such as abasic sites (AP), N7-methyl-2'-deoxyguanosine (MdG), and 2'-deoxyadenosin-N6-yl radical (dA•), have been independently generated in a site-specific manner in bottom-up-synthesized NCPs. Detailed mechanistic studies on these NCPs revealed that histones actively participate in DNA damage and repair processes in diverse ways. For instance, nucleophilic residues in the flexible histone N-terminal tails, such as Lys and N-terminal α-amine, react with electrophilic DNA damage and reactive intermediates. In some cases, transient intermediates are produced, leading to the promotion or suppression of damage and repair processes. In other examples, reactions with histones yield reversible or stable DNA-protein cross-links (DPCs). Histones also utilize acidic and basic residues, such as histidine and aspartic acid, to catalyze DNA strand cleavage through general acid/base catalysis. Alternatively, a Tyr in histone plays a vital role in nucleosomal DNA damage and repair via radical transfer. Finally, the reactivity discovered during the mechanistic studies has facilitated the development of new reagents and methods with applications in biotechnology.This research has enriched our knowledge of the roles of histone proteins in DNA damage and repair and their contributions to epigenetics and may have significant biological implications. The residues in histone N-terminal tails that react with DNA lesions also play pivotal roles in regulating the structure and function of chromatin, indicating that there may be cross-talk between DNA damage and repair in eukaryotic cells and epigenetic regulation. Also, in view of the biased amino acid composition of histones, these results provide hints about how the proteins have evolved to minimize their deleterious effects but maximize beneficial ones for maintaining genome integrity. Finally, previously unreported DPCs and histone post-translational modifications have been discovered through this research. The effects of these newly identified lesions on the structure and function of chromatin and their fates inside cells remain to be elucidated.
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Affiliation(s)
- Mengtian Ren
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Marc M. Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Chuanzheng Zhou
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
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25
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Connacher J, von Grüning H, Birkholtz L. Histone Modification Landscapes as a Roadmap for Malaria Parasite Development. Front Cell Dev Biol 2022; 10:848797. [PMID: 35433676 PMCID: PMC9010790 DOI: 10.3389/fcell.2022.848797] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/04/2022] [Indexed: 12/26/2022] Open
Abstract
Plasmodium falciparum remains the deadliest parasite species in the world, responsible for 229 million cases of human malaria in 2019. The ability of the P. falciparum parasite to progress through multiple life cycle stages and thrive in diverse host and vector species hinges on sophisticated mechanisms of epigenetic regulation of gene expression. Emerging evidence indicates such epigenetic control exists in concentric layers, revolving around core histone post-translational modification (PTM) landscapes. Here, we provide a necessary update of recent epigenome research in malaria parasites, focusing specifically on the ability of dynamic histone PTM landscapes to orchestrate the divergent development and differentiation pathways in P. falciparum parasites. In addition to individual histone PTMs, we discuss recent findings that imply functional importance for combinatorial PTMs in P. falciparum parasites, representing an operational histone code. Finally, this review highlights the remaining gaps and provides strategies to address these to obtain a more thorough understanding of the histone modification landscapes that are at the center of epigenetic regulation in human malaria parasites.
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26
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Lukasak B, Thompson RE, Mitchener MM, Feng VJ, Bagert JD, Muir TW. A Genetically Encoded Approach for Breaking Chromatin Symmetry. ACS CENTRAL SCIENCE 2022; 8:176-183. [PMID: 35233450 PMCID: PMC8875426 DOI: 10.1021/acscentsci.1c01332] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Indexed: 05/03/2023]
Abstract
Nucleosomes frequently exist as asymmetric species in native chromatin contexts. Current methods for the traceless generation of these heterotypic chromatin substrates are inefficient and/or difficult to implement. Here, we report an application of the SpyCatcher/SpyTag system as a convenient route to assemble desymmetrized nucleoprotein complexes. This genetically encoded covalent tethering system serves as an internal chaperone, maintained through the assembly process, affording traceless asymmetric nucleosomes following proteolytic removal of the tethers. The strategy allows for generation of nucleosomes containing asymmetric modifications on single or multiple histones, thereby providing facile access to a range of substrates. Herein, we use such constructs to interrogate how nucleosome desymmetrization caused by the incorporation of cancer-associated histone mutations alters chromatin remodeling processes. We also establish that our system provides access to asymmetric dinucleosomes, which allowed us to query the geometric/symmetry constraints of the unmodified histone H3 tail in stimulating the activity of the histone lysine demethylase, KDM5B. By providing a streamlined approach to generate these sophisticated substrates, our method expands the chemical biology toolbox available for interrogating the consequences of asymmetry on chromatin structure and function.
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27
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Wang ZA, Whedon SD, Wu M, Wang S, Brown EA, Anmangandla A, Regan L, Lee K, Du J, Hong JY, Fairall L, Kay T, Lin H, Zhao Y, Schwabe JWR, Cole PA. Histone H2B Deacylation Selectivity: Exploring Chromatin's Dark Matter with an Engineered Sortase. J Am Chem Soc 2022; 144:3360-3364. [PMID: 35175758 PMCID: PMC8895396 DOI: 10.1021/jacs.1c13555] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We describe a new method to produce histone H2B by semisynthesis with an engineered sortase transpeptidase. N-Terminal tail site-specifically modified acetylated, lactylated, and β-hydroxybutyrylated histone H2Bs were incorporated into nucleosomes and investigated as substrates of histone deacetylase (HDAC) complexes and sirtuins. A wide range of rates and site-specificities were observed by these enzyme forms suggesting distinct biological roles in regulating chromatin structure and epigenetics.
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Affiliation(s)
- Zhipeng A Wang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States.,Department of Biological Chemistry and Molecular Pharmcology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Samuel D Whedon
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States.,Department of Biological Chemistry and Molecular Pharmcology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Mingxuan Wu
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States.,Department of Biological Chemistry and Molecular Pharmcology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Siyu Wang
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Edward A Brown
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Ananya Anmangandla
- Howard Hughes Medical Institute; Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Liam Regan
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Kwangwoon Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States.,Department of Biological Chemistry and Molecular Pharmcology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Jianfeng Du
- The Ben May Department for Cancer Research, Chicago, Illinois 60637, United States
| | - Jun Young Hong
- Howard Hughes Medical Institute; Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Louise Fairall
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Taylor Kay
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States.,Department of Biological Chemistry and Molecular Pharmcology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Hening Lin
- Howard Hughes Medical Institute; Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Yingming Zhao
- The Ben May Department for Cancer Research, Chicago, Illinois 60637, United States
| | - John W R Schwabe
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States.,Department of Biological Chemistry and Molecular Pharmcology, Harvard Medical School, Boston, Massachusetts 02115, United States
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28
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Meanor JN, Keung AJ, Rao BM. Modified Histone Peptides Linked to Magnetic Beads Reduce Binding Specificity. Int J Mol Sci 2022; 23:ijms23031691. [PMID: 35163614 PMCID: PMC8836101 DOI: 10.3390/ijms23031691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/20/2022] [Accepted: 01/29/2022] [Indexed: 12/03/2022] Open
Abstract
Histone post-translational modifications are small chemical changes to the histone protein structure that have cascading effects on diverse cellular functions. Detecting histone modifications and characterizing their binding partners are critical steps in understanding chromatin biochemistry and have been accessed using common reagents such as antibodies, recombinant assays, and FRET-based systems. High-throughput platforms could accelerate work in this field, and also could be used to engineer de novo histone affinity reagents; yet, published studies on their use with histones have been noticeably sparse. Here, we describe specific experimental conditions that affect binding specificities of post-translationally modified histones in classic protein engineering platforms and likely explain the relative difficulty with histone targets in these platforms. We also show that manipulating avidity of binding interactions may improve specificity of binding.
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Affiliation(s)
- Jenna N. Meanor
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Campus Box 7905, Raleigh, NC 27606, USA;
| | - Albert J. Keung
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Campus Box 7905, Raleigh, NC 27606, USA;
- Correspondence: (A.J.K.); (B.M.R.)
| | - Balaji M. Rao
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Campus Box 7905, Raleigh, NC 27606, USA;
- Golden LEAF Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC 27695, USA
- Correspondence: (A.J.K.); (B.M.R.)
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29
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Bierlmeier J, Álvaro‐Benito M, Scheffler M, Sturm K, Rehkopf L, Freund C, Schwarzer D. Sortase‐vermittelte Multi‐Fragment‐Kopplung durch Ligationsstellen‐Schaltung. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202109032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jan Bierlmeier
- Interfakultäres Institut für Biochemie Universität Tübingen Auf der Morgenstelle 34 D-72076 Tübingen Deutschland
| | - Miguel Álvaro‐Benito
- Institute of Chemistry and Biochemistry Freie Universität Berlin Thielallee 63 D-14195 Berlin Deutschland
| | - Maren Scheffler
- Interfakultäres Institut für Biochemie Universität Tübingen Auf der Morgenstelle 34 D-72076 Tübingen Deutschland
| | - Kristina Sturm
- Interfakultäres Institut für Biochemie Universität Tübingen Auf der Morgenstelle 34 D-72076 Tübingen Deutschland
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology Universität Genf 30 Quai E. Ansermet 1211 Genf Schweiz
| | - Luisa Rehkopf
- Interfakultäres Institut für Biochemie Universität Tübingen Auf der Morgenstelle 34 D-72076 Tübingen Deutschland
| | - Christian Freund
- Institute of Chemistry and Biochemistry Freie Universität Berlin Thielallee 63 D-14195 Berlin Deutschland
| | - Dirk Schwarzer
- Interfakultäres Institut für Biochemie Universität Tübingen Auf der Morgenstelle 34 D-72076 Tübingen Deutschland
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30
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Griffiths RC, Smith FR, Long JE, Scott D, Williams HEL, Oldham NJ, Layfield R, Mitchell NJ. Site‐Selective Installation of N
ϵ
‐Modified Sidechains into Peptide and Protein Scaffolds via Visible‐Light‐Mediated Desulfurative C–C Bond Formation. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202110223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Rhys C. Griffiths
- School of Chemistry University of Nottingham University Park Nottingham NG7 2RD UK
| | - Frances R. Smith
- School of Chemistry University of Nottingham University Park Nottingham NG7 2RD UK
| | - Jed E. Long
- Biodiscovery Institute University of Nottingham University Park Nottingham NG7 2RD UK
| | - Daniel Scott
- School of Life Sciences, Queen's Medical Centre University of Nottingham Nottingham NG7 2UH UK
| | - Huw E. L. Williams
- Biodiscovery Institute University of Nottingham University Park Nottingham NG7 2RD UK
| | - Neil J. Oldham
- School of Chemistry University of Nottingham University Park Nottingham NG7 2RD UK
| | - Robert Layfield
- School of Life Sciences, Queen's Medical Centre University of Nottingham Nottingham NG7 2UH UK
| | - Nicholas J. Mitchell
- School of Chemistry University of Nottingham University Park Nottingham NG7 2RD UK
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31
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Idigo NJ, Voigt P. Detection and Quantification of Histone Methyltransferase Activity In Vitro. Methods Mol Biol 2022; 2529:43-61. [PMID: 35733009 DOI: 10.1007/978-1-0716-2481-4_2] [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] [Indexed: 06/15/2023]
Abstract
Histone methyltransferases (HMTs) catalyze the methylation of lysine and arginine residues in histone as well as nonhistone substrates. In vitro histone methyltransferase assays have been instrumental in identifying HMTs, and they continue to be invaluable tools for the study of these important enzymes, revealing novel substrates and modes of regulation.Here we describe a universal protocol to examine HMT activity in vitro that can be adapted to a range of HMTs, substrates, and experimental objectives. We provide protocols for the detection of activity based on incorporation of 3H-labeled methyl groups from S-adenosylmethionine (SAM), methylation-specific antibodies, and quantification of the reaction product S-adenosylhomocysteine (SAH).
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Affiliation(s)
- Nwamaka J Idigo
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Philipp Voigt
- Epigenetics Programme, Babraham Institute, Cambridge, UK.
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
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32
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Jing Y, Liu Z, Li XD. Preparation of Site-Specific Succinylated Histone Mimics to Investigate Its Impact on Nucleosome Dynamics. Methods Mol Biol 2022; 2530:141-157. [PMID: 35761047 DOI: 10.1007/978-1-0716-2489-0_10] [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] [Indexed: 06/15/2023]
Abstract
Posttranslational modifications (PTMs) of histones have been demonstrated to be the key regulating mechanism of nucleosome dynamics and chromatin structure. Lysine succinylation is a recently discovered PTM that plays critical roles in metabolism, epigenetic signaling, and is correlated with several diseases. One significant challenge in studying the effects of this modification on nucleosome dynamics is to obtain site-specifically modified histones. Here, we report the rapid site-specific incorporation of a succinylation mimic into histones, which facilitates the characterization of its impact on nucleosome dynamics with a Förster resonance energy transfer (FRET) approach.
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Affiliation(s)
- Yihang Jing
- Department of Chemistry, The University of Hong Kong, Hong Kong, P. R. China
| | - Zheng Liu
- Department of Chemistry, The University of Hong Kong, Hong Kong, P. R. China
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong, Hong Kong, P. R. China.
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33
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Leicher R, Liu S. Probing the Interaction Between Chromatin and Chromatin-Associated Complexes with Optical Tweezers. Methods Mol Biol 2022; 2478:313-327. [PMID: 36063325 PMCID: PMC10751574 DOI: 10.1007/978-1-0716-2229-2_11] [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] [Indexed: 06/15/2023]
Abstract
Single-molecule force spectroscopy is a powerful tool to analyze the architecture and interaction of large macromolecular assemblies that are refractory to high-resolution structural interrogations. Here, we describe an optical tweezers-based platform for extracting the mechanical fingerprints of individual nucleosome arrays bound with chromatin-associated complexes, such as the Polycomb repressive complex 2 (PRC2). This platform comprehensively characterizes the diverse binding modes of PRC2 on chromatin, measures their mechanical strengths, and is broadly applicable to the studies of other epigenetic machineries.
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Affiliation(s)
- Rachel Leicher
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA.
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34
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Bierlmeier J, Álvaro-Benito M, Scheffler M, Sturm K, Rehkopf L, Freund C, Schwarzer D. Sortase-Mediated Multi-Fragment Assemblies by Ligation Site Switching. Angew Chem Int Ed Engl 2021; 61:e202109032. [PMID: 34735044 PMCID: PMC9299656 DOI: 10.1002/anie.202109032] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Indexed: 11/24/2022]
Abstract
Sortase‐mediated ligation (SML) is a powerful tool of protein chemistry allowing the ligation of peptides containing LPxTG sorting motifs and N‐terminal glycine nucleophiles. The installation of a sorting motif into the product prohibits the assembly of multiple fragments by SML. Here we report multi‐fragment SML based on switchable sortase substrates. Substitution of the Leu residue by disulfide‐containing Cys(StBu) results in active sorting motifs, which are inactivatable by reduction. In combination with a photo‐protected N‐Gly nucleophile, multi‐fragment SML is enabled by repetitive cycles of SML and ligation site switching. The feasibility of this approach was demonstrated by a proof‐of‐concept four‐fragment ligation, the assembly of peptide probes for bivalent chromatin binding proteins and oligomerization of peptide antigens. Biochemical and immuno‐assays demonstrated functionality of these probes rendering them promising tools for immunology and chromatin biochemistry.
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Affiliation(s)
- Jan Bierlmeier
- Interfakultäres Institut für Biochemie, Universität Tübingen, Auf der Morgenstelle 34, 72076, Tübingen, Germany
| | - Miguel Álvaro-Benito
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Maren Scheffler
- Interfakultäres Institut für Biochemie, Universität Tübingen, Auf der Morgenstelle 34, 72076, Tübingen, Germany
| | - Kristina Sturm
- Interfakultäres Institut für Biochemie, Universität Tübingen, Auf der Morgenstelle 34, 72076, Tübingen, Germany.,Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, 30 Quai E. Ansermet, 1211, Geneva, Switzerland
| | - Luisa Rehkopf
- Interfakultäres Institut für Biochemie, Universität Tübingen, Auf der Morgenstelle 34, 72076, Tübingen, Germany
| | - Christian Freund
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Dirk Schwarzer
- Interfakultäres Institut für Biochemie, Universität Tübingen, Auf der Morgenstelle 34, 72076, Tübingen, Germany
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35
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Chemical biology approaches to study histone interactors. Biochem Soc Trans 2021; 49:2431-2441. [PMID: 34709376 PMCID: PMC9785950 DOI: 10.1042/bst20210772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 12/25/2022]
Abstract
Protein-protein interactions (PPIs) in the nucleus play key roles in transcriptional regulation and ensure genomic stability. Critical to this are histone-mediated PPI networks, which are further fine-tuned through dynamic post-translational modification. Perturbation to these networks leads to genomic instability and disease, presenting epigenetic proteins as key therapeutic targets. This mini-review will describe progress in mapping the combinatorial histone PTM landscape, and recent chemical biology approaches to map histone interactors. Recent advances in mapping direct interactors of histone PTMs as well as local chromatin interactomes will be highlighted, with a focus on mass-spectrometry based workflows that continue to illuminate histone-mediated PPIs in unprecedented detail.
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36
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Griffiths RC, Smith FR, Long JE, Scott D, Williams HEL, Oldham NJ, Layfield R, Mitchell NJ. Site-Selective Installation of N ϵ -Modified Sidechains into Peptide and Protein Scaffolds via Visible-Light-Mediated Desulfurative C-C Bond Formation. Angew Chem Int Ed Engl 2021; 61:e202110223. [PMID: 34713958 PMCID: PMC9299887 DOI: 10.1002/anie.202110223] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/13/2021] [Indexed: 01/07/2023]
Abstract
Post-translational modifications (PTMs) enhance the repertoire of protein function and mediate or influence the activity of many cellular processes. The preparation of site-specifically and homogeneously modified proteins, to apply as tools to understand the biological role of PTMs, is a challenging task. Herein, we describe a visible-light-mediated desulfurative C(sp3 )-C(sp3 ) bond forming reaction that enables the site-selective installation of Nϵ -modified sidechains into peptides and proteins of interest. Rapid, operationally simple, and tolerant to ambient atmosphere, we demonstrate the installation of a range of lysine (Lys) PTMs into model peptide systems and showcase the potential of this technology by site-selectively installing an Nϵ Ac sidechain into recombinantly expressed ubiquitin (Ub).
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Affiliation(s)
- Rhys C Griffiths
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Frances R Smith
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Jed E Long
- Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Daniel Scott
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Huw E L Williams
- Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Neil J Oldham
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Robert Layfield
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Nicholas J Mitchell
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
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37
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Bajbouj K, Al-Ali A, Ramakrishnan RK, Saber-Ayad M, Hamid Q. Histone Modification in NSCLC: Molecular Mechanisms and Therapeutic Targets. Int J Mol Sci 2021; 22:ijms222111701. [PMID: 34769131 PMCID: PMC8584007 DOI: 10.3390/ijms222111701] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 10/23/2021] [Accepted: 10/25/2021] [Indexed: 12/17/2022] Open
Abstract
Lung cancer is the leading cause of cancer mortality in both genders, with non-small cell lung cancer (NSCLC) accounting for about 85% of all lung cancers. At the time of diagnosis, the tumour is usually locally advanced or metastatic, shaping a poor disease outcome. NSCLC includes adenocarcinoma, squamous cell carcinoma, and large cell lung carcinoma. Searching for novel therapeutic targets is mandated due to the modest effect of platinum-based therapy as well as the targeted therapies developed in the last decade. The latter is mainly due to the lack of mutation detection in around half of all NSCLC cases. New therapeutic modalities are also required to enhance the effect of immunotherapy in NSCLC. Identifying the molecular signature of NSCLC subtypes, including genetics and epigenetic variation, is crucial for selecting the appropriate therapy or combination of therapies. Epigenetic dysregulation has a key role in the tumourigenicity, tumour heterogeneity, and tumour resistance to conventional anti-cancer therapy. Epigenomic modulation is a potential therapeutic strategy in NSCLC that was suggested a long time ago and recently starting to attract further attention. Histone acetylation and deacetylation are the most frequently studied patterns of epigenetic modification. Several histone deacetylase (HDAC) inhibitors (HDIs), such as vorinostat and panobinostat, have shown promise in preclinical and clinical investigations on NSCLC. However, further research on HDIs in NSCLC is needed to assess their anti-tumour impact. Another modification, histone methylation, is one of the most well recognized patterns of histone modification. It can either promote or inhibit transcription at different gene loci, thus playing a rather complex role in lung cancer. Some histone methylation modifiers have demonstrated altered activities, suggesting their oncogenic or tumour-suppressive roles. In this review, patterns of histone modifications in NSCLC will be discussed, focusing on the molecular mechanisms of epigenetic modifications in tumour progression and metastasis, as well as in developing drug resistance. Then, we will explore the therapeutic targets emerging from studying the NSCLC epigenome, referring to the completed and ongoing clinical trials on those medications.
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Affiliation(s)
- Khuloud Bajbouj
- College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates; (K.B.); (R.K.R.); (Q.H.)
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah 27272, United Arab Emirates;
| | - Abeer Al-Ali
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah 27272, United Arab Emirates;
| | - Rakhee K. Ramakrishnan
- College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates; (K.B.); (R.K.R.); (Q.H.)
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah 27272, United Arab Emirates;
| | - Maha Saber-Ayad
- College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates; (K.B.); (R.K.R.); (Q.H.)
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah 27272, United Arab Emirates;
- Faculty of Medicine, Cairo University, Cairo 11559, Egypt
- Correspondence: ; Tel.: +971-6-505-7219; Fax: +971-5-558-5879
| | - Qutayba Hamid
- College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates; (K.B.); (R.K.R.); (Q.H.)
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah 27272, United Arab Emirates;
- Meakins-Christie Laboratories, Research Institute of the McGill University Health Center, Montreal, QC H4A 3J1, Canada
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38
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Ackermann BE, Debelouchina GT. Emerging Contributions of Solid-State NMR Spectroscopy to Chromatin Structural Biology. Front Mol Biosci 2021; 8:741581. [PMID: 34708075 PMCID: PMC8544521 DOI: 10.3389/fmolb.2021.741581] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/20/2021] [Indexed: 11/13/2022] Open
Abstract
The eukaryotic genome is packaged into chromatin, a polymer of DNA and histone proteins that regulates gene expression and the spatial organization of nuclear content. The repetitive character of chromatin is diversified into rich layers of complexity that encompass DNA sequence, histone variants and post-translational modifications. Subtle molecular changes in these variables can often lead to global chromatin rearrangements that dictate entire gene programs with far reaching implications for development and disease. Decades of structural biology advances have revealed the complex relationship between chromatin structure, dynamics, interactions, and gene expression. Here, we focus on the emerging contributions of magic-angle spinning solid-state nuclear magnetic resonance spectroscopy (MAS NMR), a relative newcomer on the chromatin structural biology stage. Unique among structural biology techniques, MAS NMR is ideally suited to provide atomic level information regarding both the rigid and dynamic components of this complex and heterogenous biological polymer. In this review, we highlight the advantages MAS NMR can offer to chromatin structural biologists, discuss sample preparation strategies for structural analysis, summarize recent MAS NMR studies of chromatin structure and dynamics, and close by discussing how MAS NMR can be combined with state-of-the-art chemical biology tools to reconstitute and dissect complex chromatin environments.
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Affiliation(s)
| | - Galia T. Debelouchina
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, United States
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39
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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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40
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Konjevoda P, Štambuk N. Relational model of the standard genetic code. Biosystems 2021; 210:104529. [PMID: 34464669 DOI: 10.1016/j.biosystems.2021.104529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 11/28/2022]
Abstract
The genetic code is a set of rules that establishes mapping between triplets in messenger RNA and amino acids in proteins. The most common way to display these rules is the Standard Genetic Code (SGC) table. This paper takes an alternative approach, based on the relational data model by Edgar F. Codd (Commun. ACM, 13:377-387, 1970). The relational model (RM) proposes a distributed storage of data into a collection of tables (called relations), that can be connected by shared communality. Basic elements of the table are rows (called records or tuples), and columns (called fields or attributes). The SGC table, according to the relational data model, represents the so called unnormalized form of a table. Using normalization rules it is possible to subdivide the SGC table into four tables. The rows and columns of single tables are defined by the first and second base and individual tables by the third codon base. The result of this model is an approach to managing genetic code data, represented in terms of tuples and grouped into relations, with table structure and language consistent with first-order (predicate) logic. The RM explains that the final step in the development of the SGC was the adoption of coding function by the third base, which makes an informational/functional unit with the first base, despite the different physical location in a triplet. This enabled the synthesis of specific proteins without ambiguity, in accordance with the concept of ambiguity reduction and five phases of the general model on the origin of biological codes by Marcello Barbieri (BioSystems 181:11-19, 2019).
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Affiliation(s)
- Paško Konjevoda
- Laboratory for Epigenomics, Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia.
| | - Nikola Štambuk
- Center for Nuclear Magnetic Resonance, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia.
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Höllmüller E, Greiner K, Kienle SM, Scheffner M, Marx A, Stengel F. Interactome of Site-Specifically Acetylated Linker Histone H1. J Proteome Res 2021; 20:4443-4451. [PMID: 34351766 DOI: 10.1021/acs.jproteome.1c00396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Linker histone H1 plays a key role in chromatin organization and maintenance, yet our knowledge of the regulation of H1 functions by post-translational modifications is rather limited. In this study, we report on the generation of site-specifically mono- and di-acetylated linker histone H1.2 by genetic code expansion. We used these modified histones to identify and characterize the acetylation-dependent cellular interactome of H1.2 by affinity purification mass spectrometry and show that site-specific acetylation results in overlapping but distinct groups of interacting partners. Among these, we find multiple translational initiation factors and transcriptional regulators such as the NAD+-dependent deacetylase SIRT1, which we demonstrate to act on acetylated H1.2. Taken together, our data suggest that site-specific acetylation of H1.2 plays a role in modulating protein-protein interactions.
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Hananya N, Daley SK, Bagert JD, Muir TW. Synthesis of ADP-Ribosylated Histones Reveals Site-Specific Impacts on Chromatin Structure and Function. J Am Chem Soc 2021; 143:10847-10852. [PMID: 34264659 DOI: 10.1021/jacs.1c05429] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
ADP-ribosylation of nuclear proteins is a critical feature of various DNA damage repair pathways. Histones, particularly H3 and H2B, are major targets of ADP-ribosylation and are primarily modified on serine with a single ADP-ribose unit following DNA damage. While the overall impact of PARP1-dependent poly-ADP-ribosylation is heavily investigated, very little is known about the specific roles of histone ADP-ribosylation. Here, we report the development of an efficient and modular semisynthetic route to full-length ADP-ribosylated histones H3 and H2B, chemically installed at specific serine residues. The modified histones were used to generate various chemically defined ADP-ribosylated chromatin substrates, which were employed in biophysical assays. These studies revealed that ADP-ribosylation of serine-6 of histone H2B (H2BS6ADPr) inhibits chromatin folding and higher-order organization; notably, this effect was enhanced by ADP-ribosylation of H3S10. In addition, ADP-ribosylated nucleosomes were utilized in biochemical experiments employing a panel of lysine methyltransferase enzymes, revealing a context-dependent inhibition of histone H3K9 methylation. The availability of designer ADP-ribosylated chromatin described here is expected to facilitate further biochemical and structural studies regarding the roles of histone ADP-ribosylation in the DNA damage response.
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Affiliation(s)
- Nir Hananya
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Sara K Daley
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - John D Bagert
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Tom W Muir
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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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. [PMID: 34159701 DOI: 10.5252/embr.202152774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023] 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 München, Neuherberg, Germany
| | - Lara Zorro Shahidian
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), University of Cantabria, Santander, Spain
| | - Robert Schneider
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Faculty of Biology, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
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44
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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: 47] [Impact Index Per Article: 15.7] [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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Abstract
The field of epigenetics has exploded over the last two decades, revealing an astonishing level of complexity in the way genetic information is stored and accessed in eukaryotes. This expansion of knowledge, which is very much ongoing, has been made possible by the availability of evermore sensitive and precise molecular tools. This review focuses on the increasingly important role that chemistry plays in this burgeoning field. In an effort to make these contributions more accessible to the nonspecialist, we group available chemical approaches into those that allow the covalent structure of the protein and DNA components of chromatin to be manipulated, those that allow the activity of myriad factors that act on chromatin to be controlled, and those that allow the covalent structure and folding of chromatin to be characterized. The application of these tools is illustrated through a series of case studies that highlight how the molecular precision afforded by chemistry is being used to establish causal biochemical relationships at the heart of epigenetic regulation.
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Affiliation(s)
- John D Bagert
- Frick Chemistry Laboratory, Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA; ,
| | - Tom W Muir
- Frick Chemistry Laboratory, Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA; ,
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46
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Höllmüller E, Geigges S, Niedermeier ML, Kammer KM, Kienle SM, Rösner D, Scheffner M, Marx A, Stengel F. Site-specific ubiquitylation acts as a regulator of linker histone H1. Nat Commun 2021; 12:3497. [PMID: 34108453 PMCID: PMC8190259 DOI: 10.1038/s41467-021-23636-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 05/03/2021] [Indexed: 01/05/2023] Open
Abstract
Decoding the role of histone posttranslational modifications (PTMs) is key to understand the fundamental process of epigenetic regulation. This is well studied for PTMs of core histones but not for linker histone H1 in general and its ubiquitylation in particular due to a lack of proper tools. Here, we report on the chemical synthesis of site-specifically mono-ubiquitylated H1.2 and identify its ubiquitin-dependent interactome on a proteome-wide scale. We show that site-specific ubiquitylation of H1 at position K64 modulates interactions with deubiquitylating enzymes and the deacetylase SIRT1. Moreover, it affects H1-dependent chromatosome assembly and phase separation resulting in a more open chromatosome conformation generally associated with a transcriptionally active chromatin state. In summary, we propose that site-specific ubiquitylation plays a general regulatory role for linker histone H1. While the role of specific posttranslational modifications (PTMs) is increasingly well understood for core histones, this is not the case for linker histone H1. Here the authors show that site-specific ubiquitylation of H1 results in distinct interactomes, regulates phase separation, and modulates assembly of chromatosomes.
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Affiliation(s)
- Eva Höllmüller
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Simon Geigges
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Marie L Niedermeier
- Department of Biology, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Kai-Michael Kammer
- Department of Biology, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Simon M Kienle
- Department of Biology, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Daniel Rösner
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Martin Scheffner
- Department of Biology, University of Konstanz, Konstanz, Germany. .,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany.
| | - Andreas Marx
- Department of Chemistry, University of Konstanz, Konstanz, Germany. .,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany.
| | - Florian Stengel
- Department of Biology, University of Konstanz, Konstanz, Germany. .,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany.
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47
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Margiola S, Gerecht K, Müller MM. Semisynthetic 'designer' p53 sheds light on a phosphorylation-acetylation relay. Chem Sci 2021; 12:8563-8570. [PMID: 34221338 PMCID: PMC8221199 DOI: 10.1039/d1sc00396h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 05/18/2021] [Indexed: 12/15/2022] Open
Abstract
The tumor suppressor protein p53 is a master regulator of cell fate. The activity of p53 is controlled by a plethora of posttranslational modifications (PTMs). However, despite extensive research, the mechanisms of this regulation are still poorly understood due to a paucity of biochemical studies with p53 carrying defined PTMs. Here, we report a protein semi-synthesis approach to access site-specifically modified p53. We synthesized a set of chemically homogeneous full-length p53 carrying one (Ser20ph and Ser15ph) or two (Ser15,20ph) naturally occurring, damage-associated phosphoryl marks. Refolding and biochemical characterization of semisynthetic p53 variants confirmed their structural and functional integrity. Furthermore, we show that phosphorylation within the N-terminal domain directly enhances p300-dependent acetylation approximately twofold, consistent with the role of these marks in p53 activation. Given that the p53 N-terminus is a hotspot for PTMs, we believe that our approach will contribute greatly to a mechanistic understanding of how p53 is controlled by PTMs.
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Affiliation(s)
- Sofia Margiola
- Department of Chemistry, King's College London 7 Trinity Street London SE1 1DB UK
| | - Karola Gerecht
- Department of Chemistry, King's College London 7 Trinity Street London SE1 1DB UK
| | - Manuel M Müller
- Department of Chemistry, King's College London 7 Trinity Street London SE1 1DB UK
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49
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Freund C, Schwarzer D. Engineered Sortases in Peptide and Protein Chemistry. Chembiochem 2021; 22:1347-1356. [PMID: 33290621 PMCID: PMC8248031 DOI: 10.1002/cbic.202000745] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/07/2020] [Indexed: 12/21/2022]
Abstract
The transpeptidase sortase A of Staphylococcus aureus (Sa-SrtA) is a valuable tool in protein chemistry. The native enzyme anchors surface proteins containing a highly conserved LPxTG sorting motif to a terminal glycine residue of the peptidoglycan layer in Gram-positive bacteria. This reaction is exploited for sortase-mediated ligation (SML), allowing the site-specific linkage of synthetic peptides and recombinant proteins by a native peptide bond. However, the moderate catalytic efficiency and specificity of Sa-SrtA fueled the development of new biocatalysts for SML, including the screening of sortase A variants form microorganisms other than S. aureus and the directed protein evolution of the Sa-SrtA enzyme itself. Novel display platforms and screening formats were developed to isolate sortases with altered properties from mutant libraries. This yielded sortases with strongly enhanced catalytic activity and enzymes recognizing new sorting motifs as substrates. This minireview focuses on recent advances in the field of directed sortase evolution and applications of these tailor-made enzymes in biochemistry.
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Affiliation(s)
- Christian Freund
- Freie Universität BerlinInstitute of Chemistry and BiochemistryThielallee 6314195BerlinGermany
| | - Dirk Schwarzer
- University of TübingenInterfaculty Institute of Biochemistry (IFIB)Auf der Morgenstelle 3472076TübingenGermany
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50
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Wang L, Zhang Q, You Q. Targeting the HSP90-CDC37-kinase chaperone cycle: A promising therapeutic strategy for cancer. Med Res Rev 2021; 42:156-182. [PMID: 33846988 DOI: 10.1002/med.21807] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 03/19/2021] [Accepted: 03/31/2021] [Indexed: 12/25/2022]
Abstract
Heat shock protein 90 (HSP90) is an indispensable molecular chaperone that facilitates the maturation of numerous oncoproteins in cancer cells, including protein kinases, ribonucleoproteins, steroid hormone receptors, and transcription factors. Although over 30 HSP90 inhibitors have steadily entered clinical trials, further clinical advancement has been restricted by their limited efficacy, inevitable heat shock response, and multiple side-effects, likely induced via an ATP inhibition mechanism. Since both ATP and various co-chaperones play essential roles in the HSP90 chaperone cycle to achieve integrated function, optimal therapeutics require an understanding of the dynamic interactions among HSP90, ATP, and cochaperones. To date, continuous research has promoted the exploration of the cochaperone cell division cycle 37 (CDC37) as a kinase-specific recognizer and has shown that the HSP90-CDC37-kinase complex is particularly relevant in cancers. Indeed, disrupting the HSP90-CDC37-kinase complex, rather than totally blocking the ATP function of HSP90, is emerging as an alternative way to avoid the limitations of current inhibitors. In this review, we first briefly introduce the HSP90-CDC37-kinase cycle and present the currently available approaches for inhibitor development targeting this cycle and provide insights into selective regulation of the kinase clients of HSP90 by more directional ways.
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Affiliation(s)
- Lei Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, China.,Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, China
| | - Qiuyue Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, China.,Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, China
| | - Qidong You
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, China.,Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, China
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