251
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Abstract
Inhibiting DNA repair can have a positive outcome on therapeutic interventions
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Affiliation(s)
- Stephen P Jackson
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge CB2 1QN, UK. The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
| | - Thomas Helleday
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden.
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252
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Montgomery DC, Garlick JM, Kulkarni RA, Kennedy S, Allali-Hassani A, Kuo YM, Andrews AJ, Wu H, Vedadi M, Meier JL. Global Profiling of Acetyltransferase Feedback Regulation. J Am Chem Soc 2016; 138:6388-91. [PMID: 27149119 DOI: 10.1021/jacs.6b03036] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Lysine acetyltransferases (KATs) are key mediators of cell signaling. Methods capable of providing new insights into their regulation thus constitute an important goal. Here we report an optimized platform for profiling KAT-ligand interactions in complex proteomes using inhibitor-functionalized capture resins. This approach greatly expands the scope of KATs, KAT complexes, and CoA-dependent enzymes accessible to chemoproteomic methods. This enhanced profiling platform is then applied in the most comprehensive analysis to date of KAT inhibition by the feedback metabolite CoA. Our studies reveal that members of the KAT superfamily possess a spectrum of sensitivity to CoA and highlight NAT10 as a novel KAT that may be susceptible to metabolic feedback inhibition. This platform provides a powerful tool to define the potency and selectivity of reversible stimuli, such as small molecules and metabolites, that regulate KAT-dependent signaling.
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Affiliation(s)
- David C Montgomery
- Chemical Biology Laboratory, National Cancer Institute , Frederick, Maryland 21702, United States
| | - Julie M Garlick
- Chemical Biology Laboratory, National Cancer Institute , Frederick, Maryland 21702, United States
| | - Rhushikesh A Kulkarni
- Chemical Biology Laboratory, National Cancer Institute , Frederick, Maryland 21702, United States
| | - Steven Kennedy
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario MG5 1L7, Canada
| | | | - Yin-Ming Kuo
- Fox Chase Cancer Institute , Philadelphia, Pennsylvania 19111, United States
| | - Andrew J Andrews
- Fox Chase Cancer Institute , Philadelphia, Pennsylvania 19111, United States
| | - Hong Wu
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario MG5 1L7, Canada
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario MG5 1L7, Canada
| | - Jordan L Meier
- Chemical Biology Laboratory, National Cancer Institute , Frederick, Maryland 21702, United States.,Department of Pharmacology and Toxicology, University of Toronto , Toronto, Ontario, M5S 1A8, Canada
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253
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Li Y, Lovett D, Zhang Q, Neelam S, Kuchibhotla RA, Zhu R, Gundersen GG, Lele TP, Dickinson RB. Moving Cell Boundaries Drive Nuclear Shaping during Cell Spreading. Biophys J 2016; 109:670-86. [PMID: 26287620 DOI: 10.1016/j.bpj.2015.07.006] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 06/30/2015] [Accepted: 07/07/2015] [Indexed: 12/15/2022] Open
Abstract
The nucleus has a smooth, regular appearance in normal cells, and its shape is greatly altered in human pathologies. Yet, how the cell establishes nuclear shape is not well understood. We imaged the dynamics of nuclear shaping in NIH3T3 fibroblasts. Nuclei translated toward the substratum and began flattening during the early stages of cell spreading. Initially, nuclear height and width correlated with the degree of cell spreading, but over time, reached steady-state values even as the cell continued to spread. Actomyosin activity, actomyosin bundles, microtubules, and intermediate filaments, as well as the LINC complex, were all dispensable for nuclear flattening as long as the cell could spread. Inhibition of actin polymerization as well as myosin light chain kinase with the drug ML7 limited both the initial spreading of cells and flattening of nuclei, and for well-spread cells, inhibition of myosin-II ATPase with the drug blebbistatin decreased cell spreading with associated nuclear rounding. Together, these results show that cell spreading is necessary and sufficient to drive nuclear flattening under a wide range of conditions, including in the presence or absence of myosin activity. To explain this observation, we propose a computational model for nuclear and cell mechanics that shows how frictional transmission of stress from the moving cell boundaries to the nuclear surface shapes the nucleus during early cell spreading. Our results point to a surprisingly simple mechanical system in cells for establishing nuclear shapes.
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Affiliation(s)
- Yuan Li
- Department of Chemical Engineering, University of Florida, Gainesville, Florida
| | - David Lovett
- Department of Chemical Engineering, University of Florida, Gainesville, Florida
| | - Qiao Zhang
- Department of Chemical Engineering, University of Florida, Gainesville, Florida
| | - Srujana Neelam
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, Florida
| | | | - Ruijun Zhu
- Department of Anatomy and Cell Biology, Columbia University, New York, New York
| | - Gregg G Gundersen
- Department of Anatomy and Cell Biology, Columbia University, New York, New York
| | - Tanmay P Lele
- Department of Chemical Engineering, University of Florida, Gainesville, Florida.
| | - Richard B Dickinson
- Department of Chemical Engineering, University of Florida, Gainesville, Florida.
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254
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Abstract
The nuclear lamina (NL) is a structural component of the nuclear envelope and makes extensive contacts with integral nuclear membrane proteins and chromatin. These interactions are critical for many cellular processes, such as nuclear positioning, perception of mechanical stimuli from the cell surface, nuclear stability, 3-dimensional organization of chromatin and regulation of chromatin-binding proteins, including transcription factors. The NL is present in all nucleated metazoan cells but its composition and interactome differ between tissues. Most likely, this contributes to the broad spectrum of disease manifestations in humans with mutations in NL-related genes, ranging from muscle dystrophies to neurological disorders, lipodystrophies and progeria syndromes. We review here exciting novel insight into NL function at the cellular level, in particular in chromatin organization and mechanosensation. We also present recent observations on the relation between the NL and metabolism and the special relevance of the NL in muscle tissues. Finally, we discuss new therapeutic approaches to treat NL-related diseases.
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Affiliation(s)
- Agnieszka Dobrzynska
- a Andalusian Center for Developmental Biology (CABD) , CSIC/Junta de Andalucia/Universidad Pablo de Olavide , Seville , Spain
| | - Susana Gonzalo
- b Edward A. Doisy Department of Biochemistry and Molecular Biology , St Louis University School of Medicine , St. Louis , MO , USA
| | - Catherine Shanahan
- c BHF Center for Research Excellence , King's College London, Cardiovascular Division, James Black Center , London , UK
| | - Peter Askjaer
- a Andalusian Center for Developmental Biology (CABD) , CSIC/Junta de Andalucia/Universidad Pablo de Olavide , Seville , Spain
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255
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Czapiewski R, Robson MI, Schirmer EC. Anchoring a Leviathan: How the Nuclear Membrane Tethers the Genome. Front Genet 2016; 7:82. [PMID: 27200088 PMCID: PMC4859327 DOI: 10.3389/fgene.2016.00082] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 04/20/2016] [Indexed: 12/21/2022] Open
Abstract
It is well established that the nuclear envelope has many distinct direct connections to chromatin that contribute to genome organization. The functional consequences of genome organization on gene regulation are less clear. Even less understood is how interactions of lamins and nuclear envelope transmembrane proteins (NETs) with chromatin can produce anchoring tethers that can withstand the physical forces of and on the genome. Chromosomes are the largest molecules in the cell, making megadalton protein structures like the nuclear pore complexes and ribosomes seem small by comparison. Thus to withstand strong forces from chromosome dynamics an anchoring tether is likely to be much more complex than a single protein-protein or protein-DNA interaction. Here we will briefly review known NE-genome interactions that likely contribute to spatial genome organization, postulate in the context of experimental data how these anchoring tethers contribute to gene regulation, and posit several hypotheses for the physical nature of these tethers that need to be investigated experimentally. Significantly, disruption of these anchoring tethers and the subsequent consequences for gene regulation could explain how mutations in nuclear envelope proteins cause diseases ranging from muscular dystrophy to lipodystrophy to premature aging progeroid syndromes. The two favored hypotheses for nuclear envelope protein involvement in disease are (1) weakening nuclear and cellular mechanical stability, and (2) disrupting genome organization and gene regulation. Considerable experimental support has been obtained for both. The integration of both mechanical and gene expression defects in the disruption of anchoring tethers could provide a unifying hypothesis consistent with both.
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Affiliation(s)
| | | | - Eric C. Schirmer
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of EdinburghEdinburgh, UK
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256
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Understanding Vascular Diseases: Lessons From Premature Aging Syndromes. Can J Cardiol 2016; 32:650-8. [DOI: 10.1016/j.cjca.2015.12.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 12/02/2015] [Accepted: 12/06/2015] [Indexed: 12/18/2022] Open
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257
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Chiang TWW, le Sage C, Larrieu D, Demir M, Jackson SP. CRISPR-Cas9(D10A) nickase-based genotypic and phenotypic screening to enhance genome editing. Sci Rep 2016; 6:24356. [PMID: 27079678 PMCID: PMC4832145 DOI: 10.1038/srep24356] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 03/24/2016] [Indexed: 12/11/2022] Open
Abstract
The RNA-guided Cas9 nuclease is being widely employed to engineer the genomes of various cells and organisms. Despite the efficient mutagenesis induced by Cas9, off-target effects have raised concerns over the system's specificity. Recently a "double-nicking" strategy using catalytic mutant Cas9(D10A) nickase has been developed to minimise off-target effects. Here, we describe a Cas9(D10A)-based screening approach that combines an All-in-One Cas9(D10A) nickase vector with fluorescence-activated cell sorting enrichment followed by high-throughput genotypic and phenotypic clonal screening strategies to generate isogenic knockouts and knock-ins highly efficiently, with minimal off-target effects. We validated this approach by targeting genes for the DNA-damage response (DDR) proteins MDC1, 53BP1, RIF1 and P53, plus the nuclear architecture proteins Lamin A/C, in three different human cell lines. We also efficiently obtained biallelic knock-in clones, using single-stranded oligodeoxynucleotides as homologous templates, for insertion of an EcoRI recognition site at the RIF1 locus and introduction of a point mutation at the histone H2AFX locus to abolish assembly of DDR factors at sites of DNA double-strand breaks. This versatile screening approach should facilitate research aimed at defining gene functions, modelling of cancers and other diseases underpinned by genetic factors, and exploring new therapeutic opportunities.
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Affiliation(s)
- Ting-Wei Will Chiang
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Carlos le Sage
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
| | - Delphine Larrieu
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
| | - Mukerrem Demir
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
| | - Stephen P. Jackson
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
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258
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Sharma S, Lafontaine DLJ. 'View From A Bridge': A New Perspective on Eukaryotic rRNA Base Modification. Trends Biochem Sci 2016; 40:560-575. [PMID: 26410597 DOI: 10.1016/j.tibs.2015.07.008] [Citation(s) in RCA: 178] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 07/28/2015] [Accepted: 07/29/2015] [Indexed: 01/23/2023]
Abstract
Eukaryotic rRNA are modified frequently, although the diversity of modifications is low: in yeast rRNA, there are only 12 different types out of a possible natural repertoire exceeding 112. All nine rRNA base methyltransferases (MTases) and one acetyltransferase have recently been identified in budding yeast, and several instances of crosstalk between rRNA, tRNA, and mRNA modifications are emerging. Although the machinery has largely been identified, the functions of most rRNA modifications remain to be established. Remarkably, a eukaryote-specific bridge, comprising a single ribosomal protein (RP) from the large subunit (LSU), contacts four rRNA base modifications across the ribosomal subunit interface, potentially probing for their presence. We hypothesize in this article that long-range allosteric communication involving rRNA modifications is taking place between the two subunits during translation or, perhaps, the late stages of ribosome assembly.
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Affiliation(s)
- Sunny Sharma
- RNA Molecular Biology, FRS/FNRS, Université Libre de Bruxelles, B-6041 Charleroi-Gosselies, Belgium
| | - Denis L J Lafontaine
- RNA Molecular Biology, FRS/FNRS, Université Libre de Bruxelles, B-6041 Charleroi-Gosselies, Belgium; Center for Microscopy and Molecular Imaging, BioPark campus, B-6041 Charleroi-Gosselies, Belgium.
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259
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Kubben N, Brimacombe KR, Donegan M, Li Z, Misteli T. A high-content imaging-based screening pipeline for the systematic identification of anti-progeroid compounds. Methods 2016; 96:46-58. [PMID: 26341717 PMCID: PMC6317068 DOI: 10.1016/j.ymeth.2015.08.024] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 08/29/2015] [Accepted: 08/31/2015] [Indexed: 10/23/2022] Open
Abstract
Hutchinson-Gilford Progeria Syndrome (HGPS) is an early onset lethal premature aging disorder caused by constitutive production of progerin, a mutant form of the nuclear architectural protein lamin A. The presence of progerin causes extensive morphological, epigenetic and DNA damage related nuclear defects that ultimately disrupt tissue and organismal functions. Hypothesis-driven approaches focused on HGPS affected pathways have been used in attempts to identify druggable targets with anti-progeroid effects. Here, we report an unbiased discovery approach to HGPS by implementation of a high-throughput, high-content imaging based screening method that enables systematic identification of small molecules that prevent the formation of multiple progerin-induced aging defects. Screening a library of 2816 FDA approved drugs, we identified retinoids as a novel class of compounds that reverses aging defects in HGPS patient skin fibroblasts. These findings establish a novel approach to anti-progeroid drug discovery.
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Affiliation(s)
- Nard Kubben
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kyle R Brimacombe
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Megan Donegan
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zhuyin Li
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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260
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Liu X, Tan Y, Zhang C, Zhang Y, Zhang L, Ren P, Deng H, Luo J, Ke Y, Du X. NAT10 regulates p53 activation through acetylating p53 at K120 and ubiquitinating Mdm2. EMBO Rep 2016; 17:349-66. [PMID: 26882543 PMCID: PMC4772976 DOI: 10.15252/embr.201540505] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 01/11/2016] [Indexed: 11/10/2022] Open
Abstract
As a genome guardian, p53 maintains genome stability by arresting cells for damage repair or inducing cell apoptosis to eliminate the damaged cells in stress response. Several nucleolar proteins stabilize p53 by interfering Mdm2–p53 interaction upon cellular stress, while other mechanisms by which nucleolar proteins activate p53 remain to be determined. Here, we identify NAT10 as a novel regulator for p53 activation. NAT10 acetylates p53 at K120 and stabilizes p53 by counteracting Mdm2 action. In addition, NAT10 promotes Mdm2 degradation with its intrinsic E3 ligase activity. After DNA damage, NAT10 translocates to nucleoplasm and activates p53‐mediated cell cycle control and apoptosis. Finally, NAT10 inhibits cell proliferation and expression of NAT10 decreases in human colorectal carcinomas. Thus, our data demonstrate that NAT10 plays a critical role in p53 activation via acetylating p53 and counteracting Mdm2 action, providing a novel pathway by which nucleolar protein activates p53 as a cellular stress sensor.
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Affiliation(s)
- Xiaofeng Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing, China Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Yuqin Tan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing, China Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Chunfeng Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing, China Department of Medical Genetics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Ying Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing, China Laboratory of Genetics, Peking University School of Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Liangliang Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing, China Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Pengwei Ren
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing, China Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Hongkui Deng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing, China Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Jianyuan Luo
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing, China Department of Medical Genetics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China Department of Medical & Research Technology, School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Yang Ke
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing, China Laboratory of Genetics, Peking University School of Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xiaojuan Du
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing, China Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
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261
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Moiseeva O, Lopes-Paciencia S, Huot G, Lessard F, Ferbeyre G. Permanent farnesylation of lamin A mutants linked to progeria impairs its phosphorylation at serine 22 during interphase. Aging (Albany NY) 2016; 8:366-81. [PMID: 26922519 PMCID: PMC4789588 DOI: 10.18632/aging.100903] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 01/20/2016] [Indexed: 12/12/2022]
Abstract
Mutants of lamin A cause diseases including the Hutchinson-Gilford progeria syndrome (HGPS) characterized by premature aging. Lamin A undergoes a series of processing reactions, including farnesylation and proteolytic cleavage of the farnesylated C-terminal domain. The role of cleavage is unknown but mutations that affect this reaction lead to progeria. Here we show that interphase serine 22 phosphorylation of endogenous mutant lamin A (progerin) is defective in cells from HGPS patients. This defect can be mimicked by expressing progerin in human cells and prevented by inhibition of farnesylation. Furthermore, serine 22 phosphorylation of non-farnesylated progerin was enhanced by a mutation that disrupts lamin A head to tail interactions. The phosphorylation of lamin A or non-farnesylated progerin was associated to the formation of spherical intranuclear lamin A droplets that accumulate protein kinases of the CDK family capable of phosphorylating lamin A at serine 22. CDK inhibitors compromised the turnover of progerin, accelerated senescence of HGPS cells and reversed the effects of FTI on progerin levels. We discuss a model of progeria where faulty serine 22 phosphorylation compromises phase separation of lamin A polymers, leading to accumulation of functionally impaired lamin A structures.
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Affiliation(s)
- Olga Moiseeva
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, H3C 3J7, Canada
| | - Stéphane Lopes-Paciencia
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, H3C 3J7, Canada
| | - Geneviève Huot
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, H3C 3J7, Canada
| | - Frédéric Lessard
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, H3C 3J7, Canada
| | - Gerardo Ferbeyre
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, H3C 3J7, Canada
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262
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Wagner BK, Schreiber SL. The Power of Sophisticated Phenotypic Screening and Modern Mechanism-of-Action Methods. Cell Chem Biol 2016; 23:3-9. [PMID: 26933731 PMCID: PMC4779180 DOI: 10.1016/j.chembiol.2015.11.008] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 11/19/2015] [Accepted: 11/19/2015] [Indexed: 12/14/2022]
Abstract
The enthusiasm for phenotypic screening as an approach for small-molecule discovery has increased dramatically over the last several years. The recent increase in phenotype-based discoveries is in part due to advancements in phenotypic readouts in improved disease models that recapitulate clinically relevant biology in cell culture. Of course, a major historical barrier to using phenotypic assays in chemical biology has been the challenge in determining the mechanism of action (MoA) for compounds of interest. With the combination of medically inspired phenotypic screening and the development of modern MoA methods, we can now start implementing this approach in chemical probe and drug discovery. In this Perspective, we highlight recent advances in phenotypic readouts and MoA determination by discussing several case studies in which both activities were required for understanding the chemical biology involved and, in some cases, advancing toward clinical development.
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Affiliation(s)
- Bridget K Wagner
- Center for the Science of Therapeutics, Broad Institute, Cambridge, MA 02142, USA.
| | - Stuart L Schreiber
- Center for the Science of Therapeutics, Broad Institute, Cambridge, MA 02142, USA; Department of Chemistry and Chemical Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
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263
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Vuković LD, Jevtić P, Edens LJ, Levy DL. New Insights into Mechanisms and Functions of Nuclear Size Regulation. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 322:1-59. [PMID: 26940517 DOI: 10.1016/bs.ircmb.2015.11.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nuclear size is generally maintained within a defined range in a given cell type. Changes in cell size that occur during cell growth, development, and differentiation are accompanied by dynamic nuclear size adjustments in order to establish appropriate nuclear-to-cytoplasmic volume relationships. It has long been recognized that aberrations in nuclear size are associated with certain disease states, most notably cancer. Nuclear size and morphology must impact nuclear and cellular functions. Understanding these functional implications requires an understanding of the mechanisms that control nuclear size. In this review, we first provide a general overview of the diverse cellular structures and activities that contribute to nuclear size control, including structural components of the nucleus, effects of DNA amount and chromatin compaction, signaling, and transport pathways that impinge on the nucleus, extranuclear structures, and cell cycle state. We then detail some of the key mechanistic findings about nuclear size regulation that have been gleaned from a variety of model organisms. Lastly, we review studies that have implicated nuclear size in the regulation of cell and nuclear function and speculate on the potential functional significance of nuclear size in chromatin organization, gene expression, nuclear mechanics, and disease. With many fundamental cell biological questions remaining to be answered, the field of nuclear size regulation is still wide open.
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Affiliation(s)
- Lidija D Vuković
- Department of Molecular Biology, University of Wyoming, Laramie, WY, United States of America
| | - Predrag Jevtić
- Department of Molecular Biology, University of Wyoming, Laramie, WY, United States of America
| | - Lisa J Edens
- Department of Molecular Biology, University of Wyoming, Laramie, WY, United States of America
| | - Daniel L Levy
- Department of Molecular Biology, University of Wyoming, Laramie, WY, United States of America.
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264
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Mariani A, Mai TT, Zacharioudakis E, Hienzsch A, Bartoli A, Cañeque T, Rodriguez R. Iron-dependent lysosomal dysfunction mediated by a natural product hybrid. Chem Commun (Camb) 2016; 52:1358-60. [DOI: 10.1039/c5cc09255h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Marmycin A and artemisinin join forces as the molecular hybrid artesumycin, a new fluorescent lysosomotropic small molecule that targets lysosomal iron to kill cancer cells.
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Affiliation(s)
- A. Mariani
- Centre de Recherche de Gif
- Institut de Chimie des Substances Naturelles du CNRS
- 91198 Gif sur-Yvette
- France
| | - T. T. Mai
- Centre de Recherche de Gif
- Institut de Chimie des Substances Naturelles du CNRS
- 91198 Gif sur-Yvette
- France
- Institut Curie Research Center
| | - E. Zacharioudakis
- Centre de Recherche de Gif
- Institut de Chimie des Substances Naturelles du CNRS
- 91198 Gif sur-Yvette
- France
| | - A. Hienzsch
- Centre de Recherche de Gif
- Institut de Chimie des Substances Naturelles du CNRS
- 91198 Gif sur-Yvette
- France
| | - A. Bartoli
- Centre de Recherche de Gif
- Institut de Chimie des Substances Naturelles du CNRS
- 91198 Gif sur-Yvette
- France
| | - T. Cañeque
- Centre de Recherche de Gif
- Institut de Chimie des Substances Naturelles du CNRS
- 91198 Gif sur-Yvette
- France
- Institut Curie Research Center
| | - R. Rodriguez
- Centre de Recherche de Gif
- Institut de Chimie des Substances Naturelles du CNRS
- 91198 Gif sur-Yvette
- France
- Institut Curie Research Center
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265
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Tian X, Wang H, Guan L, Zhang Q, Zhou H, Li C, Huang B, Wu J, Tian Y. Light up Live Cell Nuclear Envelope in Real-Time Using a Two-Photon Absorption and AIE Chromophore. J Fluoresc 2015; 26:59-65. [DOI: 10.1007/s10895-015-1703-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 10/20/2015] [Indexed: 01/27/2023]
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266
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Zhang X, Liu J, Yan S, Huang K, Bai Y, Zheng S. High expression of N-acetyltransferase 10: a novel independent prognostic marker of worse outcome in patients with hepatocellular carcinoma. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:14765-14771. [PMID: 26823802 PMCID: PMC4713588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 10/21/2015] [Indexed: 06/05/2023]
Abstract
N-acetyltransferase 10 (NAT10) is a nucleolar protein involved in histone acetylation, telomerase activity regulation, DNA damage response and cytokinesis. The expression of NAT10 was found to be enhanced in several types of tumors, suggesting its correlation with tumor development. However, the specific role of NAT10 in hepatocellular carcinoma (HCC) is still unclear. The aim of this study was to investigate the expression of NAT10 in HCC patients and to assess the relationship of NAT10 expression with clinicopathological characteristics and tumor prognosis. We selected 17 pairs of HCC samples and adjacent non-neoplastic tissue for mRNA expression analysis. We also performed immunohistochemistry in 186 HCC samples to evaluate the NAT10 protein expression. Cox regression and Kaplan-Meier analysis was used to study the diagnostic and prognostic value of NAT10. The results showed that NAT10 expression was mainly localized in the nuclei/nucleoli and was significantly higher in HCC tissues than peritumoral tissues (P < 0.01). High NAT10 expression was positively correlated with histological differentiation (P < 0.01) and TNM classification (P < 0.01). Cox regression univariate and multivariable analysis revealed that expression of NAT10 in HCC was an independent prognostic factor for patient survival time. Our data suggested that NAT10 might be a promising prognostic marker and potential therapeutic target in HCC.
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Affiliation(s)
- Xiuming Zhang
- Department of Pathology, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, China
| | - Jimin Liu
- Department of Pathology, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, China
- Department of Pathology and Molecular Medicine, Faculty of Health Science, McMaster UniversityHamilton, Ontario, Canada L8S 4K1
| | - Sheng Yan
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang UniversityHangzhou 310003, China
| | - Ke Huang
- Department of Pathology, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, China
| | - Yanfeng Bai
- Department of Pathology, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou 310003, China
| | - Shusen Zheng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang UniversityHangzhou 310003, China
- Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public HealthHangzhou 310003, China
- Key Laboratory of Organ TransplantationHangzhou 310003, China
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267
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Lo Cicero A, Nissan X. Pluripotent stem cells to model Hutchinson-Gilford progeria syndrome (HGPS): Current trends and future perspectives for drug discovery. Ageing Res Rev 2015; 24:343-8. [PMID: 26474742 DOI: 10.1016/j.arr.2015.10.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 10/02/2015] [Accepted: 10/07/2015] [Indexed: 12/27/2022]
Abstract
Progeria, or Hutchinson-Gilford progeria syndrome (HGPS), is a rare, fatal genetic disease characterized by an appearance of accelerated aging in children. This syndrome is typically caused by mutations in codon 608 (p.G608G) of the LMNA, leading to the production of a mutated form of lamin A precursor called progerin. In HGPS, progerin accumulates in cells causing progressive molecular defects, including nuclear shape abnormalities, chromatin disorganization, damage to DNA and delays in cell proliferation. Here we report how, over the past five years, pluripotent stem cells have provided new insights into the study of HGPS and opened new original therapeutic perspectives to treat the disease.
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268
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Cañeque T, Gomes F, Mai TT, Maestri G, Malacria M, Rodriguez R. Synthesis of marmycin A and investigation into its cellular activity. Nat Chem 2015; 7:744-51. [PMID: 26291947 PMCID: PMC5892709 DOI: 10.1038/nchem.2302] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 06/10/2015] [Indexed: 12/29/2022]
Abstract
Anthracyclines such as doxorubicin are used extensively in the treatment of cancers. Anthraquinone-related angucyclines also exhibit antiproliferative properties and have been proposed to operate via similar mechanisms, including direct genome targeting. Here, we report the chemical synthesis of marmycin A and the study of its cellular activity. The aromatic core was constructed by means of a one-pot multistep reaction comprising a regioselective Diels-Alder cycloaddition, and the complex sugar backbone was introduced through a copper-catalysed Ullmann cross-coupling, followed by a challenging Friedel-Crafts cyclization. Remarkably, fluorescence microscopy revealed that marmycin A does not target the nucleus but instead accumulates in lysosomes, thereby promoting cell death independently of genome targeting. Furthermore, a synthetic dimer of marmycin A and the lysosome-targeting agent artesunate exhibited a synergistic activity against the invasive MDA-MB-231 cancer cell line. These findings shed light on the elusive pathways through which anthraquinone derivatives act in cells, pointing towards unanticipated biological and therapeutic applications.
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Affiliation(s)
- Tatiana Cañeque
- Centre de Recherche de Gif, Institut de Chimie des Substances Naturelles du CNRS, 1 Avenue de la Terrasse, Gif sur-Yvette 91198, France
| | - Filipe Gomes
- Centre de Recherche de Gif, Institut de Chimie des Substances Naturelles du CNRS, 1 Avenue de la Terrasse, Gif sur-Yvette 91198, France
| | - Trang Thi Mai
- Centre de Recherche de Gif, Institut de Chimie des Substances Naturelles du CNRS, 1 Avenue de la Terrasse, Gif sur-Yvette 91198, France
| | - Giovanni Maestri
- Centre de Recherche de Gif, Institut de Chimie des Substances Naturelles du CNRS, 1 Avenue de la Terrasse, Gif sur-Yvette 91198, France
- Department of Chemistry, Università degli Studi di Parma, Parco Area delle Scienze 17/a, Parma 43124, Italy
| | - Max Malacria
- Centre de Recherche de Gif, Institut de Chimie des Substances Naturelles du CNRS, 1 Avenue de la Terrasse, Gif sur-Yvette 91198, France
- Institut Parisien de Chimie Moléculaire, Sorbonne Universités, UPMC Univ Paris 06, UMR CNRS 8232, Paris CEDEX 05 75252, France
| | - Raphaël Rodriguez
- Centre de Recherche de Gif, Institut de Chimie des Substances Naturelles du CNRS, 1 Avenue de la Terrasse, Gif sur-Yvette 91198, France
- Institut Curie Research Center, Organic Synthesis and Cell Biology Group, 26 rue d’Ulm, Paris Cedex 05 75248, France
- CNRS UMR 3666, Paris 75005, France
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269
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Maizels Y, Gerlitz G. Shaping of interphase chromosomes by the microtubule network. FEBS J 2015; 282:3500-24. [PMID: 26040675 DOI: 10.1111/febs.13334] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 05/11/2015] [Accepted: 06/01/2015] [Indexed: 12/31/2022]
Abstract
It is well established that microtubule dynamics play a major role in chromosome condensation and localization during mitosis. During interphase, however, it is assumed that the metazoan nuclear envelope presents a physical barrier, which inhibits interaction between the microtubules located in the cytoplasm and the chromatin fibers located in the nucleus. In recent years, it has become apparent that microtubule dynamics alter chromatin structure and function during interphase as well. Microtubule motor proteins transport several transcription factors and exogenous DNA (such as plasmid DNA) from the cytoplasm to the nucleus. Various soluble microtubule components are able to translocate into the nucleus, where they bind various chromatin elements leading to transcriptional alterations. In addition, microtubules may apply force on the nuclear envelope, which is transmitted into the nucleus, leading to changes in chromatin structure. Thus, microtubule dynamics during interphase may affect chromatin spatial organization, as well as transcription, replication and repair.
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Affiliation(s)
- Yael Maizels
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Israel
| | - Gabi Gerlitz
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Israel
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270
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Gay S, Foiani M. Nuclear envelope and chromatin, lock and key of genome integrity. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 317:267-330. [PMID: 26008788 DOI: 10.1016/bs.ircmb.2015.03.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
More than as an inert separation between the inside and outside of the nucleus, the nuclear envelope (NE) constitutes an active toll, which controls the import and export of molecules, and also a hub for a diversity of genomic processes, such as transcription, DNA repair, and chromatin dynamics. Proteins localized at the inner surface of the NE (such as lamins, nuclear pore proteins, lamin-associated proteins) interact with chromatin in a dynamic manner, contributing to the establishment of topological domains. In this review, we address the complex interplay between chromatin and NE. We discuss the divergence of this cross talk during evolution and comment both on the current established models and the most recent findings. In particular, we focus our attention on how the NE cooperates with chromatin in protecting the genome integrity.
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Affiliation(s)
- Sophie Gay
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Marco Foiani
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy; Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano, Milan, Italy
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271
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Sharma S, Langhendries JL, Watzinger P, Kötter P, Entian KD, Lafontaine DLJ. Yeast Kre33 and human NAT10 are conserved 18S rRNA cytosine acetyltransferases that modify tRNAs assisted by the adaptor Tan1/THUMPD1. Nucleic Acids Res 2015; 43:2242-58. [PMID: 25653167 PMCID: PMC4344512 DOI: 10.1093/nar/gkv075] [Citation(s) in RCA: 252] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 01/20/2015] [Accepted: 01/20/2015] [Indexed: 01/05/2023] Open
Abstract
The function of RNA is subtly modulated by post-transcriptional modifications. Here, we report an important crosstalk in the covalent modification of two classes of RNAs. We demonstrate that yeast Kre33 and human NAT10 are RNA cytosine acetyltransferases with, surprisingly, specificity toward both 18S rRNA and tRNAs. tRNA acetylation requires the intervention of a specific and conserved adaptor: yeast Tan1/human THUMPD1. In budding and fission yeasts, and in human cells, we found two acetylated cytosines on 18S rRNA, one in helix 34 important for translation accuracy and another in helix 45 near the decoding site. Efficient 18S rRNA acetylation in helix 45 involves, in human cells, the vertebrate-specific box C/D snoRNA U13, which, we suggest, exposes the substrate cytosine to modification through Watson-Crick base pairing with 18S rRNA precursors during small subunit biogenesis. Finally, while Kre33 and NAT10 are essential for pre-rRNA processing reactions leading to 18S rRNA synthesis, we demonstrate that rRNA acetylation is dispensable to yeast cells growth. The inactivation of NAT10 was suggested to suppress nuclear morphological defects observed in laminopathic patient cells through loss of microtubules modification and cytoskeleton reorganization. We rather propose the effects of NAT10 on laminopathic cells are due to reduced ribosome biogenesis or function.
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MESH Headings
- Acetylation
- Acetyltransferases/chemistry
- Acetyltransferases/metabolism
- Amino Acid Sequence
- Cell Line
- Conserved Sequence
- Cytosine/metabolism
- Humans
- N-Terminal Acetyltransferase E/chemistry
- N-Terminal Acetyltransferase E/metabolism
- N-Terminal Acetyltransferases
- RNA, Fungal/chemistry
- RNA, Fungal/metabolism
- RNA, Plant/chemistry
- RNA, Plant/metabolism
- RNA, Ribosomal, 18S/chemistry
- RNA, Ribosomal, 18S/metabolism
- RNA, Small Nucleolar/metabolism
- RNA, Transfer/metabolism
- RNA-Binding Proteins/metabolism
- Ribosome Subunits, Small, Eukaryotic/metabolism
- Saccharomyces cerevisiae Proteins/chemistry
- Saccharomyces cerevisiae Proteins/metabolism
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Affiliation(s)
- Sunny Sharma
- Institute of Molecular Biosciences, Goethe University, 60438 Frankfurt am Main, Germany RNA Molecular Biology, F.R.S./FNRS, Université Libre de Bruxelles, B-6041 Charleroi-Gosselies, Belgium
| | - Jean-Louis Langhendries
- RNA Molecular Biology, F.R.S./FNRS, Université Libre de Bruxelles, B-6041 Charleroi-Gosselies, Belgium
| | - Peter Watzinger
- Institute of Molecular Biosciences, Goethe University, 60438 Frankfurt am Main, Germany
| | - Peter Kötter
- Institute of Molecular Biosciences, Goethe University, 60438 Frankfurt am Main, Germany
| | - Karl-Dieter Entian
- Institute of Molecular Biosciences, Goethe University, 60438 Frankfurt am Main, Germany
| | - Denis L J Lafontaine
- RNA Molecular Biology, F.R.S./FNRS, Université Libre de Bruxelles, B-6041 Charleroi-Gosselies, Belgium Center for Microscopy and Molecular Imaging, B-6041 Charleroi-Gosselies, Belgium
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272
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Abstract
![]()
Long
known for their role in histone acetylation, recent studies
have demonstrated that lysine acetyltransferases also carry out distinct
“orphan” functions. These activities impact a wide range
of biological phenomena including metabolism, RNA modification, nuclear
morphology, and mitochondrial function. Here, we review the discovery
and characterization of orphan lysine acetyltransferase functions.
In addition to highlighting the evidence and biological role for these
functions in human disease, we discuss the part emerging chemical
tools may play in investigating this versatile enzyme superfamily.
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Affiliation(s)
- David C. Montgomery
- National Cancer Institute, Chemical Biology Laboratory, Frederick, Maryland 21702-1201, United States
| | - Alexander W. Sorum
- National Cancer Institute, Chemical Biology Laboratory, Frederick, Maryland 21702-1201, United States
| | - Jordan L. Meier
- National Cancer Institute, Chemical Biology Laboratory, Frederick, Maryland 21702-1201, United States
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273
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Nuclear lamina remodelling and its implications for human disease. Cell Tissue Res 2014; 360:621-31. [DOI: 10.1007/s00441-014-2069-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 11/11/2014] [Indexed: 10/24/2022]
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274
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Ito S, Horikawa S, Suzuki T, Kawauchi H, Tanaka Y, Suzuki T, Suzuki T. Human NAT10 is an ATP-dependent RNA acetyltransferase responsible for N4-acetylcytidine formation in 18 S ribosomal RNA (rRNA). J Biol Chem 2014; 289:35724-30. [PMID: 25411247 DOI: 10.1074/jbc.c114.602698] [Citation(s) in RCA: 188] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Human N-acetyltransferase 10 (NAT10) is known to be a lysine acetyltransferase that targets microtubules and histones and plays an important role in cell division. NAT10 is highly expressed in malignant tumors, and is also a promising target for therapies against laminopathies and premature aging. Here we report that NAT10 is an ATP-dependent RNA acetyltransferase responsible for formation of N(4)-acetylcytidine (ac(4)C) at position 1842 in the terminal helix of mammalian 18 S rRNA. RNAi-mediated knockdown of NAT10 resulted in growth retardation of human cells, and this was accompanied by high-level accumulation of the 30 S precursor of 18 S rRNA, suggesting that ac(4)C1842 formation catalyzed by NAT10 is involved in rRNA processing and ribosome biogenesis.
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Affiliation(s)
- Satoshi Ito
- From the Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656 and
| | - Sayuri Horikawa
- From the Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656 and
| | | | | | - Yoshikazu Tanaka
- the Graduate School of Life Science and Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Takeo Suzuki
- From the Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656 and
| | - Tsutomu Suzuki
- From the Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656 and
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275
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Taoka M, Ishikawa D, Nobe Y, Ishikawa H, Yamauchi Y, Terukina G, Nakayama H, Hirota K, Takahashi N, Isobe T. RNA cytidine acetyltransferase of small-subunit ribosomal RNA: identification of acetylation sites and the responsible acetyltransferase in fission yeast, Schizosaccharomyces pombe. PLoS One 2014; 9:e112156. [PMID: 25402480 PMCID: PMC4234376 DOI: 10.1371/journal.pone.0112156] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 10/13/2014] [Indexed: 12/28/2022] Open
Abstract
The eukaryotic small-subunit (SSU) ribosomal RNA (rRNA) has two evolutionarily conserved acetylcytidines. However, the acetylation sites and the acetyltransferase responsible for the acetylation have not been identified. We performed a comprehensive MS-based analysis covering the entire sequence of the fission yeast, Schizosaccharomyces pombe, SSU rRNA and identified two acetylcytidines at positions 1297 and 1815 in the 3′ half of the rRNA. To identify the enzyme responsible for the cytidine acetylation, we searched for an S. pombe gene homologous to TmcA, a bacterial tRNA N-acetyltransferase, and found one potential candidate, Nat10. A temperature-sensitive strain of Nat10 with a mutation in the Walker A type ATP-binding motif abolished the cytidine acetylation in SSU rRNA, and the wild-type Nat10 supplemented to this strain recovered the acetylation, providing evidence that Nat10 is necessary for acetylation of SSU rRNA. The Nat10 mutant strain showed a slow-growth phenotype and was defective in forming the SSU rRNA from the precursor RNA, suggesting that cytidine acetylation is necessary for ribosome assembly.
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Affiliation(s)
- Masato Taoka
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo, Japan
- * E-mail: (MT); (TI)
| | - Daisuke Ishikawa
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
| | - Yuko Nobe
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo, Japan
| | - Hideaki Ishikawa
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo, Japan
- Department of Biotechnology, United Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Yoshio Yamauchi
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo, Japan
| | - Goro Terukina
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo, Japan
| | - Hiroshi Nakayama
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo, Japan
- Biomolecular Characterization Team, RIKEN Advanced Science Institute, Saitama, Japan
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
| | - Nobuhiro Takahashi
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo, Japan
- Department of Biotechnology, United Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Toshiaki Isobe
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo, Japan
- * E-mail: (MT); (TI)
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276
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Rodriguez R, Miller KM. Unravelling the genomic targets of small molecules using high-throughput sequencing. Nat Rev Genet 2014; 15:783-96. [PMID: 25311424 DOI: 10.1038/nrg3796] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Small molecules--including various approved and novel cancer therapeutics--can operate at the genomic level by targeting the DNA and protein components of chromatin. Emerging evidence suggests that functional interactions between small molecules and the genome are non-stochastic and are influenced by a dynamic interplay between DNA sequences and chromatin states. The establishment of genome-wide maps of small-molecule targets using unbiased methodologies can help to characterize and exploit drug responses. In this Review, we discuss how high-throughput sequencing strategies, such as ChIP-seq (chromatin immunoprecipitation followed by sequencing) and Chem-seq (chemical affinity capture and massively parallel DNA sequencing), are enabling the comprehensive identification of small-molecule target sites throughout the genome, thereby providing insights into unanticipated drug effects.
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Affiliation(s)
- Raphaël Rodriguez
- 1] Centre de Recherche de Gif, Institut de Chimie des Substances Naturelles du CNRS, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France. [2] Institut Curie Research Center, Organic Synthesis and Cell Biology Group, 26 rue d'Ulm, 75248, Paris Cedex 05, France. [3]
| | - Kyle M Miller
- 1] Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, 2506 Speedway Stop A5000, Austin, Texas 78712, USA. [2]
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277
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Abstract
Mutations in genes encoding nuclear envelope proteins cause a wide range of inherited diseases, many of which are neurological. We review the genetic causes and what little is known about pathogenesis of these nuclear envelopathies that primarily affect striated muscle, peripheral nerve and the central nervous system. We conclude by providing examples of experimental therapeutic approaches to these rare but important neuromuscular diseases.
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Affiliation(s)
- Howard J. Worman
- />Department of Medicine and Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY 10032 USA
| | - William T. Dauer
- />Department of Neurology and Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109 USA
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278
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Mazouzi A, Velimezi G, Loizou JI. DNA replication stress: causes, resolution and disease. Exp Cell Res 2014; 329:85-93. [PMID: 25281304 DOI: 10.1016/j.yexcr.2014.09.030] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 09/20/2014] [Accepted: 09/22/2014] [Indexed: 12/17/2022]
Abstract
DNA replication is a fundamental process of the cell that ensures accurate duplication of the genetic information and subsequent transfer to daughter cells. Various pertubations, originating from endogenous or exogenous sources, can interfere with proper progression and completion of the replication process, thus threatening genome integrity. Coordinated regulation of replication and the DNA damage response is therefore fundamental to counteract these challenges and ensure accurate synthesis of the genetic material under conditions of replication stress. In this review, we summarize the main sources of replication stress and the DNA damage signaling pathways that are activated in order to preserve genome integrity during DNA replication. We also discuss the association of replication stress and DNA damage in human disease and future perspectives in the field.
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Affiliation(s)
- Abdelghani Mazouzi
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Georgia Velimezi
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Joanna I Loizou
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria.
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279
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DeBoer J, Jagadish T, Haverland NA, Madson CJ, Ciborowski P, Belshan M. Alterations in the nuclear proteome of HIV-1 infected T-cells. Virology 2014; 468-470:409-420. [PMID: 25240327 DOI: 10.1016/j.virol.2014.08.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 08/19/2014] [Accepted: 08/27/2014] [Indexed: 01/17/2023]
Abstract
Virus infection of a cell involves the appropriation of host factors and the innate defensive response of the cell. The identification of proteins critical for virus replication may lead to the development of novel, cell-based inhibitors. In this study we mapped the changes in T-cell nuclei during human immunodeficiency virus type 1 (HIV-1) at 20 hpi. Using a stringent data threshold, a total of 13 and 38 unique proteins were identified in infected and uninfected cells, respectively, across all biological replicates. An additional 15 proteins were found to be differentially regulated between infected and control nuclei. STRING analysis identified four clusters of protein-protein interactions in the data set related to nuclear architecture, RNA regulation, cell division, and cell homeostasis. Immunoblot analysis confirmed the differential expression of several proteins in both C8166-45 and Jurkat E6-1 T-cells. These data provide a map of the response in host cell nuclei upon HIV-1 infection.
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Affiliation(s)
- Jason DeBoer
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA
| | - Teena Jagadish
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Nicole A Haverland
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Christian J Madson
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA
| | - Pawel Ciborowski
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA; The Nebraska Center for Virology, University of Nebraska, Lincoln 68583, USA
| | - Michael Belshan
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA; The Nebraska Center for Virology, University of Nebraska, Lincoln 68583, USA.
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280
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Larrieu D, Rodriguez R, Britton S. [Chemical inhibition of NAT10 corrects defects of laminopathic cells]. Med Sci (Paris) 2014; 30:745-7. [PMID: 25174749 DOI: 10.1051/medsci/20143008010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Delphine Larrieu
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, CB2 1QN Cambridge, Royaume-Uni
| | - Raphaël Rodriguez
- Institut de chimie des substances naturelles, CNRS, Gif-sur-Yvette, France
| | - Sébastien Britton
- Institut de pharmacologie et de biologie structurale, CNRS, Université de Toulouse-Université Paul Sabatier, équipe labellisée Ligue contre le cancer, 31077 Toulouse, France
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281
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Ito S, Akamatsu Y, Noma A, Kimura S, Miyauchi K, Ikeuchi Y, Suzuki T, Suzuki T. A single acetylation of 18 S rRNA is essential for biogenesis of the small ribosomal subunit in Saccharomyces cerevisiae. J Biol Chem 2014; 289:26201-26212. [PMID: 25086048 DOI: 10.1074/jbc.m114.593996] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Biogenesis of eukaryotic ribosome is a complex event involving a number of non-ribosomal factors. During assembly of the ribosome, rRNAs are post-transcriptionally modified by 2'-O-methylation, pseudouridylation, and several base-specific modifications, which are collectively involved in fine-tuning translational fidelity and/or modulating ribosome assembly. By mass-spectrometric analysis, we demonstrated that N(4)-acetylcytidine (ac(4)C) is present at position 1773 in the 18 S rRNA of Saccharomyces cerevisiae. In addition, we found an essential gene, KRE33 (human homolog, NAT10), that we renamed RRA1 (ribosomal RNA cytidine acetyltransferase 1) encoding an RNA acetyltransferase responsible for ac(4)C1773 formation. Using recombinant Rra1p, we could successfully reconstitute ac(4)C1773 in a model rRNA fragment in the presence of both acetyl-CoA and ATP as substrates. Upon depletion of Rra1p, the 23 S precursor of 18 S rRNA was accumulated significantly, which resulted in complete loss of 18 S rRNA and small ribosomal subunit (40 S), suggesting that ac(4)C1773 formation catalyzed by Rra1p plays a critical role in processing of the 23 S precursor to yield 18 S rRNA. When nuclear acetyl-CoA was depleted by inactivation of acetyl-CoA synthetase 2 (ACS2), we observed temporal accumulation of the 23 S precursor, indicating that Rra1p modulates biogenesis of 40 S subunit by sensing nuclear acetyl-CoA concentration.
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Affiliation(s)
- Satoshi Ito
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yu Akamatsu
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Akiko Noma
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Satoshi Kimura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kenjyo Miyauchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yoshiho Ikeuchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Takeo Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
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Montgomery DC, Sorum AW, Meier JL. Chemoproteomic profiling of lysine acetyltransferases highlights an expanded landscape of catalytic acetylation. J Am Chem Soc 2014; 136:8669-76. [PMID: 24836640 PMCID: PMC4227742 DOI: 10.1021/ja502372j] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
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Lysine acetyltransferases (KATs)
play a critical role in the regulation
of gene expression, metabolism, and other key cellular functions.
One shortcoming of traditional KAT assays is their inability to study
KAT activity in complex settings, a limitation that hinders efforts
at KAT discovery, characterization, and inhibitor development. To
address this challenge, here we describe a suite of cofactor-based
affinity probes capable of profiling KAT activity in biological contexts.
Conversion of KAT bisubstrate inhibitors to clickable photoaffinity
probes enables the selective covalent labeling of three phylogenetically
distinct families of KAT enzymes. Cofactor-based affinity probes report
on KAT activity in cell lysates, where KATs exist as multiprotein
complexes. Chemical affinity purification and unbiased LC–MS/MS
profiling highlights an expanded landscape of orphan lysine acetyltransferases
present in the human genome and provides insight into the global selectivity
and sensitivity of CoA-based proteomic probes that will guide future
applications. Chemoproteomic profiling provides a powerful method
to study the molecular interactions of KATs in native contexts and
will aid investigations into the role of KATs in cell state and disease.
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Affiliation(s)
- David C Montgomery
- Chemical Biology Laboratory, National Cancer Institute , Frederick, Maryland 21702, United States
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