N-Acetylation of Arginine-Rich Hepatoma Histones1

Total Page:16

File Type:pdf, Size:1020Kb

N-Acetylation of Arginine-Rich Hepatoma Histones1 [CANCER RESEARCH 31, 468-470, April 1971] N-Acetylation of Arginine-rich Hepatoma Histones1 Paul Byvoetand Harold P. Morris Cellular and Molecular Biology, Division of Biological Sciences, University of Florida, Gainesville, Florida ¡P.B.¡,and Department of Biochemistry, Howard University College of Medicine. Washington, D. C. 20001 ¡H.P.M./ SUMMARY represents a fraction of the total number of sites available for acetylation (2). Previous work in this laboratory has shown that decay rates On the other hand, Starbuck et al. (11) have purified of histones and DNA isolated from deoxyribonucleoprotein of histone fractions which were either 100% acetylated at the normal and neoplastic rat tissues were approximately equal, NH2-terminal end or not at all. In addition, when isolated indicating that not only DNA but the nucleohistone complex nuclei were incubated in the presence of radioactive acetate, as a whole is metabolically inert. In contrast, the vV-acetyl incorporation of label appeared to occur primarily in groups in the combined arginine and slightly lysine-rich e-jV-acetyllysine of histones (6, 12). Thus far, all evidence histones from these same tissues were found to turn over at would therefore lead to the conclusion that the e-jV-acetyl much faster rates than whole histones or DNA, with exception groups on the internal lysine residues are metabolically active, of the Novikoff hepatoma, in which this turnover was wheras the a-jV-acetyl groups at the NH2-terminal ends are remarkably slow, approaching that of the histones. Studies stable features of certain histone fractions, similar to those of were therefore carried out on a number of hepatomas with some other proteins, such as carbonic anhydrase (3). The varying growth rates, which indicated that the half-lives of previously mentioned in vitro experiments with isolated nuclei their histone W-acetyl groups were in general an order of also revealed that the incorporation of labeled acetate was magnitude smaller than that of the whole histones and similar most active in the f2al and ß fractions and was practically to that of most tissues studied thus far. The data derived from negligible in the lysine-rich histones (12). These data indicate very-slow-growing tumors would seem to indicate that the that the acetylation of internal lysine residues is not random histone jV-acetyl groups from hepatocyte histones exhibit a and definitely rule out the possibility of a spontaneous or rapid turnover similar to that in other tissues. artifactual process. In our previous studies, rats were given injections of alanine-14C to label the histones and tritiated acetate to label INTRODUCTION the histone TV-acetyl groups. At various time points after the injection, groups of animals were killed, and lysine-rich and It has been suggested that chemical modifications of arginine-rich (combined arginine- and slightly lysine-rich) histones introduce structural changes in the otherwise inert histone fractions isolated from various tissues and their deoxyribonucleoprotein complex which may influence the specific activities with respect to 14C and jV-acetyl-3H were flow of information from the DNA. One of these reactions determined (2). concerns the acetylation of amino groups present in the As shown in Table 1, the results of these studies indicated histone molecule. Evidence indicating the presence of 1 acetyl that uptake of acetate into ,/V-acetyl groups from lysine-rich group or less per molecule of histone and the finding that the histones was much less than that into the arginine-rich NH2-terminal amino groups of a number of more or less crude histones, which is to be expected in view of the absence of histone fractions were masked to varying degrees when e-./V-acetylgroups in the former (12). exposed to fluorodinitrobenzene, according to the method of The fact that some uptake of label occurs in the lysine-rich Sanger (9), lead to the general assumption that histones were histones is presumably due to incorporation of acetate in the acetylated only NH2-terminally. Gershey et al. (6) have a-yV-acetyl position of NH2-terminal residues. Phillips (9) has recently reported, however, that histones also contain established that the lysine-rich histone fraction is completely e-amino-acetyllysine. Experiments carried out in this acetylated at the NH2-terminal end. It is therefore not laboratory have shown that the W-acetyl groups in histones surprising that the specific activity of lysine-rich histones with turn over much faster than the histones themselves, and it respect to radioactive acetate decayed at a rate which seems therefore conceivable that the amount of ./V-acetyl approached that of the histones themselves. Accurate groups found in a pure histone species at any given time measurements of this turnover were, however, often hampered by the exceedingly low level of labeling (2). 'This research was supported in part by Grant CA-10472 to the As was already indicated, the turnover rate of Af-acetyl University of Florida, Grant CA-10729 to Howard University from the groups in the arginine-rich (combined slightly lysine-rich and National Cancer Institute, Grant P-439 from the American Cancer arginine-rich) histone fraction was found to be much faster Society, and a grant from the Florida Division of the American Cancer Society. than that of the histones (2). In view of the preceding Received May 25, 1970; accepted December 14, 1970. discussion, it seems that this rapid turnover must be attributed 468 CANCER RESEARCH VOL. 31 Downloaded from cancerres.aacrjournals.org on September 24, 2021. © 1971 American Association for Cancer Research. N-Acetylation of Arginine-ríchHepatoma Misiones Table 1 feature of hepatomas in general, as the half-lives of histone Incorporation of acetate-3 H into N-acetyl groups of histories ./V-acetyl groups in all tumors studied appeared to be an order Specific activity due to /V-acety! (acetate-3 H) of magnitude smaller than those of the whole histones and similar to that of most tissues studied thus far (2). Tissue (cpm/mg histone) Because the liver consists of a variety of cell types (4, 5), histones"665a histones75 the half-life found for histones or DNA will differ depending on the time period during which measurement takes place. In Liver ±161 ±5.5 the "short-term" studies outlined above, the 1st group of Novikoff hepatoma"Arginine-rich71 ±11Lysine-rich 34 ±4.5 animals was killed 24 hr after injection of the radioactive "Averages of 3 experimental values ±S.E.at peak activity 1 hr after amino acid. Such experiments will yield an experimental administration of radioactive acetate. half-life for DNA or histones of 100 to 200 hr. If, however, animals are killed at weekly intervals, after an incubation to the internal e-jV-acetyl groups and that the a-TV-acetyl period of 3 weeks following the administration of the tracers, groups on the NH2 -terminal residues turn over at the same rate much longer half-lives will be found, since during the long as the histones themselves. incubation period the DNA and histones of faster-turning-over The 2 arginine-rich histone fractions that are acetylated cell populations have lost their radioactivity. For ensurance of most actively incorporate radioactive acetate into the internal a reasonable uptake of radioactive precursors into DNA and e-/V-acetyl positions at approximately similar rates. Thus far, histones of hepatocytes, the animals used in such long-term no conditions have been reported that caused a differential experiments were 3 weeks old at the time of injection. The effect on the respective turnover rates. The near absence of decay of the radioactively labeled DNA and histones was turnover of TV-acetyl groups in Novikoff hepatoma histones therefore due only to dilution with newly synthesized encountered in our studies (2) would seem to indicate that in unlabeled material, since in this case no death or migration of this case both fractions were affected to the same extent. It cells occurs. The half-life obtained in such studies (Table 3) was this unexpected finding that prompted us to survey a agreed very well with the growth rate of the liver in rats of number of hepatoma lines with different growth rates to see that age (1), although it may be expected to become much longer when the animals reach adulthood.2 whether this slow turnover might be a general property of hepatomas. Because the liver cell population is varied, it was thus far In view of the similarity of jV-acetylation patterns of the not possible to decide which cell population is responsible for f2al and f3 fractions, the feasibility of the study, and the the rapid turnover of ./V-acetyl groups in liver. The present absence of e-TV-acetyl groups in lysine-rich histones, it was results indicate that the turnover of histone jV-acetyl groups in decided to carry out all experiments on the "arginine-rich" hepatomas with very slow growth rates R! and R7 appeared to histones without further fractionation. be very similar to that of normal liver. Since it can be assumed that these tumors consist of pure clones of "minimally" malignant hepatocytes, the rapid turnover of jV-acetyl groups MATERIALS AND METHODS in liver histones shown in Table 3 can in all probability be assigned to the hepatocytes, although it seems reasonable to The present studies were carried out as described previously assume that the histone W-acetyl groups in littoral cells of (1,2). Rats were given i.p. injections of 100 AiCi/kg normal liver turn over rapidly as well. This instance points out L-alanine-14C (uniformly labeled) to label the histones and 2 the experimental advantage of these slow-growing tumors, mCi/kg sodium acetate-3 H to label the histone TV-acetyl which consist of uniform populations of cells, very similar to groups.
Recommended publications
  • Evidence for Lysine Acetylation in the Coat Protein of a Polerovirus
    Journal of General Virology (2014), 95, 2321–2327 DOI 10.1099/vir.0.066514-0 Short Evidence for lysine acetylation in the coat protein of Communication a polerovirus Michelle Cilia,1,2,3 Richard Johnson,4 Michelle Sweeney,3 Stacy L. DeBlasio,1,3 James E. Bruce,4 Michael J. MacCoss4 and Stewart M. Gray1,2 Correspondence 1USDA-Agricultural Research Service, Ithaca, NY 14853, USA Michelle Cilia 2Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, [email protected] NY 14853, USA 3Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA 4Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA Virions of the RPV strain of Cereal yellow dwarf virus-RPV were purified from infected oat tissue and analysed by MS. Two conserved residues, K147 and K181, in the virus coat protein, were confidently identified to contain epsilon-N-acetyl groups. While no functional data are available for K147, K181 lies within an interfacial region critical for virion assembly and stability. The signature immonium ion at m/z 126.0919 demonstrated the presence of N-acetyllysine, and the sequence fragment ions enabled an unambiguous assignment of the epsilon-N-acetyl modification on K181. Received 4 April 2014 We hypothesize that selection favours acetylation of K181 in a fraction of coat protein monomers Accepted 13 June 2014 to stabilize the capsid by promoting intermonomer salt bridge formation. Potato leafroll virus (PLRV) and the barley/cereal/maize encapsidation of one species’ RNA in the virion of another yellow dwarf viruses, members of the Luteoviridae and species. Such manipulation can result in an expansion of referred to hereafter as luteovirids, are globally important potential aphid species that can transmit the virus.
    [Show full text]
  • N-Acetylation of Arginine-Rich Hepatoma Histones1
    [CANCER RESEARCH 31, 468-470, April 1971] N-Acetylation of Arginine-rich Hepatoma Histones1 Paul Byvoetand Harold P. Morris Cellular and Molecular Biology, Division of Biological Sciences, University of Florida, Gainesville, Florida ¡P.B.¡,and Department of Biochemistry, Howard University College of Medicine. Washington, D. C. 20001 ¡H.P.M./ SUMMARY represents a fraction of the total number of sites available for acetylation (2). Previous work in this laboratory has shown that decay rates On the other hand, Starbuck et al. (11) have purified of histones and DNA isolated from deoxyribonucleoprotein of histone fractions which were either 100% acetylated at the normal and neoplastic rat tissues were approximately equal, NH2-terminal end or not at all. In addition, when isolated indicating that not only DNA but the nucleohistone complex nuclei were incubated in the presence of radioactive acetate, as a whole is metabolically inert. In contrast, the vV-acetyl incorporation of label appeared to occur primarily in groups in the combined arginine and slightly lysine-rich e-jV-acetyllysine of histones (6, 12). Thus far, all evidence histones from these same tissues were found to turn over at would therefore lead to the conclusion that the e-jV-acetyl much faster rates than whole histones or DNA, with exception groups on the internal lysine residues are metabolically active, of the Novikoff hepatoma, in which this turnover was wheras the a-jV-acetyl groups at the NH2-terminal ends are remarkably slow, approaching that of the histones. Studies stable features of certain histone fractions, similar to those of were therefore carried out on a number of hepatomas with some other proteins, such as carbonic anhydrase (3).
    [Show full text]
  • Global Lysine Acetylome Analysis of LPS-Stimulated Hepg2 Cells Identified Hyperacetylation of PKM2 As a Metabolic Regulator in Sepsis
    International Journal of Molecular Sciences Article Global Lysine Acetylome Analysis of LPS-Stimulated HepG2 Cells Identified Hyperacetylation of PKM2 as a Metabolic Regulator in Sepsis Ann-Yae Na 1, Sanjita Paudel 1, Soyoung Choi 1, Jun Hyung Lee 2, Min-Sik Kim 2, Jong-Sup Bae 1 and Sangkyu Lee 1,* 1 BK21 FOUR Community-Based Intelligent Novel Drug Discovery Education Unit, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 41566, Korea; [email protected] (A.-Y.N.); [email protected] (S.P.); [email protected] (S.C.); [email protected] (J.-S.B.) 2 Department of New Biology, Daegu Gyeongbuk Institute of Science & Technology, Daegu 42988, Korea; [email protected] (J.H.L.); [email protected] (M.-S.K.) * Correspondence: [email protected]; Tel.: +82-53-950-8571; Fax: +82-53-950-8557 Abstract: Sepsis-induced liver dysfunction (SILD) is a common event and is strongly associated with mortality. Establishing a causative link between protein post-translational modification and diseases is challenging. We studied the relationship among lysine acetylation (Kac), sirtuin (SIRTs), and the factors involved in SILD, which was induced in LPS-stimulated HepG2 cells. Protein hyperacetylation was observed according to SIRTs reduction after LPS treatment for 24 h. We identified 1449 Kac sites based on comparative acetylome analysis and quantified 1086 Kac sites on 410 proteins for Citation: Na, A.-Y.; Paudel, S.; Choi, S.; Lee, J.H.; Kim, M.-S.; Bae, J.-S.; Lee, acetylation. Interestingly, the upregulated Kac proteins are enriched in glycolysis/gluconeogenesis S. Global Lysine Acetylome Analysis pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG) category.
    [Show full text]
  • Engineering an Acetyllysine Reader with Photocrosslinking Amino Acid for Interactome Profiling
    Electronic Supplementary Material (ESI) for ChemComm. This journal is © The Royal Society of Chemistry 2021 Engineering an acetyllysine reader with photocrosslinking amino acid for interactome profiling Anirban Roy,a Soumen Barman,a Jyotirmayee Padhan and Babu Sudhamalla* Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India 741246 aEqual contribution Table of Contents 1. General materials, methods and equipment S2 2. Protein-peptide docking studies S2 3. Molecular modeling and molecular dynamics (MD) simulations S3 4. Mutagenesis, expression and purification of ATAD2B bromodomain S4 5. Fluorescence polarization (FP) assay S5 6. Isothermal titration calorimetry (ITC) S5 7. Circular dichroism spectroscopy S6 8. Thermal shift assay S6 9. Photo-crosslinking experiment with histone peptides and in-gel fluorescence S6 10. Mammalian cell culture S7 11. Acid extraction of histones S7 12. Photocrosslinking with hyperacetylated histone H4 and Western blotting S8 13. Preparation of HeLa cell lysate S8 14. Photocrosslinking with HeLa cell lysate and Western blotting S9 15. Supplementary figures and tables S10 16. References S24 S1 1. General materials, methods and equipment All the plasmids for bacterial expression are obtained as gifts from individual laboratories or purchased from addgene. Details of these constructs are given in sections below. Mutagenic primers are obtained from Sigma-Aldrich (Table S1). Commercially available competent bacterial cells were used for protein expression and mutagenesis. HeLa cells, obtained from the American Type Culture Collection (ATCC) and used in the current study following manufacturer’s protocol. All the antibodies used in the current study are purchased from established vendors and used following manufacturer’s protocol.
    [Show full text]
  • Synthesized Histones H3 and H4 (Chromatin/Nucleosome Assembly/Deblocking and Microsequencing) RICHARD E
    Proc. Natl. Acad. Sci. USA Vol. 92, pp. 1237-1241, February 1995 Cell Biology Conservation of deposition-related acetylation sites in newly synthesized histones H3 and H4 (chromatin/nucleosome assembly/deblocking and microsequencing) RICHARD E. SOBEL*, RICHARD G. COOKt, CAROLYN A. PERRY*, ANTHONY T. ANNUNZIATOt, AND C. DAVID ALLIS*§ *Department of Biology, Syracuse University, Syracuse, NY 13244; tDepartment of Microbiology and Immunology, Baylor College of Medicine, Houston, TX 77030; and *Department of Biology, Boston College, Chestnut Hill, MA 02167 Communicated by Salih J. Wakil, Baylor College of Medicine, Houston, 7X, October 12, 1994 ABSTRACT Newly synthesized histone H4 is deposited in deposited into macronuclei (4). By stain and by label, histone a diacetylated isoform in a wide variety of organisms. In extracted from these micronuclei is greatly enriched in di- Tetrahymena a specific pair of residues, lysines 4 and 11, have acetylated H4 and mono- and diacetylated forms of H3. been shown to undergo this modification in vivo. In this report, Because micronuclei are transcriptionally inactive, acetylation we demonstrate that the analogous residues, lysines 5 and 12, of newly synthesized H3 and H4 in micronuclei is clearly are acetylated in Drosophila and HeLa 114. These data strongly distinct from transcription-related acetylation in this system. suggest that deposition-related acetylation sites in H4 have Despite evidence suggesting a conserved pattern of depo- been highly, perhaps absolutely, conserved. In Tetrahymena sition-related H4 diacetylation, very few studies have at- and Drosophila newly synthesized histone H3 is also deposited tempted to ascertain the sites of diacetylation in newly syn- in several modified forms.
    [Show full text]
  • Measurement of Acetylation Turnover at Distinct Lysines in Human Histones Identifies Long-Lived Acetylation Sites
    ARTICLE Received 5 Feb 2013 | Accepted 26 Jun 2013 | Published 29 Jul 2013 DOI: 10.1038/ncomms3203 Measurement of acetylation turnover at distinct lysines in human histones identifies long-lived acetylation sites Yupeng Zheng1, Paul M. Thomas1 & Neil L. Kelleher1,2,3 Histone acetylation has long been determined as a highly dynamic modification associated with open chromatin and transcriptional activation. Here we develop a metabolic labelling scheme using stable isotopes to study the kinetics of acetylation turnover at 19 distinct lysines on histones H3, H4 and H2A. Using human HeLa S3 cells, the analysis reveals 12 sites of histone acetylation with fast turnover and 7 sites stable over a 30 h experiment. The sites showing fast turnover (anticipated from classical radioactive measurements of whole histones) have half-lives between B1–2 h. To support this finding, we use a broad-spectrum deacetylase inhibitor to verify that only fast turnover sites display 2–10-fold increases in acetylation whereas long-lived sites clearly do not. Most of these stable sites lack extensive functional studies or localization within global chromatin, and their role in non-genetic mechanisms of inheritance is as yet unknown. 1 Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA. 2 Division of Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA. 3 Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA. Correspondence and requests for materials should be addressed to N.L.K. (email: [email protected]). NATURE COMMUNICATIONS | 4:2203 | DOI: 10.1038/ncomms3203 | www.nature.com/naturecommunications 1 & 2013 Macmillan Publishers Limited.
    [Show full text]
  • Epigenetic Reader Domain
    Epigenetic Reader Domain Epigenetic regulators of gene expression and chromatin state include so-called writers, erasers, and readers of chromatin modifications.Well-characterized examples of reader domains include bromodomains typically binding acetyllysine and chromatin organization modifier (chromo), malignant brain tumor (MBT), plant homeodomain (PHD), and Tudor domains generally associating with methyllysine. Research on epigenetic readers has been tremendously influenced by the discovery of selective inhibitors targeting the bromodomain and extraterminal motif (BET) family of acetyl-lysine readers. The human genome encodes 46 proteins containing 61 bromodomains clustered into eight families. Distinct experimental approaches are used to identify the first BET inhibitors, GSK 525762A and (+)-JQ-1. The Polycomb group (PcG) protein, enhancer of zeste homologue 2 (EZH2), has an essential role in promoting histone H3 lysine 27 trimethylation (H3K27me3) and epigenetic gene silencing. This function of EZH2 is important for cell proliferation and inhibition of cell differentiation, and is implicated in cancer progression. Cyclin-dependent kinases regulate epigenetic gene silencing through phosphorylation of EZH2. In many types of cancers including lymphomas and leukemia, EZH2 is postulated to exert its oncogenic effects via aberrant histone and DNA methylation, causing silencing of tumor suppressor genes. p300/CBP is not only a transcriptional adaptor but also a histone acetyltransferase. www.MedChemExpress.com 1 Epigenetic Reader Domain Inhibitors & Modulators (+)-JQ-1 (+)-JQ-1-aldehyde (JQ1) Cat. No.: HY-13030 Cat. No.: HY-131633A (+)-JQ-1 (JQ1) is a potent, specific, and (+)-JQ-1-aldehyde is the aldehyde form of (+)-JQ1. reversible BET bromodomain inhibitor, with (+)-JQ-1-aldehyde can be uesd as a precursor to IC50s of 77 and 33 nM for the first and second synthesize PROTACs, which targets BET bromodomain (BRD4(1/2)).
    [Show full text]
  • Download.Php) 936
    bioRxiv preprint doi: https://doi.org/10.1101/2020.09.21.306696; this version posted September 21, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. bioRxiv preprint doi: https://doi.org/10.1101/2020.09.21.306696; this version posted September 21, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 A common binding motif in the ET domain of BRD3 forms polymorphic structural 2 interfaces with host and viral proteins 3 4 Sriram Aiyer1,2,#,¶, G.V.T. Swapna1,2,¶, Li-Chung Ma1,2 , Gaohua Liu2, ‡, Jingzhou Hao2,3, 5 Gordon Chalmers3, Brian C. Jacobs1, Gaetano T. Montelione2,3,*, Monica J. Roth1,2,* 6 7 1Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State 8 University of New Jersey, 675 Hoes Lane, Piscataway, NJ, 08854 USA, 2Department of 9 Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The 10 State University of New Jersey, 675 Hoes Lane, Piscataway, NJ, 08854 USA. 3Department of 11 Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, 12 Rensselaer Polytechnic Institute, Troy, NY, 12180 USA 13 14 #Present address: Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La 15 Jolla, CA, 92037, USA. 16 ‡Present address: Nexomics Bioscience, Inc. 5 Crescent Ave, Rocky Hill, NJ 08553 17 COI Statement. GL is an officer of Nexomics Biosciences, Inc. GTM is a founder of Nexomics 18 Biosciences, Inc.
    [Show full text]
  • Quantitative Analysis of Histone Modifications: Formaldehyde Is a Source of Pathological N6- Formyllysine That Is Refractory to Histone Deacetylases
    Quantitative Analysis of Histone Modifications: Formaldehyde Is a Source of Pathological N6- Formyllysine That Is Refractory to Histone Deacetylases The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Edrissi, Bahar, Koli Taghizadeh, and Peter C. Dedon. “Quantitative Analysis of Histone Modifications: Formaldehyde Is a Source of Pathological N6-Formyllysine That Is Refractory to Histone Deacetylases.” Ed. James Swenberg. PLoS Genetics 9.2 (2013): e1003328. As Published http://dx.doi.org/10.1371/journal.pgen.1003328 Publisher Public Library of Science Version Final published version Citable link http://hdl.handle.net/1721.1/78350 Terms of Use Creative Commons Attribution Detailed Terms http://creativecommons.org/licenses/by/2.5/ Quantitative Analysis of Histone Modifications: Formaldehyde Is a Source of Pathological N6- Formyllysine That Is Refractory to Histone Deacetylases Bahar Edrissi1, Koli Taghizadeh2, Peter C. Dedon1,2* 1 Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America, 2 Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America Abstract Aberrant protein modifications play an important role in the pathophysiology of many human diseases, in terms of both dysfunction of physiological modifications and the formation of pathological modifications by reaction of proteins with endogenous electrophiles. Recent
    [Show full text]
  • A Chemical Biology Toolbox to Study Protein Methyltransferases and Epigenetic Signaling
    ARTICLE https://doi.org/10.1038/s41467-018-07905-4 OPEN A chemical biology toolbox to study protein methyltransferases and epigenetic signaling Sebastian Scheer 1, Suzanne Ackloo 2, Tiago S. Medina3, Matthieu Schapira 2,4, Fengling Li2, Jennifer A. Ward 5,6, Andrew M. Lewis 5,6, Jeffrey P. Northrop1, Paul L. Richardson 7, H. Ümit Kaniskan 8, Yudao Shen8, Jing Liu 8, David Smil 2, David McLeod 9, Carlos A. Zepeda-Velazquez9, Minkui Luo 10,11, Jian Jin 8, Dalia Barsyte-Lovejoy 2, Kilian V.M. Huber 5,6, Daniel D. De Carvalho3,12, Masoud Vedadi2,4, Colby Zaph 1, Peter J. Brown 2 & Cheryl H. Arrowsmith2,3,12 1234567890():,; Protein methyltransferases (PMTs) comprise a major class of epigenetic regulatory enzymes with therapeutic relevance. Here we present a collection of chemical probes and associated reagents and data to elucidate the function of human and murine PMTs in cellular studies. Our collection provides inhibitors and antagonists that together modulate most of the key regulatory methylation marks on histones H3 and H4, providing an important resource for modulating cellular epigenomes. We describe a comprehensive and comparative character- ization of the probe collection with respect to their potency, selectivity, and mode of inhi- bition. We demonstrate the utility of this collection in CD4+ T cell differentiation assays revealing the potential of individual probes to alter multiple T cell subpopulations which may have implications for T cell-mediated processes such as inflammation and immuno-oncology. In particular, we demonstrate a role for DOT1L in limiting Th1 cell differentiation and main- taining lineage integrity.
    [Show full text]
  • The Role of Dietary Histone Deacetylases (Hdacs) Inhibitors in Health and Disease
    Nutrients 2014, 6, 4273-4301; doi:10.3390/nu6104273 OPEN ACCESS nutrients ISSN 2072-6643 www.mdpi.com/journal/nutrients Review The Role of Dietary Histone Deacetylases (HDACs) Inhibitors in Health and Disease Shalome A. Bassett 1,2,* and Matthew P. G. Barnett 1,2 1 Food Nutrition & Health Team, Food & Bio-based Products Group, AgResearch Limited, Grasslands Research Centre, Tennent Drive, Palmerston North 4442, New Zealand; E-Mail: [email protected] 2 Nutrigenomics New Zealand, Private Bag 92019, Auckland 1142, New Zealand * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +64-6-351-8056; Fax: +64-6-351-8032. Received: 31 July 2014; in revised form: 6 October 2014 / Accepted: 6 October 2014 / Published: 15 October 2014 Abstract: Modification of the histone proteins associated with DNA is an important process in the epigenetic regulation of DNA structure and function. There are several known modifications to histones, including methylation, acetylation, and phosphorylation, and a range of factors influence each of these. Histone deacetylases (HDACs) remove the acetyl group from lysine residues within a range of proteins, including transcription factors and histones. Whilst this means that their influence on cellular processes is more complex and far-reaching than histone modifications alone, their predominant function appears to relate to histones; through deacetylation of lysine residues they can influence expression of genes encoded by DNA linked to the histone molecule. HDAC inhibitors in turn regulate the activity of HDACs, and have been widely used as therapeutics in psychiatry and neurology, in which a number of adverse outcomes are associated with aberrant HDAC function.
    [Show full text]
  • Synthesis and Evaluation of a Stable Isostere of Malonyllysine
    bioRxiv preprint doi: https://doi.org/10.1101/2020.08.23.263285; this version posted August 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Synthesis and Evaluation of a Stable Isostere of Malonyllysine Sarah E. Bergholtz,[a]# Yihang Jing,[a]# Rhushikesh A. Kulkarni,[a]# Thomas T. Zengeya,[a] and Jordan L. Meier*[a] [a]Chemical Biology Laboratory, National Cancer Institute, Frederick MD, 21702, USA.. *Email: [email protected]; These authors contributed equally Abstract: Lysine malonylation is a recently characterized posttranslational modification involved in the regulation of energy metabolism and gene expression. Two unique features of this posttranslational modification are its negative charge and potential susceptibility to decarboxylation, both of which pose possible challenges to its study. As a step towards addressing these challenges, here we report the synthesis and evaluation of a stable isostere of malonyllysine. First, we find that synthetic substitution of the malonyl group with a tetrazole isostere results in amino acids resistant to thermal decarboxylation. Next, we demonstrate that protected variants of this amino acid are readily incorporated into peptides. Finally, we show that tetrazole isosteres of malonyllysine can be recognized by anti-malonyllysine antibodies, validating their ability to mimic features of the endogenous lysine modification. Overall, this study establishes a new chemical strategy for stably mimicking a metabolite-derived posttranslational modification, providing a foothold for tool development and functional analyses. bioRxiv preprint doi: https://doi.org/10.1101/2020.08.23.263285; this version posted August 24, 2020.
    [Show full text]