DOCSLIB.ORG

Epigenetické Procesy Během Reparace DNA

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Epigenetické Procesy Během Reparace DNA PŘÍRODOVĚDECKÁ FAKULTA Epigenetické procesy během reparace DNA Disertační práce ALENA SVOBODOVÁ KOVAŘÍKOVÁ Vedoucí práce: doc. Bártová Eva, RNDr., Ph.D., DSc. ÚSTAV EXPERIMENTÁLNÍ BIOLOGIE BIOFYZIKÁLNÍ ÚSTAV, AKADEMIE VĚD ČESKÉ REPUBLIKY Oddělení molekulární cytologie a cytometrie Brno 2019 Bibliografický záznam Autor: Mgr. Alena Svobodová Kovaříková Přírodovědecká fakulta, Masarykova univerzita Ústav experimentální biologie Název práce: Epigenetické procesy během reparace DNA Studijní program: PřF D-MBBG Molekulární a buněčná biologie a genetika Studijní obor: PřF MBBG Molekulární a buněčná biologie a genetika Vedoucí práce: doc. Bártová Eva, RNDr., Ph.D., DSc. Akademický rok: 2018/2019 Počet stran: 123 Klíčová slova: Oprava DNA; epigenetika; chromatin; histony; metyltransferázy; Suv39h1/h2; H4K20me3; H3K9me3; HP1β; Dnmt1; m6A; 5mC; 5hmC; 5caC; METTL3; METTL14 Bibliographic Entry Author: Mgr. Alena Svobodová Kovaříková Faculty of Science, Masaryk University Department of Experimental Biology Title of Thesis: Epigenetic Processes during DNA repair Degree programme: PřF D-MBBG Molecular and Cell Biology and Genetics Field of Study: PřF MBBG Molecular and Cell Biology and Genetics Supervisor: doc. Bártová Eva, RNDr., Ph.D., DSc. Academic Year: 2018/2019 Number of Pages: 123 Keywords: DNA repair; epigenetics; chromatin; histones; methyltransferases; Suv39h1/h2; H4K20me3; H3K9me3; Dnmt1; HP1β, m6A; 5mC; 5hmC; 5caC; METTL3; METTL14 Abstrakt Schopnost buňky rozpoznat a odstranit chyby v sekvenci DNA je jednou ze základních podmínek přežití každého organizmu. Během evoluce se vyvinuly různě složité a přísně řízené mechanismy opravy DNA, které buňky využívají ve stresových situacích. Narušení některého kroku z těchto fyziologických dějů může vést k rozvoji celé řady onemocnění. Nejen mnohé opravné proteiny, ale i epigenetické značky navázané na histonech, DNA a RNA regulují tyto složité procesy, souhrnně označené jako odpověď na poškození DNA (DDR). Význam epigenetiky pro tuto oblast výzkumu je obrovský, avšak konkrétní funkce epigenetických modifikací nejsou zcela objasněny, protože chromatin podléhá četným úpravám. Tato závěrečná práce přispívá k pochopení změn na úrovni chromatinu, ke kterým dochází při poškození DNA a při následné opravě. První část experimentální práce se věnuje histonovým modifikacím, především H3K9 trimetylaci a H4K20 trimetylaci, a jejich úloze v opravné dráze nehomologního spojování konců, NHEJ. V našich experimentech jsme prokázali vzájemnou interakci těchto histonových značek a stěžejního proteinu 53BP1. Navíc jsme pozorovali inhibiční vliv delece genu pro histonové metyltransferázy Suv39h1/h2 na utváření reparačních ohnisek proteinu 53BP1. Další část předkládané práce je zaměřená na rozdíly v metylaci DNA v souvislosti s disfunkcí enzymů Suv39h1/h2 a při poškození chromatinu. Ukázali jsme, že stres může v zasažené oblasti buněčného jádra vyvolat aktivní demetylaci DNA, doprovázenou tvorbou 5hmC a 5caC. Poslední část experimentální práce se zabývá distribucí vybraných posttranskripčních 6 1 modifikací RNA (m A, m A, m3G/TMG) a jejich přítomností v místě poškození DNA. Zjistili jsme pozitivní korelaci mezi množstvím hypermetylovaného 6-adeninu v RNA a správnou funkcí metyltransferáz Suv39h1/h2 v místech lokálních lézí DNA. Navíc velice rychlá akumulace m6A RNA je během opravy DNA následována redukcí hladiny m3G/TMG v poškozeném chromatinu. Abstract The ability to recognize and eliminate errors in the DNA sequence is one of the basic preconditions for the survival of each organism. In stress situations, cells take advantage of many complex and strictly regulated mechanisms developed during evolution. Malfunction of any step in these physiological processes may lead to a number of diseases. Not just proteins, but also epigenetic markers bound to proteins, DNA, and RNA, regulate these complex processes, collectively called DNA-damage response (DDR). The epigenetic impact on this research topic is huge. However, the impacts of specific epigenetic modifications are not yet clear because chromatin is subject to many modifications. This thesis contributes to our understanding of chromatin modifications appearing after DNA damage and its consequent repair. The first part of my experimental work is focused on histone modifications, especially H3K9 trimethylation and H4K20 trimethylation, and their role in nonhomologous end-joining (NHEJ) repair pathway. In our experiments, we provided evidence for a mutual interaction between these histone marks and the 53BP1 oncoprotein. Furthermore, the influence of the Suv39h1/h2 (major histone H3K9 methyltransferases) depletion on the formation of repair foci consisting of 53BP1 was observed in Suv39h1/h2 knock out cells. The second part of this thesis is focused on the relationship between DNA methylation at cytosine residues and dysfunction of Suv39h1/h2 enzymes. We have shown that stress may cause active DNA demethylation, accompanied by increased levels of 5hmC and 5caC in the cell nucleus. The last part of the experimental work deals with the role of certain posttranscriptional modifications of 6 1 RNA (m A, m A, m3G/TMG) in DNA repair processes. We observed a reduction of m6A (position 6 of a purine cycle of adenine) RNA levels in local DNA lesions in Suv39h1/h2 deficient cells. Finally, we also observed that fast accumulation of m6A RNA during DNA repair processes was followed by depletion of m3G/TMG level in damaged chromatin Poděkování Na tomto místě bych ráda poděkovala své školitelce doc. RNDr. Evě Bártové, Ph.D., DSc. za odborné vedení, cenné připomínky a čas, který mi během mého doktorského studia věnovala. Velice si také cením toho, že mi umožnila pracovat na Biofyzikálním ústavě AVČR, v. v. i., kde jsem získala nové zkušenosti v oblasti buněčné biologie a epigenetiky. Dále bych chtěla poděkovat kolegům z Oddělení molekulární cytologie a cytometrie, zejména Mgr. Denise Komůrkové, Ph.D., Mgr. Lence Stixové, Ph.D. a Mgr. Soni Legartové, Ph.D. za jejich rady a pomoc při řešení technických problémů. Velké poděkování patři také mojí rodině, především manželovi, kteří mě po celou dobu podporovali a v závěru studia věnovali svůj čas čtení i úpravám této práce. Prohlášení Prohlašuji, že jsem svoji disertační práci vypracovala samostatně s využitím informačních zdrojů, které jsou v práci citovány. Brno 30. srpna 2019 ……………………………… Jméno Příjmení: Alena Svobodová Kovaříková Použité publikace: Svobodova Kovarikova, A., Legartova, S., Krejci, J., and Bartova, E. (2018). H3K9me3 and H4K20me3 represent the epigenetic landscape for 53BP1 binding to DNA lesions. Aging 10, 2585-2605. Plná verze: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6224238/ IF: 5.515 Prohlášení: Prohlašuji, že můj podíl na publikaci činí 70 % (příprava designu studie, kultivace buněčných linií, transfekce buněk plazmidovou DNA, konfokální mikroskopie, indukce poškození UVA a γ-zářením, imunofluorescenční barvení, imunodetekce pomocí westernového přenosu, analýza dat, psaní některých částí textu). Svobodova Kovarikova, A., Stixova, L., Kovarik, A., Komurkova, D., Legartova, S., and Bartova, E. (2019). Pronounced methylation of N6-adenosine in RNAs and reduced level of m3G/TMG in small RNAs appear before the active DNA demethylation at UV-induced DNA lesions. Plná verze: odesláno v odborném periodiku Prohlášení: Prohlašuji, že můj podíl na publikaci činí 65 % (příprava designu studie, kultivace buněčných linií, transfekce buněk plazmidovou DNA, konfokální mikroskopie, indukce poškození UVA a γ-zářením, imunofluorescenční barvení, imunodetekce pomocí westernového přenosu, analýza dat, psaní některých částí textu). OBSAH 1 ÚVOD ................................................................................................................................... 16 2 TEORETICKÁ ČÁST ........................................................................................................ 17 2.1 Metylace DNA ............................................................................................................... 17 2.1.1 Metylace cytosinu u savců ...................................................................................... 19 2.1.2 Savčí DNA metyltransferázy (Dnmt) ..................................................................... 19 2.1.3 Metyl-CpG vázající proteiny .................................................................................. 25 2.2 Demetylace 5mC a jeho deriváty ................................................................................... 25 2.3 Metylace adeninu 6mA v DNA ...................................................................................... 27 2.4 Metylace RNA................................................................................................................ 28 2.5 Histonové modifikace a jejich funkční význam ............................................................. 30 2.5.1 Acetylace histonů .................................................................................................... 31 2.5.2 Metylace histonů a její funkční význam ................................................................. 32 2.6 Význam epigenetiky pro opravné mechanismy poškozené DNA .................................. 36 2.6.1 Jednořetězcové zlomy (SSB) v DNA a jejich opravné mechanismy ...................... 37 2.6.2 Dvouřetězcové zlomy a mechanismy jejich opravy ............................................... 40 2.6.3 Nukleotidové excizní opravy (NER) ...................................................................... 44 2.6.4 Epigenetické modifikace
Load more

Recommended publications
  • Computational Modeling of Lysine Post-Translational Modification: an Overview Md
    c and S eti ys h te nt m y s S B Hasan MM et al., Curr Synthetic Sys Biol 2018, 6:1 t i n o e l Current Synthetic and o r r g DOI: 10.4172/2332-0737.1000137 u y C ISSN: 2332-0737 Systems Biology CommentaryResearch Article OpenOpen Access Access Computational Modeling of Lysine Post-Translational Modification: An Overview Md. Mehedi Hasan 1*, Mst. Shamima Khatun2, and Hiroyuki Kurata1,3 1Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan 2Department of Statistics, Laboratory of Bioinformatics, Rajshahi University-6205, Bangladesh 3Biomedical Informatics R&D Center, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan Commentary hot spot for PTMs, and a number of protein lysine modifications could occur in both histone and non-histone proteins [11,12]. For instance, Living organisms have a magnificent ordered and complex lysine methylation in non-histone proteins can regulate the protein structure. In regulating the cellular functions, post-translational activity and protein structure stability [13]. In 2004, the Nobel Prize in modifications (PTMs) are critical molecular measures. They alter Chemistry was awarded jointly to Aaron Ciechanover, Avram Hershko protein conformation, modulating their activity, stability and and Irwin Rose for the discovery of lysine ubiquitin-mediated protein localization. Up to date, more than 300 types of PTMs are experimentally degradation [14]. discovered in vivo and in vitro pathways [1,2]. Major and common PTMs are methylation, ubiquitination, succinylation, phosphorylation, Moreover, in biological process, lysine can be modified by the glycosylation, acetylation, and sumoylation.
    [Show full text]
  • Loss of Conserved Ubiquitylation Sites in Conserved Proteins During Human Evolution
    INTERNATIONAL JOURNAL OF MOleCular meDICine 42: 2203-2212, 2018 Loss of conserved ubiquitylation sites in conserved proteins during human evolution DONGBIN PARK, CHUL JUN GOH, HYEIN KIM, JI SEOK LEE and YOONSOO HAHN Department of Life Science, Chung‑Ang University, Seoul 06974, Republic of Korea Received January 30, 2018; Accepted July 6, 2018 DOI: 10.3892/ijmm.2018.3772 Abstract. Ubiquitylation of lysine residues in proteins serves Introduction a pivotal role in the efficient removal of misfolded or unused proteins and in the control of various regulatory pathways Ubiquitylation, in which the highly conserved 76‑residue poly- by monitoring protein activity that may lead to protein peptide ubiquitin is covalently attached to a lysine residue of degradation. The loss of ubiquitylated lysines may affect substrate proteins, mediates the targeted destruction of ubiq- the ubiquitin‑mediated regulatory network and result in the uitylated proteins by the ubiquitin‑proteasome system (1‑4). emergence of novel phenotypes. The present study analyzed The ubiquitin‑mediated protein degradation pathway serves a mouse ubiquitylation data and orthologous proteins from crucial role in the efficient and specific removal of misfolded 62 mammals to identify 193 conserved ubiquitylation sites from proteins and certain key regulatory proteins (5,6). Ubiquitin 169 proteins that were lost in the Euarchonta lineage leading and other ubiquitin‑like proteins, including autophagy‑related to humans. A total of 8 proteins, including betaine homo- protein 8, Ubiquitin‑like
    [Show full text]
  • Metabolomics-Assisted Proteomics Identifies Succinylation and SIRT5 As Important Regulators of Cardiac Function
    Metabolomics-assisted proteomics identifies succinylation and SIRT5 as important regulators of cardiac function Sushabhan Sadhukhana, Xiaojing Liub,c,d, Dongryeol Ryue, Ornella D. Nelsona, John A. Stupinskif, Zhi Lia, Wei Cheng, Sheng Zhangg, Robert S. Weissf, Jason W. Locasaleb,c,d, Johan Auwerxe,1, and Hening Lina,h,1 aDepartment of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853; bDuke Cancer Institute, Duke University School of Medicine, Durham, NC 27710; cDuke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27710; dDepartment of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710; eLaboratory of Integrative and Systems Physiology, School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; fDepartment of Biomedical Sciences, Cornell University, Ithaca, NY 14853; gProteomics & Mass Spectrometry Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853; and hHoward Hughes Medical Institute, Cornell University, Ithaca, NY 14853 Edited by Kevan M. Shokat, University of California, San Francisco, CA, and approved March 9, 2016 (received for review October 7, 2015) Cellular metabolites, such as acyl-CoA, can modify proteins, leading SIRT4 and SIRT5 have very weak deacetylase activities (14). SIRT5 to protein posttranslational modifications (PTMs). One such PTM is possesses unique enzymatic activity on hydrolyzing negatively lysine succinylation, which is regulated by sirtuin 5 (SIRT5). Although charged
    [Show full text]
  • SUMO and Transcriptional Regulation: the Lessons of Large-Scale Proteomic, Modifomic and Genomic Studies
    molecules Review SUMO and Transcriptional Regulation: The Lessons of Large-Scale Proteomic, Modifomic and Genomic Studies Mathias Boulanger 1,2 , Mehuli Chakraborty 1,2, Denis Tempé 1,2, Marc Piechaczyk 1,2,* and Guillaume Bossis 1,2,* 1 Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; [email protected] (M.B.); [email protected] (M.C.); [email protected] (D.T.) 2 Equipe Labellisée Ligue Contre le Cancer, Paris, France * Correspondence: [email protected] (M.P.); [email protected] (G.B.) Abstract: One major role of the eukaryotic peptidic post-translational modifier SUMO in the cell is transcriptional control. This occurs via modification of virtually all classes of transcriptional actors, which include transcription factors, transcriptional coregulators, diverse chromatin components, as well as Pol I-, Pol II- and Pol III transcriptional machineries and their regulators. For many years, the role of SUMOylation has essentially been studied on individual proteins, or small groups of proteins, principally dealing with Pol II-mediated transcription. This provided only a fragmentary view of how SUMOylation controls transcription. The recent advent of large-scale proteomic, modifomic and genomic studies has however considerably refined our perception of the part played by SUMO in gene expression control. We review here these developments and the new concepts they are at the origin of, together with the limitations of our knowledge. How they illuminate the SUMO-dependent Citation: Boulanger, M.; transcriptional mechanisms that have been characterized thus far and how they impact our view of Chakraborty, M.; Tempé, D.; SUMO-dependent chromatin organization are also considered.
    [Show full text]
  • Ubiquitin Modifications
    npg Cell Research (2016) 26:399-422. REVIEW www.nature.com/cr Ubiquitin modifications Kirby N Swatek1, David Komander1 1Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK Protein ubiquitination is a dynamic multifaceted post-translational modification involved in nearly all aspects of eukaryotic biology. Once attached to a substrate, the 76-amino acid protein ubiquitin is subjected to further modi- fications, creating a multitude of distinct signals with distinct cellular outcomes, referred to as the ‘ubiquitin code’. Ubiquitin can be ubiquitinated on seven lysine (Lys) residues or on the N-terminus, leading to polyubiquitin chains that can encompass complex topologies. Alternatively or in addition, ubiquitin Lys residues can be modified by ubiq- uitin-like molecules (such as SUMO or NEDD8). Finally, ubiquitin can also be acetylated on Lys, or phosphorylated on Ser, Thr or Tyr residues, and each modification has the potential to dramatically alter the signaling outcome. While the number of distinctly modified ubiquitin species in cells is mind-boggling, much progress has been made to characterize the roles of distinct ubiquitin modifications, and many enzymes and receptors have been identified that create, recognize or remove these ubiquitin modifications. We here provide an overview of the various ubiquitin modifications present in cells, and highlight recent progress on ubiquitin chain biology. We then discuss the recent findings in the field of ubiquitin acetylation and phosphorylation, with a focus on Ser65-phosphorylation and its role in mitophagy and Parkin activation. Keywords: ubiquitin; proteasomal degradation; phosphorylation; post-translational modification; Parkin Cell Research (2016) 26:399-422.
    [Show full text]
  • SUCLA2 Mutations Cause Global Protein Succinylation Contributing To
    ARTICLE https://doi.org/10.1038/s41467-020-19743-4 OPEN SUCLA2 mutations cause global protein succinylation contributing to the pathomechanism of a hereditary mitochondrial disease ✉ Philipp Gut 1,2,17 , Sanna Matilainen3,17, Jesse G. Meyer4,14,17, Pieti Pällijeff3, Joy Richard2, Christopher J. Carroll5, Liliya Euro 3, Christopher B. Jackson 3, Pirjo Isohanni3,6, Berge A. Minassian7,8, Reem A. Alkhater9, Elsebet Østergaard10, Gabriele Civiletto2, Alice Parisi2, Jonathan Thevenet2, Matthew J. Rardin4,15, Wenjuan He1, Yuya Nishida1, John C. Newman 1, Xiaojing Liu11,16, Stefan Christen2, ✉ ✉ Sofia Moco 2, Jason W. Locasale 11, Birgit Schilling 4,18 , Anu Suomalainen 3,12,13,18 & 1234567890():,; ✉ Eric Verdin 1,4,18 Mitochondrial acyl-coenzyme A species are emerging as important sources of protein modification and damage. Succinyl-CoA ligase (SCL) deficiency causes a mitochondrial encephalomyopathy of unknown pathomechanism. Here, we show that succinyl-CoA accumulates in cells derived from patients with recessive mutations in the tricarboxylic acid cycle (TCA) gene succinyl-CoA ligase subunit-β (SUCLA2), causing global protein hyper- succinylation. Using mass spectrometry, we quantify nearly 1,000 protein succinylation sites on 366 proteins from patient-derived fibroblasts and myotubes. Interestingly, hyper- succinylated proteins are distributed across cellular compartments, and many are known targets of the (NAD+)-dependent desuccinylase SIRT5. To test the contribution of hyper- succinylation to disease progression, we develop a zebrafish model of the SCL deficiency and find that SIRT5 gain-of-function reduces global protein succinylation and improves survival. Thus, increased succinyl-CoA levels contribute to the pathology of SCL deficiency through post-translational modifications.
    [Show full text]
  • The E3 Ligase TRIM32 Is an Effector of the RAS Family Gtpase RAP2
    The E3 Ligase TRIM32 is an effector of the RAS family GTPase RAP2 Berna Demiray A thesis submitted towards the degree of Doctor of Philosophy Cancer Institute University College London 2014 Declaration I, Berna Demiray, confirm that the work presented in this thesis is my own. Where information has been derived from other sources, I confirm that this has been indicated. London, 2014 The E3 Ligase TRIM32 is an Effector of the RAS family GTPase RAP2 Classical RAS oncogenes are mutated in approximately 30% of human tumours and RAP proteins are closely related to classical RAS proteins. RAP1 has an identical effector domain to RAS whereas RAP2 differs by one amino acid. RAP2 not only shares effectors with other classical RAS family members, but it also has its own specific effectors that do not bind to RAP1 or classical RAS family proteins. Thus, although closely related, RAP2 performs distinct functions, although these have been poorly characterised. Using RAP2 as bait in Tandem Affinity Purifications, we have identified several RAP2 interacting proteins including TRIM32; a protein implicated in diverse pathological processes such as Limb-Girdle Muscular Dystrophy (LGMD2H), and Bardet-Biedl syndrome (BBS). TRIM32 was shown to interact specifically with RAP2 in an activation- and effector domain-dependent manner; demonstrating stronger interaction with the RAP2 V12 mutant than the wild-type RAP2 and defective binding to the effector mutant RAP2 V12A38. The interaction was mapped to the C-terminus of TRIM32 (containing the NHL domains) while mutations found in LGMD2H (R394H, D487N, ∆588) were found to disrupt binding to RAP2. The TRIM32 P130S mutant linked to BBS did not affect binding to RAP2, suggesting that the RAP2-TRIM32 interaction may be functionally involved in LGMD2H.
    [Show full text]
  • Oxidative Stress-Triggered Interactions Between the Succinyl- and Acetyl
    Oxidative stress-triggered interactions between the succinyl- and acetyl-proteomes of rice leaves Heng Zhou1, Iris Finkemeier2, Wenxue Guan1, Maria-Armineh Tossounian3,4,5, Bo Wei3,4,5,6,7, David Young3,4,5, Jingjing Huang3,4,5,6,7, Joris Messens3,4,5, Xibin Yang8, Jun Zhu8, Michael H. Wilson9, Wenbiao Shen1, Yanjie Xie1,9,*, Christine H Foyer9,* 1 Laboratory Center of Life Sciences, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China. 2 Institute of Plant Biology and Biotechnology, Westfaelische Wilhelms University Muenster, 48149 Muenster, Germany 3 VIB-VUB Center for Structural Biology, B-1050 Brussels, Belgium. 4 Brussels Center for Redox Biology, B-1050 Brussels, Belgium. 5 Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium. 6 VIB-UGent Center for Plant Systems Biology, Technologiepark 927, B-9052 Ghent, Belgium. 7 Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium. 8 Jingjie PTM Biolab (Hangzhou) Co. Ltd, Hangzhou 310018, China. 9 Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK Running title: Redox mediated succinylome/acetylome interactions This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process which may lead to differences between this version and the Version of Record. Please cite this article as doi: 10.1111/pce.13100 This article is protected by copyright. All rights reserved. Summary Statement Protein post-transcriptional modifications (PTMs) such as lysine succinylation and acetylation regulating protein functions in response to metabolic and environmental cues.
    [Show full text]
  • Protein Interactions Allow Functional Regulation of Homocysteine Metabolism
    HIGHLIGHTS - Protein interactions allow functional regulation of homocysteine metabolism - Homocysteine metabolism establishes pathway interplays through protein interactions - Intermolecular interactions within homocysteine metabolism may support substrate channeling - Homocysteine metabolism interaction networks are altered in oncogenesis - Proteins of homocysteine metabolism interact with oncogenes for gene regulation PROTEIN-PROTEIN INTERACTIONS INVOLVING ENZYMES OF THE MAMMALIAN METHIONINE AND HOMOCYSTEINE METABOLISM Francisco Portillo1,2,3,4, Jesús Vázquez5,6, María A. Pajares2,7* 1Instituto de Investigaciones Biomédicas Alberto Sols (CSIC-UAM), Arturo Duperier 4, 28029 Madrid, Spain 2Instituto de Investigación Sanitaria La Paz (IdiPAZ), Paseo de la Castellana 261, 28046 Madrid, Spain 3Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid, Arzobispo Morcillo 4, 28029 Madrid, Spain 4Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain. 5Laboratory of Cardiovascular Proteomics, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández de Almagro 3, 28029 Madrid, Spain. 6CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain. 7Departamento de Biología Estructural y Química, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain. *Corresponding author: Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain. (Phone: 34-918373112; FAX: 34-915360432; email: [email protected]). ABBREVIATIONS: AdoMet, S-adenosylmethionine; AdoHcy, S- adenosylhomocysteine; AHCY, S-adenosylhomocysteine hydrolase; AP, affinity 1 purification; BHMT and BHMT2, betaine homocysteine S-methyltransferases 1 and 2; CBS, cystathionine b-synthase; CTH, cystathionine g-lyase; GSH and GSSG, glutathione reduced and oxidized forms; Hcy, homocysteine; MAT, methionine adenosyltransferase; MS, mass spectrometry; MTR, methionine synthase; NNMT, nicotinamide N- methyltransferase; PDRG1, p53 and DNA damage-regulated gene 1.
    [Show full text]
  • First Comprehensive Proteome Analysis of Lysine Crotonylation In
    www.nature.com/scientificreports OPEN First comprehensive proteome analysis of lysine crotonylation in seedling leaves of Nicotiana Received: 12 January 2017 Accepted: 25 April 2017 tabacum Published: xx xx xxxx Hangjun Sun1, Xiaowei Liu1, Fangfang Li1, Wei Li2, Jing Zhang2, Zhixin Xiao3, Lili Shen1, Ying Li1, Fenglong Wang1 & Jinguang Yang1 Histone crotonylation is a new lysine acylation type of post-translational modification (PTM) enriched at active gene promoters and potential enhancers in yeast and mammalian cells. However, lysine crotonylation in nonhistone proteins and plant cells has not yet been studied. In the present study, we performed a global crotonylation proteome analysis of Nicotiana tabacum (tobacco) using high- resolution LC-MS/MS coupled with highly sensitive immune-affinity purification. A total of 2044 lysine modification sites distributed on 637 proteins were identified, representing the most abundant lysine acylation proteome reported in the plant kingdom. Similar to lysine acetylation and succinylation in plants, lysine crotonylation was related to multiple metabolism pathways, such as carbon metabolism, the citrate cycle, glycolysis, and the biosynthesis of amino acids. Importantly, 72 proteins participated in multiple processes of photosynthesis, and most of the enzymes involved in chlorophyll synthesis were modified through crotonylation. Numerous crotonylated proteins were implicated in the biosynthesis, folding, and degradation of proteins through the ubiquitin-proteasome system. Several crotonylated proteins related to chromatin organization are also discussed here. These data represent the first report of a global crotonylation proteome and provide a promising starting point for further functional research of crotonylation in nonhistone proteins. Post-translational modification (PTM) is a covalent modification process resulting from the proteolytic cleavage or addition of a functional group to one amino acid.
    [Show full text]
  • Narita Et Al., NRMCB 2019 AAM
    Functions and mechanisms of non-histone protein acetylation Narita, Takeo; Weinert, Brian T; Choudhary, Chunaram Published in: Nature Reviews. Molecular Cell Biology DOI: 10.1038/s41580-018-0081-3 Publication date: 2019 Document version Peer reviewed version Citation for published version (APA): Narita, T., Weinert, B. T., & Choudhary, C. (2019). Functions and mechanisms of non-histone protein acetylation. Nature Reviews. Molecular Cell Biology, 20, 156-174. https://doi.org/10.1038/s41580-018-0081-3 Download date: 26. sep.. 2021 Functions and mechanisms of non-histone protein acetylation Takeo Narita, Brian T. Weinert, Chunaram Choudhary* The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark *Correspondence should be addressed to: CC, [email protected] Abstract | N-ε-lysine acetylation was discovered more than half a century ago as a posttranslational modification of histones and has been extensively studied in the context of transcription regulation. In the past decade, proteomic analyses have revealed that non-histone proteins are frequently acetylated and constitute a major portion of the acetylome in mammalian cells. Indeed, non-histone protein acetylation is involved in key cellular processes relevant to physiology and disease, such as gene transcription, DNA damage repair, cell division, signal transduction, protein folding, autophagy and metabolism. Acetylation affects protein functions through diverse mechanisms, including by regulating protein stability, enzymatic activity, subcellular localization, cross-talk with other posttranslational modifications, and by controlling protein–protein and protein–DNA interactions. In this Review, we discuss recent progress in our understanding of the scope, functional diversity and mechanisms of non-histone protein acetylation.
    [Show full text]
  • Succinyl-Proteome Profiling of Dendrobium Officinale, an Important Traditional Chinese Orchid Herb, Revealed Involvement of Succ
    Feng et al. BMC Genomics (2017) 18:598 DOI 10.1186/s12864-017-3978-x RESEARCH ARTICLE Open Access Succinyl-proteome profiling of Dendrobium officinale, an important traditional Chinese orchid herb, revealed involvement of succinylation in the glycolysis pathway Shangguo Feng1,2, Kaili Jiao1,2, Hong Guo1,2, Mengyi Jiang1,2, Juan Hao1,2, Huizhong Wang1,2* and Chenjia Shen1,2* Abstract Background: Lysine succinylation is a ubiquitous and important protein post-translational modification in various eukaryotic and prokaryotic cells. However, its functions in Dendrobium officinale, an important traditional Chinese orchid herb with high polysaccharide contents, are largely unknown. Results: In our study, LC-MS/MS was used to identify the peptides that were enriched by immune-purification with a high-efficiency succinyl-lysine antibody. In total, 314 lysine succinylation sites in 207 proteins were identified. A gene ontology analysis showed that these proteins are associated with a wide range of cellular functions, from metabolic processes to stimuli responses. Moreover, two types of conserved succinylation motifs, ‘***Ksuc******K**’ and ‘****EKsuc***’, were identified. Our data showed that lysine succinylation occurred on five key enzymes in the glycolysis pathway. The numbers of average succinylation sites on these five enzymes in plants were lower than those in bacteria and mammals. Interestingly, two active site amino acids residues, K103 and K225, could be succinylated in fructose-bisphosphate aldolase, indicating a potential function of lysine succinylation in the regulation of glycolytic enzyme activities. Furthermore, the protein–protein interaction network for the succinylated proteins showed that several functional terms, such as glycolysis, TCA cycle, oxidative phosphorylation and ribosome, are consisted.
    [Show full text]