DOCSLIB.ORG

Functional Role of N-Terminal Extension of Human AP Endonuclease 1 in Coordination of Base Excision DNA Repair Via Protein–Protein Interactions

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Functional Role of N-Terminal Extension of Human AP Endonuclease 1 in Coordination of Base Excision DNA Repair Via Protein–Protein Interactions International Journal of Molecular Sciences Article Functional Role of N-Terminal Extension of Human AP Endonuclease 1 In Coordination of Base Excision DNA Repair via Protein–Protein Interactions Nina Moor 1, Inna Vasil’eva 1 and Olga Lavrik 1,2,* 1 Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; [email protected] (N.M.); [email protected] (I.V.) 2 Novosibirsk State University, 630090 Novosibirsk, Russia * Correspondence: [email protected] Received: 12 February 2020; Accepted: 27 April 2020; Published: 28 April 2020 Abstract: Human apurinic/apyrimidinic endonuclease 1 (APE1) has multiple functions in base excision DNA repair (BER) and other cellular processes. Its eukaryote-specific N-terminal extension plays diverse regulatory roles in interaction with different partners. Here, we explored its involvement in interaction with canonical BER proteins. Using fluorescence based-techniques, we compared binding affinities of the full-length and N-terminally truncated forms of APE1 (APE1ND35 and APE1ND61) for functionally and structurally different DNA polymerase β (Polβ), X-ray repair cross-complementing protein 1 (XRCC1), and poly(adenosine diphosphate (ADP)-ribose) polymerase 1 (PARP1), in the absence and presence of model DNA intermediates. Influence of the N-terminal truncation on binding the AP site-containing DNA was additionally explored. These data suggest that the interaction domain for proteins is basically formed by the conserved catalytic core of APE1. The N-terminal extension being capable of dynamically interacting with the protein and DNA partners is mostly responsible for DNA-dependent modulation of protein–protein interactions. Polβ, XRCC1, and PARP1 were shown to more efficiently regulate the endonuclease activity of the full-length protein than that of APE1ND61, further suggesting contribution of the N-terminal extension to BER coordination. Our results advance the understanding of functional roles of eukaryote-specific protein extensions in highly coordinated BER processes. Keywords: APE1; protein–protein interactions; base excision repair; multifunctional disordered protein; fluorescence techniques 1. Introduction Apurinic/apyrimidinic endonuclease 1 (APE1) is an essential protein in mammals with multiple functions in base excision DNA repair (BER), regulation of gene expression, RNA metabolism, and other specific cellular processes [1–3]. BER is the primary mechanism for correcting apurinic/apyrimidinic (AP) sites (created through N-glycosidic bond cleavage), modified bases, and single-strand breaks (SSBs) [4,5]. The major enzymatic function of APE1 in BER is the incision of AP sites, one of the most abundant types of oxidative DNA damage [6]. Additional activities of APE1, 30-diesterase, and 30-50-exonuclease contribute to removing terminal blocking groups in BER DNA intermediates and to proofreading DNA mismatches introduced by DNA polymerase β (Polβ)[1,3]. APE1 is also capable of incising DNA at certain base lesions (nucleotide incision repair) and RNA at abasic site and specific regions, as well as of processing abasic and oxidized ribonucleotides embedded in the DNA [1–3,7,8]. A redox activity of APE1 is responsible for the regulation of DNA-binding activities of different transcription factors [1,2]. The DNA repair and redox activities of APE1 can Int. J. Mol. Sci. 2020, 21, 3122; doi:10.3390/ijms21093122 www.mdpi.com/journal/ijms Int. J. Mol. Sci. 2020, 21, x 2 of 19 Int. J. Mol. Sci. 2020, 21, 3122 2 of 18 of APE1 can play a collaborative role in different processes [9,10]. Interactions with multiple protein playpartners a collaborative that modulate role diverse in different enzymatic processes activities [9,10]. of Interactions APE1 and with mediate multiple its regulatory protein partners function that in modulatetranscription diverse are enzymatic highly activitiesinterconnected of APE1 andand mediate dynamically its regulatory regulated function inthrough transcription various are highlypost-translational interconnected modifications and dynamically of APE1 regulated [1,2,11–13]. through Dysregulation various post-translational of multifunctional modifications activities of ofAPE1 APE1 is [associated1,2,11–13]. with Dysregulation various human of multifunctional pathologies, making activities APE1 of APE1 a potential is associated therapeutic with various target human[1,5,12,14]. pathologies, making APE1 a potential therapeutic target [1,5,12,14]. The humanhuman APE1APE1 is is composed composed of of two two structural structural domains domains and and a disordered a disordered N-terminal N-terminal region region [15], formed[15], formed mostly mostly by the by sequence the sequence highly conservedhighly conserved in mammals in mammals (Figure1). (Figure The catalytically 1). The catalytically active core responsibleactive core forresponsible the enzyme for activities the enzyme in BER activities is created in by BER the universally is created conservedby the universally sequence 62–318conserved [16]. Thesequence region 62–318 required [16]. for The the redoxregion activity required of APE1for the is re indox the N-terminalactivity of APE1 domain is [in1]. the The N-terminal unique disordered domain region[1]. The comprises unique thedisordered nuclear localizationregion comprises signal and the multiple nuclear post-translational localization signal modification and multiple sites. Thispost-translational region, enriched modification in lysine residues,sites. This contributes region, enriched to APE1 in lysine interaction residues, with contributes various DNA to /APE1RNA structuresinteractionand with to acetylation-mediatedvarious DNA/RNA structures modulation an ofd theto acetylation-mediated enzyme DNA repair activitymodulationin vitro of andthe inenzyme vivo [ 17DNA–21 ].repair Ubiquitination activity in vitro and and acetylation in vivo of[17–21]. specific Ubiquitination Lys residues and of the acetylation N-terminal of specific region modulateLys residues the of expression the N-terminal level andregion diff modulateerent functions the expression of APE1 inlevel vivo andvia different proteolytic functions degradation of APE1 or limitedin vivo N-terminalvia proteolytic proteolysis, degradation respectively or limited [22,23 N-terminal]. The conserved proteolysis, catalytic respectively core and the [22,23]. N-terminal The extensionconserved arecatalytic both required core and for the the N-terminal APE1 function extens ation telomeric are both DNA required substrates for the and APE1 their function protective at proteintelomeric complexes DNA substrates [24,25]. and The their N-terminal protective extension protein of complexes APE1 contributes [24,25]. toThe a diN-terminalfferent extent extension to the interactionof APE1 contributes with proteins to a different involved extent in RNA to the processing interaction and with ribosome proteins biogenesis involved [in26 RNA]; its interactionprocessing withand ribosome nucleophosmin biogenesis (NPM1) [26]; is veryits interaction unstable to with be detected nucleophosmin in the absence (NPM1) of the is remainingvery unstable C-terminal to be portiondetected [ 20in]. the The absence first 35 of residues the remaining are critical C-terminal for the portion physical [20]. interaction The first of 35 APE1 residues with are X-ray critical repair for cross-complementingthe physical interaction protein of APE1 1 (XRCC1) with functioningX-ray repair as cross-complementing a scaffold protein of BERprotein [27 ].1 However,(XRCC1) involvementfunctioning as of a the scaffold N-terminal protein extension of BER of[27]. APE1 However, in the interaction involvement with of otherthe N-terminal canonical BERextension proteins of stillAPE1 remains in the interaction unexplored. with other canonical BER proteins still remains unexplored. Figure 1. Structural organization of human apurinicapurinic/apy/apyrimidinicrimidinic endonuclease 1 (APE1). Protein is composed ofof twotwo structural structural domains domains and and disordered disordered N-terminal N-terminal region region invisible invisible in crystal in crystal structures structures [15]. Sequence[15]. Sequence 62–318 62–318 responsible responsible for for AP AP endonuclease endonuclease activity activity is is conserved conserved in in pro-pro- andand eukaryotes; firstfirst 35 residues of of N-terminal N-terminal eukaryote-specific eukaryote-specific extension extension (residues (residues 1–61) 1–61) are are highly highly conserved conserved in inmammals mammals [16]. [ 16Isoelectric]. Isoelectric points points(calculated (calculated using Ex usingPASy ExPASyproteomics proteomics server) of server)full-length of full-lengthprotein, its protein,N-terminally its N-terminally truncated truncatedforms (APE1N forms (APE1NΔ35, APE1ND35, APE1NΔ61), Dthe61), entire the entire extension, extension, and and its mammalian-specificmammalian-specific fragment fragment are are presented. presented. We demonstrated the usefulness of fluorescence-based techniques for the detection and We demonstrated the usefulness of fluorescence-based techniques for the detection and quantification of physical interactions between various BER proteins, and for the detection of modulation quantification of physical interactions between various BER proteins, and for the detection of of protein–protein interactions by DNA intermediates [28]. In the present study, we used the same modulation of protein–protein interactions by DNA intermediates [28]. In the present
Load more

Recommended publications
  • Structure and Function of Nucleases in DNA Repair: Shape, Grip and Blade of the DNA Scissors
    Oncogene (2002) 21, 9022 – 9032 ª 2002 Nature Publishing Group All rights reserved 0950 – 9232/02 $25.00 www.nature.com/onc Structure and function of nucleases in DNA repair: shape, grip and blade of the DNA scissors Tatsuya Nishino1 and Kosuke Morikawa*,1 1Department of Structural Biology, Biomolecular Engineering Research Institute (BERI), 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan DNA nucleases catalyze the cleavage of phosphodiester mismatched nucleotides. They also recognize the bonds. These enzymes play crucial roles in various DNA replication or recombination intermediates to facilitate repair processes, which involve DNA replication, base the following reaction steps through the cleavage of excision repair, nucleotide excision repair, mismatch DNA strands (Table 1). repair, and double strand break repair. In recent years, Nucleases can be regarded as molecular scissors, new nucleases involved in various DNA repair processes which cleave phosphodiester bonds between the sugars have been reported, including the Mus81 : Mms4 (Eme1) and the phosphate moieties of DNA. They contain complex, which functions during the meiotic phase and conserved minimal motifs, which usually consist of the Artemis : DNA-PK complex, which processes a V(D)J acidic and basic residues forming the active site. recombination intermediate. Defects of these nucleases These active site residues coordinate catalytically cause genetic instability or severe immunodeficiency. essential divalent cations, such as magnesium, Thus, structural biology on various nuclease actions is calcium, manganese or zinc, as a cofactor. However, essential for the elucidation of the molecular mechanism the requirements for actual cleavage, such as the types of complex DNA repair machinery. Three-dimensional and the numbers of metals, are very complicated, but structural information of nucleases is also rapidly are not common among the nucleases.
    [Show full text]
  • Structural Comparison of AP Endonucleases from The
    Biochimie 128-129 (2016) 20e33 Contents lists available at ScienceDirect Biochimie journal homepage: www.elsevier.com/locate/biochi Research paper Structural comparison of AP endonucleases from the exonuclease III family reveals new amino acid residues in human AP endonuclease 1 that are involved in incision of damaged DNA Modesto Redrejo-Rodríguez a, 1, 2, Armelle Vigouroux b, 1, Aibek Mursalimov e, 1, Inga Grin a, c, d, 1, Doria Alili a, Zhanat Koshenov e, Zhiger Akishev f, Andrei Maksimenko a, Amangeldy K. Bissenbaev f, Bakhyt T. Matkarimov e, Murat Saparbaev a, * * Alexander A. Ishchenko a, , Solange Morera b, a Laboratoire «StabiliteGenetique et Oncogenese» CNRS, UMR 8200, Univ. Paris-Sud, Universite Paris-Saclay, Gustave Roussy Cancer Campus, Equipe Labellisee Ligue Contre le Cancer, F-94805 Villejuif Cedex, France b Institute for Integrative Biology of the Cell (I2BC), CNRS CEA Univ Paris-Sud, Universite Paris-Saclay, Gif-sur-Yvette 91198, France c SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia d Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia e National Laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan f Department of Molecular Biology and Genetics, Faculty of Biology, Al-Farabi Kazakh National University, Almaty 530038, Kazakhstan article info abstract Article history: Oxidatively damaged DNA bases are substrates for two overlapping repair pathways: DNA glycosylase- Received 15 December 2015 initiated base excision repair (BER) and apurinic/apyrimidinic (AP) endonuclease-initiated nucleotide Accepted 20 June 2016 incision repair (NIR). In the BER pathway, an AP endonuclease cleaves DNA at AP sites and 30-blocking Available online 22 June 2016 moieties generated by DNA glycosylases, whereas in the NIR pathway, the same AP endonuclease incises DNA 50 to an oxidized base.
    [Show full text]
  • Human AP Endonuclease (APE)/Buffer
    Human Apurinic/Apyrimidinic Endonuclease (APE) Catalog Number: EN004 Specifications and Use Contents Component Size Human APE 200 Units in 0.2 mL 10X DDR Buffer 2 (100 mM HEPES-KOH (pH 7.4), 1 M KCl, 100 mM MgCl2) 1 mL Description ♦ Human APE (also known as Ref-1) is the apurinic/apyrimidinic (AP) endonuclease required for efficient DNA base excision repair (BER). Following the removal of a damaged base by a DNA glycosylase, APE cleaves the AP site to allow resynthesis and ligation to complete repair. In addition, APE/Ref-1 acts as a factor that regulates the redox state of multiple transcription factors, including c-Jun, c-Fos, NF-κB, and p53. Source ♦ A cDNA corresponding to amino acid residues 2-318 of human APE was fused to a sequence encoding a 6X histidine epitope tag at the N-terminus. The recombinant fusion protein was expressed in E. coli. Unit Definition ♦ One unit is the amount of enzyme required to cleave the tetrahydrofuran (THF) synthetic AP Site Oligonucleotide (Cat. # 3854-100-OL) indicated below at the rate of 1 pmole/hour at 37° C. Comparable results were observed when the AP Site Oligonucleotide was used (Cat. # 3851-100-OL). ♦ Sequence: 5' CCTGCCCTGTHFGCAGCTGTGGG 3' 3' GGACGGGAC ACGTCGACACCC Specificity ♦ Human APE catalyzes the cleavage of the phosphodiester bond either 3’ or 5’ to an AP site. Assay Conditions ♦ Serial dilutions of human APE are incubated for 1 hour at 37° C in a 20 µL reaction containing 1X DDR Buffer 2 and 4 pmole THF-AP Site Oligonucleotide (Cat. # 3854-100-OL) labeled with 32P and annealed with 4 pmole Oligo Complement B (Cat.
    [Show full text]
  • African Swine Fever Virus Protein Pe296r Is a DNA Repair Apurinic
    JOURNAL OF VIROLOGY, May 2006, p. 4847–4857 Vol. 80, No. 10 0022-538X/06/$08.00ϩ0 doi:10.1128/JVI.80.10.4847–4857.2006 Copyright © 2006, American Society for Microbiology. All Rights Reserved. African Swine Fever Virus Protein pE296R Is a DNA Repair Apurinic/Apyrimidinic Endonuclease Required for Virus Growth in Swine Macrophages Modesto Redrejo-Rodrı´guez, Ramo´n Garcı´a-Escudero,† Rafael J. Ya´n˜ez-Mun˜oz,‡ Marı´a L. Salas, and Jose´ Salas* Centro de Biologı´a Molecular Severo Ochoa (Consejo Superior de Investigaciones Cientı´ficas-Universidad Auto´noma de Madrid), Universidad Auto´noma de Madrid, Cantoblanco, 28049 Madrid, Spain Received 15 December 2005/Accepted 21 February 2006 We show here that the African swine fever virus (ASFV) protein pE296R, predicted to be a class II apurinic/apyrimidinic (AP) endonuclease, possesses endonucleolytic activity specific for AP sites. Biochemical characterization of the purified recombinant enzyme indicated that the Km and catalytic efficiency values for the endonucleolytic reaction are in the range of those reported for Escherichia coli endonuclease IV (endo IV) and human Ape1. In addition to endonuclease activity, the ASFV enzyme has a proofreading 3؅35؅ exonuclease activity that is considerably more efficient in the elimination of a mismatch than in that of a correctly paired base. The three-dimensional structure predicted for the pE296R protein underscores the structural similarities between endo IV and the viral protein, supporting a common mechanism for the cleavage reaction. During infection, the protein is expressed at early times and accumulates at later times. The early enzyme is localized in the nucleus and the cytoplasm, while the late protein is found only in the cytoplasm.
    [Show full text]
  • Mechanism and Regulation Igh Chain Class Switch Recombination
    IgH Chain Class Switch Recombination: Mechanism and Regulation Janet Stavnezer and Carol E. Schrader This information is current as J Immunol 2014; 193:5370-5378; ; of September 26, 2021. doi: 10.4049/jimmunol.1401849 http://www.jimmunol.org/content/193/11/5370 Downloaded from References This article cites 133 articles, 66 of which you can access for free at: http://www.jimmunol.org/content/193/11/5370.full#ref-list-1 Why The JI? Submit online. http://www.jimmunol.org/ • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average by guest on September 26, 2021 Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2014 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. Th eJournal of Brief Reviews Immunology IgH Chain Class Switch Recombination: Mechanism and Regulation Janet Stavnezer and Carol E. Schrader IgH class switching occurs rapidly after activation of with an S region farther downstream. S regions are G rich and mature naive B cells, resulting in a switch from expres- have a high density of WGCW (A/T-G-C-A/T) motifs, the sion of IgM and IgD to expression of IgG, IgE, or IgA; preferred target for activation-induced cytidine deaminase this switch improves the ability of Abs to remove the (AID), the enzyme that initiates CSR by deaminating cytosines pathogen that induces the humoral immune response.
    [Show full text]
  • Uracil in Duplex DNA Is a Substrate for the Nucleotide Incision Repair
    Uracil in duplex DNA is a substrate for the nucleotide PNAS PLUS incision repair pathway in human cells Paulina Proroka,b, Doria Alilib, Christine Saint-Pierrec, Didier Gasparuttoc, Dmitry O. Zharkovd,e, Alexander A. Ishchenkob, Barbara Tudeka,f,1, and Murat K. Saparbaevb,1 aInstitute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; bGroupe Réparation de l’ADN, Centre National de la Recherche Scientifique Unité Mixte de Recherche 8200, Université Paris-Sud, Institut de Cancérologie Gustave Roussy, F-94805 Villejuif Cedex, France; cLaboratoire Lésions des Acides Nucléiques, Service de Chimie Inorganique et Biologique/Unité Mixte de Recherche E3 Commissariat à l’Energie Atomique–Université Joseph Fourier, Institut Nanosciences et Cryogénie, F-38054 Grenoble, France; dSiberian Branch of the Russian Academy of Sciences, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia; eDepartment of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia; and fInstitute of Genetics and Biotechnology, University of Warsaw, 00-927, Warsaw, Poland Edited by James E. Cleaver, University of California, San Francisco, CA, and approved August 13, 2013 (received for review March 25, 2013) Spontaneous hydrolytic deamination of cytosine to uracil (U) in and leave an apurinic/apyrimidinic (AP) site, which in turn is DNA is a constant source of genome instability in cells. This cleaved by an AP endonuclease to generate a single-stranded mutagenic process is greatly enhanced at high temperatures and break flankedwith3′-hydroxyl (3′-OH) and 5′-deoxyribose in single-stranded DNA. If not repaired, these uracil residues give phosphate (5′-dRp) groups. Next, using the 3′-OH terminus, a rise to C→T transitions, which are the most common spontaneous DNA polymerase initiates repair synthesis to incorporate reg- mutations occurring in living organisms and are frequently found ular nucleotides and to remove the 5′-dRp group.
    [Show full text]
  • BCR-ABL1 Kinase Inhibits Uracil DNA Glycosylase UNG2 to Enhance Oxidative DNA Damage and Stimulate Genomic Instability
    Leukemia (2013) 27, 629–634 & 2013 Macmillan Publishers Limited All rights reserved 0887-6924/13 www.nature.com/leu ORIGINAL ARTICLE BCR-ABL1 kinase inhibits uracil DNA glycosylase UNG2 to enhance oxidative DNA damage and stimulate genomic instability A Slupianek1, R Falinski1, P Znojek1, T Stoklosa1,2, S Flis1, V Doneddu3, D Pytel1,5, E Synowiec4, J Blasiak4, A Bellacosa3 and T Skorski1 Tyrosine kinase inhibitors (TKIs) revolutionized the treatment of chronic myeloid leukemia in chronic phase (CML-CP). Unfortunately, 25% of TKI-naive patients and 50–90% of patients developing TKI-resistance carry CML clones expressing TKI-resistant BCR-ABL1 kinase mutants. We reported that CML-CP leukemia stem and progenitor cell populations accumulate high amounts of reactive oxygen species, which may result in accumulation of uracil derivatives in genomic DNA. Unfaithful and/or inefficient repair of these lesions generates TKI-resistant point mutations in BCR-ABL1 kinase. Using an array of specific substrates and inhibitors/blocking antibodies we found that uracil DNA glycosylase UNG2 were inhibited in BCR-ABL1-transformed cell lines and CD34 þ CML cells. The inhibitory effect was not accompanied by downregulation of nuclear expression and/or chromatin association of UNG2. The effect was BCR-ABL1 kinase-specific because several other fusion tyrosine kinases did not reduce UNG2 activity. Using UNG2-specific inhibitor UGI, we found that reduction of UNG2 activity increased the number of uracil derivatives in genomic DNA detected by modified comet assay and facilitated accumulation of ouabain-resistant point mutations in reporter gene Na þ /K þ ATPase. In conclusion, we postulate that BCR-ABL1 kinase-mediated inhibition of UNG2 contributes to accumulation of point mutations responsible for TKI resistance causing the disease relapse, and perhaps also other point mutations facilitating malignant progression of CML.
    [Show full text]
  • Rotational Dynamics of DNA on the Nucleosome Surface Markedly Impact Accessibility to a DNA Repair Enzyme
    Rotational dynamics of DNA on the nucleosome surface markedly impact accessibility to a DNA repair enzyme John M. Hinz, Yesenia Rodriguez, and Michael J. Smerdon1 Biochemistry and Biophysics, School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520 Edited by Philip C. Hanawalt, Stanford University, Stanford, CA, and approved January 26, 2010 (received for review December 16, 2009) Histones play a crucial role in the organization of DNA in the Although the density of chromatin is an essential factor for its nucleus, but their presence can prevent interactions with DNA role in organizing DNA, its presence can be problematic for binding proteins responsible for repair of DNA damage. Uracil is an normal DNA metabolic processes, including DNA repair and abundant mutagenic lesion recognized by uracil DNA glycosylase transcription (8, 10, 12–15). DNA associated with nucleosomes is (UDG) in the first step of base excision repair (BER). In nucleosome constrained, and the general helical mobility necessary for access core particles (NCPs), we find substantial differences in UDG- to binding factors is impeded (12). In addition, the DNA in directed cleavage at uracils rotationally positioned toward (U-In) direct contact with histones is occluded from interaction with or away from (U-Out) the histone core, or midway between these other proteins, as intervals of the helix along the histone core orientations (U-Mid). Whereas U-Out NCPs show a cleavage rate surface are buried away from the solvent and thus virtually just below that of naked DNA, U-In and U-Mid NCPs have markedly inaccessible (13, 16). slower rates of cleavage.
    [Show full text]
  • Ciona Intestinalis
    Funakoshi et al. Genes and Environment (2017) 39:27 DOI 10.1186/s41021-017-0087-7 SHORT REPORT Open Access CiAPEX2 and CiP0, candidates of AP endonucleases in Ciona intestinalis, have 3′-5′ exonuclease activity and contribute to protection against oxidative stress Masafumi Funakoshi, Daisuke Nambara, Yuichiro Hayashi and Qiu-Mei Zhang-Akiyama* Abstract Apurinic/apyrimidinic (AP) sites are one of the most frequent DNA lesions. AP sites inhibit transcription and DNA replication, and induce cell death. AP endonucleases are key enzymes in AP site repair. Several types of AP endonucleases have been reported, such as AP endonuclease 2 (APEX2) and ribosomal protein P0 (P0). However, it is not known how the functions and roles differ among AP endonucleases. To clarify the difference of roles among AP endonucleases, we conducted biochemical analysis focused on APEX2 and P0 homologues in Ciona intestinalis.Amino acid sequence analysis suggested that CiAPEX2 and CiP0 are AP endonuclease homologues. Although we could not detect AP endonuclease or 3′-phosphodiesterase activity, these two purified proteins exhibited 3′-5′ exonuclease activity. This 3′-5′ exonuclease activity was sensitive to ethylenediaminetetraacetic acid (EDTA), and the efficiency of this activity was influenced by the 3′-terminus of substrate DNA. Both CiAPEX2 and CiP0 degraded not only a 5′-protruding DNA end, but also nicked DNA, which is generated through AP endonuclease 1 (APEX1) cleavage. These two genes partially complemented the growth rate of AP endonuclease-deficient Escherichia coli treated with hydrogen peroxide. These results indicate that 3′-5′ exonuclease activity is an evolutionarily conserved enzymatic activity of APEX2 and P0 homologues and this enzymatic activity may be important for AP endonucleases.
    [Show full text]
  • A Dual Face of APE1 in the Maintenance of Genetic Stability in Monocytes: an Overview of the Current Status and Future Perspectives
    G C A T T A C G G C A T genes Review A Dual Face of APE1 in the Maintenance of Genetic Stability in Monocytes: An Overview of the Current Status and Future Perspectives Gabriela Betlej 1,* , Ewelina Bator 1 , Antoni Pyrkosz 2 and Aleksandra Kwiatkowska 1 1 Institute of Physical Culture Studies, College of Medical Sciences, University of Rzeszow, 35-959 Rzeszow, Poland; [email protected] (E.B.); [email protected] (A.K.) 2 Medical College, University of Rzeszow, 35-959 Rzeszow, Poland; [email protected] * Correspondence: [email protected]; Tel.: +48-17-872-32-50 Received: 6 May 2020; Accepted: 8 June 2020; Published: 11 June 2020 Abstract: Monocytes, which play a crucial role in the immune system, are characterized by an enormous sensitivity to oxidative stress. As they lack four key proteins responsible for DNA damage response (DDR) pathways, they are especially prone to reactive oxygen species (ROS) exposure leading to oxidative DNA lesions and, consequently, ROS-driven apoptosis. Although such a phenomenon is of important biological significance in the regulation of monocyte/macrophage/dendritic cells’ balance, it also a challenge for monocytic mechanisms that have to provide and maintain genetic stability of its own DNA. Interestingly, apurinic/apyrimidinic endonuclease 1 (APE1), which is one of the key proteins in two DDR mechanisms, base excision repair (BER) and non-homologous end joining (NHEJ) pathways, operates in monocytic cells, although both BER and NHEJ are impaired in these cells. Thus, on the one hand, APE1 endonucleolytic activity leads to enhanced levels of both single- and double-strand DNA breaks (SSDs and DSBs, respectively) in monocytic DNA that remain unrepaired because of the impaired BER and NHEJ.
    [Show full text]
  • Genetic and Biochemical Characterization of Human AP Endonuclease 1 Mutants Deficient in Nucleotide Incision Repair Activity
    Genetic and Biochemical Characterization of Human AP Endonuclease 1 Mutants Deficient in Nucleotide Incision Repair Activity Aurore Gelin1, Modesto Redrejo-Rodrı´guez2, Jacques Laval2, Olga S. Fedorova3, Murat Saparbaev2, Alexander A. Ishchenko2* 1 CNRS UMR8126, Universite´ Paris-Sud, Institut de Cance´rologie Gustave Roussy, Villejuif, France, 2 CNRS UMR8200 Groupe «Re´paration de l9ADN», Universite´ Paris-Sud, Institut de Cance´rologie Gustave Roussy, Villejuif, France, 3 Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Abstract Background: Human apurinic/apyrimidinic endonuclease 1 (APE1) is a key DNA repair enzyme involved in both base excision repair (BER) and nucleotide incision repair (NIR) pathways. In the BER pathway, APE1 cleaves DNA at AP sites and 39- blocking moieties generated by DNA glycosylases. In the NIR pathway, APE1 incises DNA 59 to a number of oxidatively damaged bases. At present, physiological relevance of the NIR pathway is fairly well established in E. coli, but has yet to be elucidated in human cells. Methodology/Principal Finding: We identified amino acid residues in the APE1 protein that affect its function in either the BER or NIR pathway. Biochemical characterization of APE1 carrying single K98A, R185A, D308A and double K98A/R185A amino acid substitutions revealed that all mutants exhibited greatly reduced NIR and 39R59 exonuclease activities, but were capable of performing BER functions to some extent. Expression of the APE1 mutants deficient in the NIR and exonuclease activities reduced the sensitivity of AP endonuclease-deficient E. coli xth nfo strain to an alkylating agent, methylmethanesulfonate, suggesting that our APE1 mutants are able to repair AP sites.
    [Show full text]
  • Analysis of the Dna Repair/Ribosomal Protein Ap3/Po Gene in Drosophila (Homologue to Human Po)
    Loyola University Chicago Loyola eCommons Dissertations Theses and Dissertations 1993 Analysis of the Dna Repair/Ribosomal Protein Ap3/Po Gene in Drosophila (Homologue to Human Po) David T. Grabowski Loyola University Chicago Follow this and additional works at: https://ecommons.luc.edu/luc_diss Part of the Molecular Biology Commons Recommended Citation Grabowski, David T., "Analysis of the Dna Repair/Ribosomal Protein Ap3/Po Gene in Drosophila (Homologue to Human Po)" (1993). Dissertations. 3110. https://ecommons.luc.edu/luc_diss/3110 This Dissertation is brought to you for free and open access by the Theses and Dissertations at Loyola eCommons. It has been accepted for inclusion in Dissertations by an authorized administrator of Loyola eCommons. For more information, please contact [email protected]. This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 License. Copyright © 1993 David T. Grabowski .LIBRARY ·LOYOLA UNIVERSITY MEDICAL CENTER ANALYSIS OF THE DNA REPAIR/RIBOSOMAL PROTEIN AP3/PO GENE IN DROSOPHILA (HOMOLOGUE TO HUMAN PO) by David T. Grabowski A Dissertation submitted to the Faculty of the Graduate School of Loyola University of Chicago in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy January 1993 Copyright by David T. Grabowski, 1992 All rights reserved. ii ACKNOWLEDGEMENTS I would like to express my gratitude to my director, Dr. Mark R. Kelley for his guidence and his excellent example as a research scientist. My thanks are also extended to members of my committee, Drs. Allen Frankfater, Bill Simmons, Leonard Erickson, and Deborah Hoshizaki for their advice, technical help and constructive criticism of these studies.
    [Show full text]