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Chan RWY, Serpas L, Ni M, Volpi S, Hiraki LT, Tam LS, Rashidfarrokhi A, Wong PCH, Tam LHP, Wang Y, Jiang P, Cheng ASH, Peng W, Han DSC, Tse PPP, Lau PK, Lee WS, Magnasco A, Buti E, Sisirak V, AlMutairi N, Chan KCA, Chiu RWK, Reizis B, Lo YMD. Plasma DNA Profile Associated with DNASE1L3 Gene Mutations: Clinical Observations, Relationships to Nuclease Substrate Preference, and In Vivo Correction. Am J Hum Genet 2020; 107:882-894. [PMID: 33022220 PMCID: PMC7674998 DOI: 10.1016/j.ajhg.2020.09.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/16/2020] [Indexed: 12/30/2022] Open
Abstract
Plasma DNA fragmentomics is an emerging area in cell-free DNA diagnostics and research. In murine models, it has been shown that the extracellular DNase, DNASE1L3, plays a role in the fragmentation of plasma DNA. In humans, DNASE1L3 deficiency causes familial monogenic systemic lupus erythematosus with childhood onset and anti-dsDNA reactivity. In this study, we found that human patients with DNASE1L3 disease-associated gene variations showed aberrations in size and a reduction of a "CC" end motif of plasma DNA. Furthermore, we demonstrated that DNA from DNASE1L3-digested cell nuclei showed a median length of 153 bp with CC motif frequencies resembling plasma DNA from healthy individuals. Adeno-associated virus-based transduction of Dnase1l3 into Dnase1l3-deficient mice restored the end motif profiles to those seen in the plasma DNA of wild-type mice. Our findings demonstrate that DNASE1L3 is an important player in the fragmentation of plasma DNA, which appears to act in a cell-extrinsic manner to regulate plasma DNA size and motif frequency.
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Affiliation(s)
- Rebecca W Y Chan
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China; Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Lee Serpas
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Meng Ni
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China; Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Stefano Volpi
- Clinica Pediatrica e Reumatologia, Centro per le malattie Autoinfiammatorie e Immunodeficienze, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Giannina Gaslini, Via G. Gaslini 5, 16147 Genova, Italy; Dipartimento di Neuroscienze, Riabilitazione, Oftalmologia, Genetica e Scienze Materno-Infantili (DINOGMI), Università degli Studi di Genova, 16132 Genova, Italy
| | - Linda T Hiraki
- Division of Rheumatology, The Hospital for Sick Children, Toronto, ON M5G 1X5, Canada
| | - Lai-Shan Tam
- Department of Medicine & Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Ali Rashidfarrokhi
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Priscilla C H Wong
- Department of Medicine & Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Lydia H P Tam
- Department of Medicine & Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Yueyang Wang
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Peiyong Jiang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China; Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Alice S H Cheng
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China; Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Wenlei Peng
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China; Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Diana S C Han
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China; Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Patty P P Tse
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China; Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Pik Ki Lau
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China; Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Wing-Shan Lee
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China; Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Alberto Magnasco
- Division of Nephrology, Dialysis and Transplantation, Istituto di Ricovero e Cura a Carattere Scientifico, Istituto Giannina Gaslini, 16147 Genova, Italy
| | - Elisa Buti
- Nefrologia e Dialisi, Azienda Ospedaliero Universitaria Meyer, 50139 Firenze, Italy
| | - Vanja Sisirak
- CNRS-UMR 5164, ImmunoConcEpt, Université de Bordeaux, 33076 Bordeaux, France
| | - Nora AlMutairi
- Sabah Hospital, Jaber Al Ahmad Al Jaber Al Sabah Hospital, Kuwait
| | - K C Allen Chan
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China; Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Rossa W K Chiu
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China; Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Boris Reizis
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA.
| | - Y M Dennis Lo
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China; Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China.
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Soni C, Perez OA, Voss WN, Pucella JN, Serpas L, Mehl J, Ching KL, Goike J, Georgiou G, Ippolito GC, Sisirak V, Reizis B. Plasmacytoid Dendritic Cells and Type I Interferon Promote Extrafollicular B Cell Responses to Extracellular Self-DNA. Immunity 2020; 52:1022-1038.e7. [PMID: 32454024 PMCID: PMC7306002 DOI: 10.1016/j.immuni.2020.04.015] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 03/13/2020] [Accepted: 04/23/2020] [Indexed: 01/06/2023]
Abstract
Class-switched antibodies to double-stranded DNA (dsDNA) are prevalent and pathogenic in systemic lupus erythematosus (SLE), yet mechanisms of their development remain poorly understood. Humans and mice lacking secreted DNase DNASE1L3 develop rapid anti-dsDNA antibody responses and SLE-like disease. We report that anti-DNA responses in Dnase1l3-/- mice require CD40L-mediated T cell help, but proceed independently of germinal center formation via short-lived antibody-forming cells (AFCs) localized to extrafollicular regions. Type I interferon (IFN-I) signaling and IFN-I-producing plasmacytoid dendritic cells (pDCs) facilitate the differentiation of DNA-reactive AFCs in vivo and in vitro and are required for downstream manifestations of autoimmunity. Moreover, the endosomal DNA sensor TLR9 promotes anti-dsDNA responses and SLE-like disease in Dnase1l3-/- mice redundantly with another nucleic acid-sensing receptor, TLR7. These results establish extrafollicular B cell differentiation into short-lived AFCs as a key mechanism of anti-DNA autoreactivity and reveal a major contribution of pDCs, endosomal Toll-like receptors (TLRs), and IFN-I to this pathway.
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Affiliation(s)
- Chetna Soni
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Oriana A Perez
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - William N Voss
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Joseph N Pucella
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Lee Serpas
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Justin Mehl
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Krystal L Ching
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Jule Goike
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - George Georgiou
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Gregory C Ippolito
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Department of Oncology, Dell Medical School, University of Texas at Austin, Austin, TX 78712, USA
| | - Vanja Sisirak
- CNRS-UMR 5164, ImmunoConcEpt, Université de Bordeaux, 33076 Bordeaux, France.
| | - Boris Reizis
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Medicine, New York University Grossman School of Medicine, New York, NY 10016, USA.
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Olsen MB, Hildrestrand GA, Scheffler K, Vinge LE, Alfsnes K, Palibrk V, Wang J, Neurauter CG, Luna L, Johansen J, Øgaard JDS, Ohm IK, Slupphaug G, Kuśnierczyk A, Fiane AE, Brorson SH, Zhang L, Gullestad L, Louch WE, Iversen PO, Østlie I, Klungland A, Christensen G, Sjaastad I, Sætrom P, Yndestad A, Aukrust P, Bjørås M, Finsen AV. NEIL3-Dependent Regulation of Cardiac Fibroblast Proliferation Prevents Myocardial Rupture. Cell Rep 2017; 18:82-92. [PMID: 28052262 DOI: 10.1016/j.celrep.2016.12.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 10/06/2016] [Accepted: 12/01/2016] [Indexed: 12/15/2022] Open
Abstract
Myocardial infarction (MI) triggers a reparative response involving fibroblast proliferation and differentiation driving extracellular matrix modulation necessary to form a stabilizing scar. Recently, it was shown that a genetic variant of the base excision repair enzyme NEIL3 was associated with increased risk of MI in humans. Here, we report elevated myocardial NEIL3 expression in heart failure patients and marked myocardial upregulation of Neil3 after MI in mice, especially in a fibroblast-enriched cell fraction. Neil3-/- mice show increased mortality after MI caused by myocardial rupture. Genome-wide analysis of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) reveals changes in the cardiac epigenome, including in genes related to the post-MI transcriptional response. Differentially methylated genes are enriched in pathways related to proliferation and myofibroblast differentiation. Accordingly, Neil3-/- ruptured hearts show increased proliferation of fibroblasts and myofibroblasts. We propose that NEIL3-dependent modulation of DNA methylation regulates cardiac fibroblast proliferation and thereby affects extracellular matrix modulation after MI.
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Affiliation(s)
- Maria B Olsen
- Research Institute of Internal Medicine, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; Center for Heart Failure Research, University of Oslo, 0317 Oslo, Norway; K.G. Jebsen Inflammation Research Centre, University of Oslo, 0317 Oslo, Norway
| | - Gunn A Hildrestrand
- Department of Microbiology, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway
| | - Katja Scheffler
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Leif Erik Vinge
- Research Institute of Internal Medicine, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; Department of Cardiology, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; Center for Heart Failure Research, University of Oslo, 0317 Oslo, Norway
| | - Katrine Alfsnes
- Research Institute of Internal Medicine, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; Center for Heart Failure Research, University of Oslo, 0317 Oslo, Norway; K.G. Jebsen Inflammation Research Centre, University of Oslo, 0317 Oslo, Norway
| | - Vuk Palibrk
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Junbai Wang
- Department of Pathology, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway
| | - Christine G Neurauter
- Department of Microbiology, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway
| | - Luisa Luna
- Department of Microbiology, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway
| | - Jostein Johansen
- Bioinformatics Core Facility-BioCore , Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Jonas D S Øgaard
- Research Institute of Internal Medicine, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway
| | - Ingrid K Ohm
- Research Institute of Internal Medicine, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; Center for Heart Failure Research, University of Oslo, 0317 Oslo, Norway
| | - Geir Slupphaug
- Proteomics and Metabolomics Core Facility-PROMEC, Norwegian University of Science and Technology, 7491 Trondheim, Norway; Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Anna Kuśnierczyk
- Proteomics and Metabolomics Core Facility-PROMEC, Norwegian University of Science and Technology, 7491 Trondheim, Norway; Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Arnt E Fiane
- Department of Cardiothoracic Surgery, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway
| | - Sverre-Henning Brorson
- Department of Pathology, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway
| | - Lili Zhang
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway
| | - Lars Gullestad
- Research Institute of Internal Medicine, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; Department of Cardiology, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; Center for Heart Failure Research, University of Oslo, 0317 Oslo, Norway
| | - William E Louch
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; Center for Heart Failure Research, University of Oslo, 0317 Oslo, Norway
| | - Per Ole Iversen
- Department of Haematology, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; Department of Nutrition, University of Oslo, 0317 Oslo, Norway
| | - Ingunn Østlie
- Department of Pathology, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway
| | - Arne Klungland
- Department of Microbiology, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway
| | - Geir Christensen
- Department of Cardiology, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; Center for Heart Failure Research, University of Oslo, 0317 Oslo, Norway
| | - Ivar Sjaastad
- Department of Cardiology, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; Center for Heart Failure Research, University of Oslo, 0317 Oslo, Norway
| | - Pål Sætrom
- Bioinformatics Core Facility-BioCore , Norwegian University of Science and Technology, 7491 Trondheim, Norway; Department of Computer and Information Science, Norwegian University of Science and Technology, 7491 Trondheim, Norway; Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Arne Yndestad
- Research Institute of Internal Medicine, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; Center for Heart Failure Research, University of Oslo, 0317 Oslo, Norway; K.G. Jebsen Inflammation Research Centre, University of Oslo, 0317 Oslo, Norway
| | - Pål Aukrust
- Research Institute of Internal Medicine, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; K.G. Jebsen Inflammation Research Centre, University of Oslo, 0317 Oslo, Norway
| | - Magnar Bjørås
- Department of Microbiology, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway.
| | - Alexandra V Finsen
- Research Institute of Internal Medicine, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; Department of Cardiology, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway; Center for Heart Failure Research, University of Oslo, 0317 Oslo, Norway
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Massaad MJ, Zhou J, Tsuchimoto D, Chou J, Jabara H, Janssen E, Glauzy S, Olson BG, Morbach H, Ohsumi TK, Schmitz K, Kyriacos M, Kane J, Torisu K, Nakabeppu Y, Notarangelo LD, Chouery E, Megarbane A, Kang PB, Al-Idrissi E, Aldhekri H, Meffre E, Mizui M, Tsokos GC, Manis JP, Al-Herz W, Wallace SS, Geha RS. Deficiency of base excision repair enzyme NEIL3 drives increased predisposition to autoimmunity. J Clin Invest 2016; 126:4219-4236. [PMID: 27760045 DOI: 10.1172/jci85647] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 09/06/2016] [Indexed: 12/17/2022] Open
Abstract
Alterations in the apoptosis of immune cells have been associated with autoimmunity. Here, we have identified a homozygous missense mutation in the gene encoding the base excision repair enzyme Nei endonuclease VIII-like 3 (NEIL3) that abolished enzymatic activity in 3 siblings from a consanguineous family. The NEIL3 mutation was associated with fatal recurrent infections, severe autoimmunity, hypogammaglobulinemia, and impaired B cell function in these individuals. The same homozygous NEIL3 mutation was also identified in an asymptomatic individual who exhibited elevated levels of serum autoantibodies and defective peripheral B cell tolerance, but normal B cell function. Further analysis of the patients revealed an absence of LPS-responsive beige-like anchor (LRBA) protein expression, a known cause of immunodeficiency. We next examined the contribution of NEIL3 to the maintenance of self-tolerance in Neil3-/- mice. Although Neil3-/- mice displayed normal B cell function, they exhibited elevated serum levels of autoantibodies and developed nephritis following treatment with poly(I:C) to mimic microbial stimulation. In Neil3-/- mice, splenic T and B cells as well as germinal center B cells from Peyer's patches showed marked increases in apoptosis and cell death, indicating the potential release of self-antigens that favor autoimmunity. These findings demonstrate that deficiency in NEIL3 is associated with increased lymphocyte apoptosis, autoantibodies, and predisposition to autoimmunity.
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Pawaria S, Moody KL, Busto P, Nündel K, Baum R, Sharma S, Gravallese EM, Fitzgerald KA, Marshak-Rothstein A. An unexpected role for RNA-sensing toll-like receptors in a murine model of DNA accrual. Clin Exp Rheumatol 2015; 33:S70-S73. [PMID: 26457825 PMCID: PMC4731237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 09/01/2015] [Indexed: 06/05/2023]
Abstract
OBJECTIVES The goal of this study was to determine whether endosomal Toll-like receptors (TLRs) contribute to the clinical manifestation of systemic autoimmunity exhibited by mice that lack the lysosomal nuclease DNaseII. METHODS DNaseII/IFNaR double deficient mice were intercrossed with Unc93b13d/3d mice to generate DNaseII-/-mice with non-functional endosomal TLRs. The resulting triple deficient mice were evaluated for arthritis, autoantibody production, splenomegaly, and extramedullary haematopoiesis. B cells from both strains were evaluated for their capacity to respond to endogenous DNA by using small oligonucleotide based TLR9D ligands and a novel class of bifunctional anti-DNA antibodies. RESULTS Mice that fail to express DNaseII, IFNaR, and Unc93b1 still develop arthritis but do not make autoantibodies, develop splenomegaly, or exhibit extramedullary haematopoiesis. DNaseII-/- IFNaR-/- B cells can respond to synthetic ODNs, but not to endogenous dsDNA. CONCLUSIONS RNA-reactive TLRs, presumably TLR7, are required for autoantibody production, splenomegaly, and extramedullary haematopoiesis in the DNaseII-/- model of systemic autoimmunity.
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Affiliation(s)
- Sudesh Pawaria
- Department of Medicine, University of Massachusetts School of Medicine, Worcester, MA, USA
| | - Krishna L Moody
- Department of Medicine, University of Massachusetts School of Medicine, Worcester, and Department of Microbiology, Boston University School of Medicine, Boston, USA
| | - Patricia Busto
- Department of Medicine, University of Massachusetts School of Medicine, Worcester, MA, USA
| | - Kerstin Nündel
- Department of Medicine, University of Massachusetts School of Medicine, Worcester, MA, USA
| | - Rebecca Baum
- Department of Medicine, University of Massachusetts School of Medicine, Worcester, MA, USA
| | - Shruti Sharma
- Department of Medicine, University of Massachusetts School of Medicine, Worcester, MA, USA
| | - Ellen M Gravallese
- Department of Medicine, University of Massachusetts School of Medicine, Worcester, MA, USA
| | - Katherine A Fitzgerald
- Department of Medicine, University of Massachusetts School of Medicine, Worcester, MA, USA
| | - Ann Marshak-Rothstein
- Department of Medicine, University of Massachusetts School of Medicine, Worcester, MA, USA.
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Mishra M, Sharma A, Shukla AK, Pragya P, Murthy RC, de Pomerai D, Dwivedi UN, Chowdhuri DK. Transcriptomic analysis provides insights on hexavalent chromium induced DNA double strand breaks and their possible repair in midgut cells of Drosophila melanogaster larvae. Mutat Res 2013; 747-748:28-39. [PMID: 23628323 DOI: 10.1016/j.mrfmmm.2013.04.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Revised: 04/16/2013] [Accepted: 04/19/2013] [Indexed: 06/02/2023]
Abstract
Hexavalent chromium [Cr(VI)] is a well known mutagen and carcinogen. Since genomic instability due to generation of double strand breaks (DSBs) is causally linked to carcinogenesis, we tested a hypothesis that Cr(VI) causes in vivo generation of DSBs and elicits DNA damage response. We fed repair proficient Drosophila melanogaster (Oregon R(+)) larvae Cr(VI) (20.0μg/ml) mixed food for 24 and 48h and observed a significant (p<0.05) induction of DSBs in their midgut cells after 48h using neutral Comet assay. Global gene expression profiling in Cr(VI)-exposed Oregon R(+) larvae unveiled mis-regulation of DSBs responsive repair genes both after 24 and 48h. In vivo generation of DSBs in exposed Drosophila was confirmed by an increased pH2Av immunostaining along with the activation of cell cycle regulation genes. Analysis of mis-regulated genes grouped under DSB response by GOEAST indicated the participation of non-homologous end joining (NHEJ) DSB repair pathway. We selected two strains, one mutant (ligIV) and another ku80-RNAi (knockdown of ku80), whose functions are essentially linked to NHEJ-DSB repair pathway. As a proof of principle, we compared the DSBs generation in larvae of these two strains with that of repair proficient Oregon R(+). Along with this, DSBs generation in spn-A and okr [essential genes in homologous recombination repair (HR) pathway] mutants was also tested for the possible involvement of HR-DSB repair. A significantly increased DSBs generation in the exposed ku80-RNAi and ligIV (mutant) larvae because of impaired repair, concomitant with an insignificant DSBs generation in okr and spn-A mutant larvae indicates an active participation of NHEJ repair pathway. The study, first of its kind to our knowledge, while providing evidences for in vivo generation of DSBs in Cr(VI) exposed Drosophila larvae, assumes significance for its relevance to higher organisms due to causal link between DSB generation and Cr(VI)-induced carcinogenesis.
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Affiliation(s)
- Manish Mishra
- Embryotoxicology Section and Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research CSIR-IITR, Lucknow 226001, Uttar Pradesh, India
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7
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Giralt A, Sanchis D, Cherubini M, Ginés S, Cañas X, Comella JX, Alberch J. Neurobehavioral characterization of Endonuclease G knockout mice reveals a new putative molecular player in the regulation of anxiety. Exp Neurol 2013; 247:122-9. [PMID: 23603365 DOI: 10.1016/j.expneurol.2013.03.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2013] [Revised: 03/27/2013] [Accepted: 03/31/2013] [Indexed: 01/03/2023]
Abstract
Endonuclease G (EndoG) has been largely related with a role in the modulation of a caspase-independent cell death pathway in many cellular systems. However, whether this protein plays a specific role in the brain remains to be elucidated. Here we have characterized the behavioral phenotype of EndoG(-/-) null mice and the expression of the nuclease among brain regions. EndoG(-/-) mice showed normal neurological function, learning, motor coordination and spontaneous behaviors. However, these animals displayed lower activity in a running wheel and, strikingly, they were consistently less anxious compared to EndoG(+/+) mice in different tests for anxiety such as plus maze and dark-light test. We next evaluated the expression of EndoG in different brain regions of wild type mice and found that it was expressed in all over but specially enriched in the striatum. Further, subcellular biochemical experiments in neocortical samples from wild type mice revealed that EndoG is localized in pre-synaptic compartments but not in post-synaptic compartments. Altogether these findings suggest that EndoG could play a highly specific role in the regulation of anxiety by modulating synaptic components.
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Affiliation(s)
- Albert Giralt
- Departament de Biologia Cel·lular, Immunologia i Neurociències, Facultat de Medicina, Universitat de Barcelona, Spain
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Ward TA, Dudášová Z, Sarkar S, Bhide MR, Vlasáková D, Chovanec M, McHugh PJ. Components of a Fanconi-like pathway control Pso2-independent DNA interstrand crosslink repair in yeast. PLoS Genet 2012; 8:e1002884. [PMID: 22912599 PMCID: PMC3415447 DOI: 10.1371/journal.pgen.1002884] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 06/22/2012] [Indexed: 12/20/2022] Open
Abstract
Fanconi anemia (FA) is a devastating genetic disease, associated with genomic instability and defects in DNA interstrand cross-link (ICL) repair. The FA repair pathway is not thought to be conserved in budding yeast, and although the yeast Mph1 helicase is a putative homolog of human FANCM, yeast cells disrupted for MPH1 are not sensitive to ICLs. Here, we reveal a key role for Mph1 in ICL repair when the Pso2 exonuclease is inactivated. We find that the yeast FANCM ortholog Mph1 physically and functionally interacts with Mgm101, a protein previously implicated in mitochondrial DNA repair, and the MutSα mismatch repair factor (Msh2-Msh6). Co-disruption of MPH1, MGM101, MSH6, or MSH2 with PSO2 produces a lesion-specific increase in ICL sensitivity, the elevation of ICL-induced chromosomal rearrangements, and persistence of ICL-associated DNA double-strand breaks. We find that Mph1-Mgm101-MutSα directs the ICL-induced recruitment of Exo1 to chromatin, and we propose that Exo1 is an alternative 5′-3′ exonuclease utilised for ICL repair in the absence of Pso2. Moreover, ICL-induced Rad51 chromatin loading is delayed when both Pso2 and components of the Mph1-Mgm101-MutSα and Exo1 pathway are inactivated, demonstrating that the homologous recombination stages of ICL repair are inhibited. Finally, the FANCJ- and FANCP-related factors Chl1 and Slx4, respectively, are also components of the genetic pathway controlled by Mph1-Mgm101-MutSα. Together this suggests that a prototypical FA–related ICL repair pathway operates in budding yeast, which acts redundantly with the pathway controlled by Pso2, and is required for the targeting of Exo1 to chromatin to execute ICL repair. Individuals with Fanconi anemia (FA) suffer from bone marrow failure and from elevated rates of haematological and solid malignancy. Moreover, FA patients exhibit extreme sensitivity to DNA interstrand cross-links (ICLs), but not other forms of DNA damage. Despite recent progress in identifying and characterising FA factors, little is known about the mechanistic basis of the ICL repair defect in FA. The identification and characterisation of FA–like pathways in simple model eukaryotes, amenable to genetic dissection, would clearly accelerate progress. Here, we have identified an ICL repair pathway in budding yeast that has significant similarities to the FA pathway and that acts in parallel to an established pathway controlled by the Pso2 exonuclease. We have discovered that a key component of this pathway, the FANCM-like helicase, Mph1, interacts and collaborates with a mismatch repair factor (MutSα) and a novel nuclear DNA repair factor Mgm101 to control ICL repair. We also found that a central role of these factors is to recruit Exonuclease 1 (Exo1) to ICL-damaged chromatin, and propose that this factor acts redundantly with Pso2 to execute the exonucleolytic processing of ICLs. Our findings reveal new mechanistic insights into the control of ICL repair by FA–like proteins in an important model organism.
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Affiliation(s)
- Thomas A. Ward
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Zuzana Dudášová
- Laboratory of Molecular Genetics, Cancer Research Institute, Bratislava, Slovak Republic
| | - Sovan Sarkar
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Mangesh R. Bhide
- Department of Microbiology and Immunology, University of Veterinary Medicine, Košice, Slovak Republic
| | - Danuša Vlasáková
- Laboratory of Molecular Genetics, Cancer Research Institute, Bratislava, Slovak Republic
| | - Miroslav Chovanec
- Laboratory of Molecular Genetics, Cancer Research Institute, Bratislava, Slovak Republic
| | - Peter J. McHugh
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- * E-mail:
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9
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McDermott-Roe C, Ye J, Ahmed R, Sun XM, Serafín A, Ware J, Bottolo L, Muckett P, Cañas X, Zhang J, Rowe GC, Buchan R, Lu H, Braithwaite A, Mancini M, Hauton D, Martí R, García-Arumí E, Hubner N, Jacob H, Serikawa T, Zidek V, Papousek F, Kolar F, Cardona M, Ruiz-Meana M, García-Dorado D, Comella JX, Felkin LE, Barton PJR, Arany Z, Pravenec M, Petretto E, Sanchis D, Cook SA. Endonuclease G is a novel determinant of cardiac hypertrophy and mitochondrial function. Nature 2011; 478:114-8. [PMID: 21979051 PMCID: PMC3189541 DOI: 10.1038/nature10490] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2011] [Accepted: 08/17/2011] [Indexed: 12/31/2022]
Abstract
Left ventricular mass (LVM) is a highly heritable trait and an independent risk factor for all-cause mortality. So far, genome-wide association studies have not identified the genetic factors that underlie LVM variation, and the regulatory mechanisms for blood-pressure-independent cardiac hypertrophy remain poorly understood. Unbiased systems genetics approaches in the rat now provide a powerful complementary tool to genome-wide association studies, and we applied integrative genomics to dissect a highly replicated, blood-pressure-independent LVM locus on rat chromosome 3p. Here we identified endonuclease G (Endog), which previously was implicated in apoptosis but not hypertrophy, as the gene at the locus, and we found a loss-of-function mutation in Endog that is associated with increased LVM and impaired cardiac function. Inhibition of Endog in cultured cardiomyocytes resulted in an increase in cell size and hypertrophic biomarkers in the absence of pro-hypertrophic stimulation. Genome-wide network analysis unexpectedly implicated ENDOG in fundamental mitochondrial processes that are unrelated to apoptosis. We showed direct regulation of ENDOG by ERR-α and PGC1α (which are master regulators of mitochondrial and cardiac function), interaction of ENDOG with the mitochondrial genome and ENDOG-mediated regulation of mitochondrial mass. At baseline, the Endog-deleted mouse heart had depleted mitochondria, mitochondrial dysfunction and elevated levels of reactive oxygen species, which were associated with enlarged and steatotic cardiomyocytes. Our study has further established the link between mitochondrial dysfunction, reactive oxygen species and heart disease and has uncovered a role for Endog in maladaptive cardiac hypertrophy.
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Affiliation(s)
- Chris McDermott-Roe
- Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 ONN, UK
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10
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Kim MS, Kondo T, Takada I, Youn MY, Yamamoto Y, Takahashi S, Matsumoto T, Fujiyama S, Shirode Y, Yamaoka I, Kitagawa H, Takeyama KI, Shibuya H, Ohtake F, Kato S. DNA demethylation in hormone-induced transcriptional derepression. Nature 2009; 461:1007-12. [PMID: 19829383 DOI: 10.1038/nature08456] [Citation(s) in RCA: 199] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2008] [Accepted: 08/24/2009] [Indexed: 12/23/2022]
Abstract
Epigenetic modifications at the histone level affect gene regulation in response to extracellular signals. However, regulated epigenetic modifications at the DNA level, especially active DNA demethylation, in gene activation are not well understood. Here we report that DNA methylation/demethylation is hormonally switched to control transcription of the cytochrome p450 27B1 (CYP27B1) gene. Reflecting vitamin-D-mediated transrepression of the CYP27B1 gene by the negative vitamin D response element (nVDRE), methylation of CpG sites ((5m)CpG) is induced by vitamin D in this gene promoter. Conversely, treatment with parathyroid hormone, a hormone known to activate the CYP27B1 gene, induces active demethylation of the (5m)CpG sites in this promoter. Biochemical purification of a complex associated with the nVDRE-binding protein (VDIR, also known as TCF3) identified two DNA methyltransferases, DNMT1 and DNMT3B, for methylation of CpG sites, as well as a DNA glycosylase, MBD4 (ref. 10). Protein-kinase-C-phosphorylated MBD4 by parathyroid hormone stimulation promotes incision of methylated DNA through glycosylase activity, and a base-excision repair process seems to complete DNA demethylation in the MBD4-bound promoter. Such parathyroid-hormone-induced DNA demethylation and subsequent transcriptional derepression are impaired in Mbd4(-/-) mice. Thus, the present findings suggest that methylation switching at the DNA level contributes to the hormonal control of transcription.
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Affiliation(s)
- Mi-Sun Kim
- ERATO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchisi, Saitama 332-0012, Japan
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11
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Kawane K. [Molecular mechanisms and physiological roles of DNA degradation]. Seikagaku 2009; 81:765-779. [PMID: 19882947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Affiliation(s)
- Kohki Kawane
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Sakyo, Kyoto, Japan
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12
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Kawane K, Ohtani M, Miwa K, Kizawa T, Kanbara Y, Yoshioka Y, Yoshikawa H, Nagata S. Chronic polyarthritis caused by mammalian DNA that escapes from degradation in macrophages. Nature 2006; 443:998-1002. [PMID: 17066036 DOI: 10.1038/nature05245] [Citation(s) in RCA: 355] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2006] [Accepted: 09/14/2006] [Indexed: 11/09/2022]
Abstract
A large amount of chromosomal DNA is degraded during programmed cell death and definitive erythropoiesis. DNase II is an enzyme that digests the chromosomal DNA of apoptotic cells and nuclei expelled from erythroid precursor cells after macrophages have engulfed them. Here we show that DNase II-/-IFN-IR-/- mice and mice with an induced deletion of the DNase II gene develop a chronic polyarthritis resembling human rheumatoid arthritis. A set of cytokine genes was strongly activated in the affected joints of these mice, and their serum contained high levels of anti-cyclic citrullinated peptide antibody, rheumatoid factor and matrix metalloproteinase-3. Early in the pathogenesis, expression of the gene encoding tumour necrosis factor (TNF)-alpha was upregulated in the bone marrow, and administration of anti-TNF-alpha antibody prevented the development of arthritis. These results indicate that if macrophages cannot degrade mammalian DNA from erythroid precursors and apoptotic cells, they produce TNF-alpha, which activates synovial cells to produce various cytokines, leading to the development of chronic polyarthritis.
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Affiliation(s)
- Kohki Kawane
- Department of Genetics, Osaka University, Osaka 565-0871, Japan
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13
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Stumpf M, Waskow C, Krötschel M, van Essen D, Rodriguez P, Zhang X, Guyot B, Roeder RG, Borggrefe T. The mediator complex functions as a coactivator for GATA-1 in erythropoiesis via subunit Med1/TRAP220. Proc Natl Acad Sci U S A 2006; 103:18504-9. [PMID: 17132730 PMCID: PMC1693692 DOI: 10.1073/pnas.0604494103] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Mediator complex forms the bridge between transcriptional activators and RNA polymerase II. Mediator subunit Med1/TRAP220 is a key component of Mediator originally found to associate with nuclear hormone receptors. Med1 deficiency causes lethality at embryonic day 11.5 because of defects in heart and placenta development. Here we show that Med1-deficient 10.5 days postcoitum embryos are anemic but have normal numbers of hematopoietic progenitor cells. Med1-deficient progenitor cells have a defect in forming erythroid burst-forming units (BFU-E) and colony-forming units (CFU-E), but not in forming myeloid colonies. At the molecular level, we demonstrate that Med1 interacts physically with the erythroid master regulator GATA-1. In transcription assays, Med1 deficiency leads to a defect in GATA-1-mediated transactivation. In chromatin immunoprecipitation experiments, we find Mediator components at GATA-1-occupied enhancer sites. Thus, we conclude that Mediator subunit Med1 acts as a pivotal coactivator for GATA-1 in erythroid development.
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Affiliation(s)
- Melanie Stumpf
- *Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology, Stübeweg 51, 79108 Freiburg, Germany
- Department of Immunology, University Clinics Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Claudia Waskow
- Department of Immunology, University Clinics Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
- Molecular Immunology, The Rockefeller University, 1230 York Avenue, New York, NY 10021
| | - Marit Krötschel
- *Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology, Stübeweg 51, 79108 Freiburg, Germany
- Department of Immunology, University Clinics Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Dominic van Essen
- *Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology, Stübeweg 51, 79108 Freiburg, Germany
| | - Patrick Rodriguez
- *Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology, Stübeweg 51, 79108 Freiburg, Germany
| | | | - Boris Guyot
- Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom; and
| | | | - Tilman Borggrefe
- *Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology, Stübeweg 51, 79108 Freiburg, Germany
- Department of Immunology, University Clinics Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
- To whom reprint requests should be addressed.
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14
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Seong CS, Varela-Ramirez A, Aguilera RJ. DNase II deficiency impairs innate immune function in Drosophila. Cell Immunol 2006; 240:5-13. [PMID: 16854402 PMCID: PMC2430755 DOI: 10.1016/j.cellimm.2006.05.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2006] [Revised: 05/11/2006] [Accepted: 05/12/2006] [Indexed: 01/08/2023]
Abstract
DNase II enzymes are highly conserved proteins that are required for the degradation of DNA within phagolysosomes. Engulfment of apoptotic cells and/or bacteria by phagocytic cells requires the function of DNase II to completely destroy ingested DNA. Mutation of the dnase II gene results in an increase of undegraded apoptotic DNA within phagocytic cells in mice and nematodes. Additionally, reduction of DNase II enzymatic activity in Drosophila melanogaster has been shown to lead to increased accumulation of DNA in the ovaries. Due to the importance of DNA clearance during infection, we hypothesized that a severe reduction of DNase II activity would result in diminished immune function and viability. To test this hypothesis, we knocked down DNase II activity in flies using RNAi. As expected, expression of a dnase II-RNAi construct in flies resulted in a dramatic reduction of DNase II activity and a significant decrease in total hemocyte numbers. Furthermore, infection of dnase II-RNAi flies with Gram negative or positive bacteria resulted in a severe reduction in fly viability. These results confirm that DNase II and the ability to clear macromolecular DNA is essential for maintaining proper immune function in Drosophila.
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Affiliation(s)
- Chang-Soo Seong
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX 79968-0519, USA
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15
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Flajollet S, Lefebvre B, Rachez C, Lefebvre P. Distinct Roles of the Steroid Receptor Coactivator 1 and of MED1 in Retinoid-induced Transcription and Cellular Differentiation. J Biol Chem 2006; 281:20338-48. [PMID: 16723356 DOI: 10.1074/jbc.m603023200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Retinoic acid receptors (RARs) are the molecular relays of retinoid action on transcription, cellular differentiation and apoptosis. Transcriptional activation of retinoid-regulated promoters requires the dismissal of corepressors and the recruitment of coactivators to promoter-bound RAR. RARs recruit in vitro a plethora of coactivators whose actual contribution to retinoid-induced transcription is poorly characterized in vivo. Embryonal carcinoma P19 cells, which are highly sensitive to retinoids, were depleted from archetypical coactivators by RNAi. SRC1-deficient P19 cells showed severely compromised retinoid-induced responses, in agreement with the supposed role of SRC1 as a RAR coactivator. Unexpectedly, Med1/TRAP220/DRIP205-depleted cells exhibited an exacerbated response to retinoids, both in terms transcriptional responses and of cellular differentiation. Med1 depletion affected TFIIH and cdk9 detection at the prototypical retinoid-regulated RARbeta2 promoter, and favored a higher RNA polymerase II detection in transcribed regions of the RARbeta2 gene. Furthermore, the nature of the ligand impacted strongly on the ability of RARs to interact with a given coactivator and to activate transcription in intact cells. Thus RAR accomplishes transcriptional activation as a function of the ligand structure, by recruiting regulatory complexes which control distinct molecular events at retinoid-regulated promoters.
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16
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Okabe Y, Kawane K, Akira S, Taniguchi T, Nagata S. Toll-like receptor-independent gene induction program activated by mammalian DNA escaped from apoptotic DNA degradation. ACTA ACUST UNITED AC 2006; 202:1333-9. [PMID: 16301743 PMCID: PMC2212973 DOI: 10.1084/jem.20051654] [Citation(s) in RCA: 210] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Deoxyribonuclease (DNase) II in macrophages cleaves the DNA of engulfed apoptotic cells and of nuclei expelled from erythroid precursor cells. DNase II–deficient mouse embryos accumulate undigested DNA in macrophages, and die in feto because of the activation of the interferonβ (IFNβ) gene. Here, we found that the F4/80-positive macrophages in DNase II−/− fetal liver specifically produce a set of cytokines such as IFNβ, TNFα, and CXCL10. Whereas, IFN-inducible genes (2′5′-oligo(A) synthetase, IRF7, and ISG15) were expressed not only in macrophages but also in other F4/80-negative cells. When DNase II−/− macrophages or embryonal fibroblasts engulfed apoptotic cells, they expressed the IFNβ and CXCL10 genes. The ablation of Toll-like receptor (TLR) 3 and 9, or their adaptor molecules (MyD88 and TRIF), had no effect on the lethality of the DNase II−/− mice. These results indicate that there is a TLR-independent sensing mechanism to activate the innate immunity for the endogenous DNA escaping lysosomal degradation.
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Affiliation(s)
- Yasutaka Okabe
- Department of Genetics, Osaka University Medical School, Japan
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17
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Park SW, Li G, Lin YP, Barrero MJ, Ge K, Roeder RG, Wei LN. Thyroid hormone-induced juxtaposition of regulatory elements/factors and chromatin remodeling of Crabp1 dependent on MED1/TRAP220. Mol Cell 2005; 19:643-53. [PMID: 16137621 DOI: 10.1016/j.molcel.2005.08.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2005] [Revised: 07/20/2005] [Accepted: 08/10/2005] [Indexed: 11/24/2022]
Abstract
The cellular retinoic acid binding protein I gene is induced by thyroid hormone (T3) through a T3 response element (TRE) approximately 1 kb upstream of the basal promoter. The upstream region is organized into a positioned nucleosomal array with the N1 nucleosome spanning the GC box region. T3 induces apparent interactions between chromatin segments containing the TRE and the GC box regions and the sliding of upstream nucleosomes toward N1 with concomitant N1 remodeling. Concurrently, the chromatin-remodeling factor BRM is replaced by BRG1 and histones are hyperacetylated. All these events are abolished in Med1/Trap220 null cells, indicating a key role for TRAP/Mediator in these processes. A MED1/TRAP220-containing Mediator complex constitutively occupies the GC box region but not the TRE, serving as a nexus for distal and proximal factors. This indicates new TRAP/Mediator functions in facilitating ultimate recruitment and function of RNA polymerase II and the general transcription machinery.
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Affiliation(s)
- Sung Wook Park
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
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18
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Takata KI, Shimanouchi K, Yamaguchi M, Murakami S, Ishikawa G, Takeuchi R, Kanai Y, Ruike T, Nakamura RI, Abe Y, Sakaguchi K. Damaged DNA binding protein 1 in Drosophila defense reactions. Biochem Biophys Res Commun 2004; 323:1024-31. [PMID: 15381102 DOI: 10.1016/j.bbrc.2004.08.182] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2004] [Indexed: 10/26/2022]
Abstract
We have focused attention on functions of Drosophila damaged DNA binding protein 1 (D-DDB1) in Drosophila hematopoiesis and previously reported that its whole body dsRNA over-expression using a GAL4-UAS targeted expression system results in melanotic tumors and complete lethality. Since the lesions appear to arise as a normal and heritable response to abnormal development, forming groups of cells that are recognized by the immune system and encapsulated in melanized cuticle, D-DDB1 appears to be an essential development-associated factor in Drosophila. To probe the possibility that it contributes to hemocyte development, we used a collagen promoter-GAL4 strain to over-express dsRNA of D-DDB1 in Drosophila hemocytes. The D-DDB1 gene silencing caused melanotic tumors and mortality at the end of larval development. Similarly, it interfered with melanization and synthesis of antimicrobial peptides. Transgenic flies with D-DDB1 gene silencing were found to accumulate abnormal large blood cells, reminiscent of human leukemia, suggesting that D-DDB1 has functions in hemocyte development.
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Affiliation(s)
- Kei-ichi Takata
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda-shi, Chiba-ken 278-8510, Japan
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19
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Yoshida H, Okabe Y, Kawane K, Fukuyama H, Nagata S. Lethal anemia caused by interferon-beta produced in mouse embryos carrying undigested DNA. Nat Immunol 2004; 6:49-56. [PMID: 15568025 DOI: 10.1038/ni1146] [Citation(s) in RCA: 293] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2004] [Accepted: 11/09/2004] [Indexed: 01/09/2023]
Abstract
The livers of DNase II-deficient mouse embryos contain many macrophages carrying undigested DNA, and the embryos die in utero. Here we report that erythroid precursor cells underwent apoptosis in the livers of DNase II-deficient embryos and that in the liver, interferon-beta mRNA was expressed by the resident macrophages. When the DNase II-deficient mice were crossed with mice deficient in type I interferon receptor, the resultant 'double-mutant' mice were born healthy. The double-mutant embryos expressed interferon-beta mRNA, but the expression of a subset of the interferon-responsive genes dysregulated in DNase II-deficient embryos was restored to normal. These results indicate that the inability to degrade DNA derived from erythroid precursors results in interferon-beta production that induces expression of a specific set of interferon-responsive genes associated with embryonic lethality in DNase II-deficient mice.
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Affiliation(s)
- Hideyuki Yoshida
- Department of Genetics, Osaka University Medical School, 2-2 Yamada-oka, Suita, Osaka 565-0871, Japan
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20
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Abstract
Class switch recombination (CSR) is a region-specific, transcriptionally regulated, nonhomologous recombinational process that is initiated by activation-induced cytidine deaminase (AID). The initial lesions in the switch (S) regions are processed and resolved, leading to a recombination of the two S regions involved. The mechanism involved in the repair and ligation of the broken DNA ends is however still unclear. Here, we describe that switching is less efficient in cells from patients with Mre11 deficiency (Ataxia-Telangiectasia-like disorder, ATLD) and, more importantly, that the switch recombination junctions resulting from the in vivo switching events are aberrant. There was a trend toward an increased usage of microhomology (> or =4 bp) at the switch junctions in both ATLD and Nijmegen breakage syndrome (NBS) patients. However, the DNA ends were not joined as "perfectly" as those from Ataxia-Telangiectasia (A-T) patients and 1-2 bp mutations or insertions were often observed. In switch junctions from ATLD patients, there were fewer base substitutions due to transitions and, most strikingly, the substitutions that occurred most often in controls, C --> T transitions, never occurred at, or close to, the junctions derived from the ATLD patients. In switch junctions from NBS patients, all base substitutions were observed at the G/C nucleotides, and transitions were preferred. These data suggest that the Mre11-Rad50-Nbs1 complex (Mre11 complex) is involved in the nonhomologous end joining pathway in CSR and that Mre11, Nbs1, and protein mutated in ataxia-telangiectasia (ATM) might have both common and independent roles in this process.
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Affiliation(s)
- Aleksi Lähdesmäki
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet at Huddinge Hospital, SE-14186 Stockholm, Sweden
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21
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Zhang J, Dong M, Li L, Fan Y, Pathre P, Dong J, Lou D, Wells JM, Olivares-Villagómez D, Van Kaer L, Wang X, Xu M. Endonuclease G is required for early embryogenesis and normal apoptosis in mice. Proc Natl Acad Sci U S A 2003; 100:15782-7. [PMID: 14663139 PMCID: PMC307645 DOI: 10.1073/pnas.2636393100] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Endonuclease G (EndoG) is a nuclear-encoded mitochondrial protein reported to be important for both nuclear DNA fragmentation during apoptosis and mitochondrial DNA replication. To evaluate the in vivo function of EndoG, we have investigated the effects of EndoG deficiency in cells and mice. We found that EndoG homozygous mutant embryos die between embryonic days 2.5 and 3.5. Mitochondrial DNA copy numbers in ovulated oocytes from EndoG heterozygous mutant and wild-type mice are similar, suggesting that EndoG is involved in a cellular function unrelated to mitochondrial DNA replication. Interestingly, we found that cells from EndoG heterozygous mutant mice exhibit increased resistance to both tumor necrosis factor alpha- and staurosporine-induced cell death. Moreover, spontaneous cell death of spermatogonia in EndoG heterozygous mutant mice is significantly reduced compared with wild-type mice. DNA fragmentation is also reduced in EndoG+/- thymocytes and splenocytes compared with wild-type cells, as well as in EndoG+/- thymus in vivo compared with that of the wild-type mice, on activation of apoptosis. These findings indicate that EndoG is essential during early embryogenesis and plays a critical role in normal apoptosis and nuclear DNA fragmentation.
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Affiliation(s)
- Jianhua Zhang
- Department of Cell Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA.
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Sansom OJ, Zabkiewicz J, Bishop SM, Guy J, Bird A, Clarke AR. MBD4 deficiency reduces the apoptotic response to DNA-damaging agents in the murine small intestine. Oncogene 2003; 22:7130-6. [PMID: 14562041 DOI: 10.1038/sj.onc.1206850] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
MBD4 was originally identified through its methyl binding domain, but has more recently been characterized as a thymine DNA glycosylase that interacts with the mismatch repair (MMR) protein MLH1. In vivo, MBD4 functions to reduce the mutability of methyl-CpG sites in the genome and mice deticient in MBD4 show increased intestinal tumorigenesis on an Apc(Min/+) background. As MLH1 and other MMR proteins have been functionally linked to apoptosis, we asked whether MBD4 also plays a role in mediating the apoptotic response within the murine small intestine. Mice deficient for MBD4 showed significantly reduced apoptotic responses 6 h following treatment with a range of cytotoxic agents including gamma-irradiation, cisplatin, temozolomide and 5-fluorouracil (5-FU). This leads to increased clonogenic survival in vivo in Mbd4(-/-) mice following exposure to either 5-FU or cisplatin. We next analysed the apoptotic response to 5-FU and temozolomide in doubly mutant Mbd4(-/-), Mlh1(-/-) mice but observed no additive decrease. The results imply that MBD4 and MLH1 lie in the same pathway and therefore that MMR-dependent apoptosis is mediated through MBD4. MBD4 deficiency also reduced the normal apoptotic response to gamma-irradiation, which we show is independent of Mlh1 status (at least in the murine small intestine), so suggesting that the reliance upon MBD4 may extend beyond MMR-mediated apoptosis. Our results establish a novel functional role for MBD4 in the cellular response to DNA damage and may have implications for its role in suppressing neoplasia.
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Affiliation(s)
- Owen James Sansom
- Cardiff School of Biosciences, Cardiff University, PO Box 911, Cardiff CF10 3US, UK
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23
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Abstract
Loss of deoxyribonuclease I (Dnase1) function is associated with systemic lupus erythematosus (SLE) in humans and mice; however, no coding mutations in Dnase1 are found in polygenic murine models. Instead, both MRL-lpr strains and NZB/W F1 hybrids are homozygous for T89I missense in the macrophage-DNASE, desoxyribonuclease I-like 3 (Dnase1l3). By in vitro expression studies, this substitution decreases this enzyme's nuclease activity against free DNA by only approximately twofold; however, the mutation has a greater effect on the capacity of media conditioned with Dnase1l3 to confer a barrier to liposomal gene transfection to HeLa cells. The 89I substitution decreases the Dnase1l3 barrier function in vitro by eightfold (P < 0.01). In splenocytes and BM-derived macrophages of SLE mice, while cellular Dnase1l3 levels are induced relative to C57BL/6 (control) mice, levels of FD-nuclease activity are similar. Finally, media conditioned by MRL and NZB/W F1 macrophages, relative to control, contains a weak interferon-gamma (IFN-gamma) inducible Dnase1l3-associated barrier to transfection. This barrier function is hypothesized to reflect the inability of SLE mice to degrade membrane-enveloped DNA-associated antigens, such as apoptotic bodies, which are predicted to stimulate the characteristic autoimmunity of SLE. Our results for these two generally independent models strongly suggest that Dnase1l3 deficiency increases the susceptibility of these mice to polygenic SLE.
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Affiliation(s)
- A Wilber
- Division of Genetics and Metabolism, Southern Illinois University School of Medicine, Springfield, IL 62794, USA
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24
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Abstract
Previous studies have shown that expansion-prone repeats form structures that inhibit human flap endonuclease (FEN-1). We report here that faulty processing by FEN-1 initiates repeat instability in mammalian cells. Disease-length CAG tracts in Huntington's disease mice heterozygous for FEN-1 display a tendency toward expansions over contractions during intergenerational inheritance compared to those in homozygous wild-type mice. Further, with regard to human cells expressing a nuclease-defective FEN-1, we provide direct evidence that an unprocessed FEN-1 substrate is a precursor to instability. In cells with no endogenous defects in DNA repair, exogenous nuclease-defective FEN-1 causes repeat instability and aberrant DNA repair. Inefficient flap processing blocks the formation of Rad51/BRCA1 complexes but invokes repair by other pathways.
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Affiliation(s)
- Craig Spiro
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic and Foundation, Rochester, Minnesota 55905, USA
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25
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Nishimoto S, Kawane K, Watanabe-Fukunaga R, Fukuyama H, Ohsawa Y, Uchiyama Y, Hashida N, Ohguro N, Tano Y, Morimoto T, Fukuda Y, Nagata S. Nuclear cataract caused by a lack of DNA degradation in the mouse eye lens. Nature 2003; 424:1071-4. [PMID: 12944971 DOI: 10.1038/nature01895] [Citation(s) in RCA: 142] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2003] [Accepted: 07/04/2003] [Indexed: 02/03/2023]
Abstract
The eye lens is composed of fibre cells, which develop from the epithelial cells on the anterior surface of the lens. Differentiation into a lens fibre cell is accompanied by changes in cell shape, the expression of crystallins and the degradation of cellular organelles. The loss of organelles is believed to ensure the transparency of the lens, but the molecular mechanism behind this process is not known. Here we show that DLAD ('DNase II-like acid DNase', also called DNase IIbeta) is expressed in human and murine lens cells, and that mice deficient in the DLAD gene are incapable of degrading DNA during lens cell differentiation--the undigested DNA accumulates in the fibre cells. The DLAD-/- mice develop cataracts of the nucleus lentis, and their response to light on electroretinograms is severely reduced. These results indicate that DLAD is responsible for the degradation of nuclear DNA during lens cell differentiation, and that if DNA is left undigested in the lens, it causes cataracts of the nucleus lentis, blocking the light path.
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Affiliation(s)
- Sogo Nishimoto
- Department of Genetics, Osaka University Medical School, Osaka 565-0871, Japan.
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26
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Abstract
Phagocytic cells inhibit the growth of intracellular pathogens by producing nitric oxide (NO). NO causes cell filamentation, induction of the SOS response, and DNA replication arrest in the Gram-negative bacterium Salmonella enterica. NO also induces double-stranded chromosomal breaks in replication-arrested Salmonella lacking a functional RecBCD exonuclease. This DNA damage depends on actions of additional DNA repair proteins, the RecG helicase, and RuvC endonuclease. Introduction of a recG mutation restores both resistance to NO and the ability of an attenuated recBC mutant Salmonella strain to cause lethal infection in mice, demonstrating that bacterial DNA replication is inhibited during host-pathogen interactions. Inhibition of DNA replication during nitrosative stress is invariably accompanied by zinc mobilization, implicating DNA-binding zinc metalloproteins as critical targets of NO-related antimicrobial activity.
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Affiliation(s)
- Jeffrey M. Schapiro
- Departments of Laboratory Medicine
andMicrobiology, University of Washington
School of Medicine, Seattle, WA 98195-7242;
andDepartment of Microbiology, North Carolina
State University, Raleigh, NC 27695-7615
| | - Stephen J. Libby
- Departments of Laboratory Medicine
andMicrobiology, University of Washington
School of Medicine, Seattle, WA 98195-7242;
andDepartment of Microbiology, North Carolina
State University, Raleigh, NC 27695-7615
| | - Ferric C. Fang
- Departments of Laboratory Medicine
andMicrobiology, University of Washington
School of Medicine, Seattle, WA 98195-7242;
andDepartment of Microbiology, North Carolina
State University, Raleigh, NC 27695-7615
- To whom correspondence should be addressed. E-mail:
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27
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Handa N, Kobayashi I. Accumulation of large non-circular forms of the chromosome in recombination-defective mutants of Escherichia coli. BMC Mol Biol 2003; 4:5. [PMID: 12718760 PMCID: PMC156651 DOI: 10.1186/1471-2199-4-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2003] [Accepted: 04/28/2003] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Double-strand breakage of chromosomal DNA is obviously a serious threat to cells because various activities of the chromosome depend on its integrity. However, recent experiments suggest that such breakage may occur frequently during "normal" growth in various organisms - from bacteria through vertebrates, possibly through arrest of a replication fork at some endogenous DNA damage. RESULTS In order to learn how the recombination processes contribute to generation and processing of the breakage, large (> 2000 kb) linear forms of Escherichia coli chromosome were detected by pulsed-field gel electrophoresis in various recombination-defective mutants. The mutants were analyzed in a rich medium, in which the wild-type strain showed fewer of these huge broken chromosomes than in a synthetic medium, and the following results were obtained: (i) Several recB and recC null mutants (in an otherwise rec+ background) accumulated these huge linear forms, but several non-null recBCD mutants (recD, recC1001, recC1002, recC1003, recC1004, recC2145, recB2154, and recB2155) did not. (ii) In a recBC sbcA background, in which RecE-mediated recombination is active, recA, recJ, recQ, recE, recT, recF, recO, and recR mutations led to their accumulation. The recJ mutant accumulated many linear forms, but this effect was suppressed by a recQ mutation. (iii) The recA, recJ, recQ, recF and recR mutations led to their accumulation in a recBC sbcBC background. The recJ mutation showed the largest amount of these forms. (iv) No accumulation was detected in mutants affecting resolution of Holliday intermediates, recG, ruvAB and ruvC, in any of these backgrounds. CONCLUSION These results are discussed in terms of stepwise processing of chromosomal double-strand breaks.
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Affiliation(s)
- Naofumi Handa
- Division of Molecular Biology, Institute of Medical Science, University of Tokyo, Shirokanedai, Tokyo 108-8639 Japan.
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28
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Bardwell PD, Martin A, Wong E, Li Z, Edelmann W, Scharff MD. Cutting edge: the G-U mismatch glycosylase methyl-CpG binding domain 4 is dispensable for somatic hypermutation and class switch recombination. J Immunol 2003; 170:1620-4. [PMID: 12574322 DOI: 10.4049/jimmunol.170.4.1620] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Affinity maturation of the humoral response is accomplished by somatic hypermutation and class switch recombination (CSR) of Ig genes. Activation-induced cytidine deaminase likely initiates these processes by deamination of cytidines in the V and switch regions of Ig genes. This activity is expected to produce G-U mismatches that can be substrates for MutS homolog 2/MutS homolog 6 heterodimers and for uracil DNA glycosylase. However, G-T and G-U mismatches are also substrates of the methyl-CpG binding domain 4 (Mbd4) glycosylase. To determine whether Mbd4 functions downstream of activation-induced cytidine deaminase activity, we examined somatic hypermutation and CSR in Mbd4(-/-) mice. In this study, we report that CSR, as analyzed by an in vitro switch assay and by in vivo immunizations, is unaffected in Mbd4(-/-) mice. In addition, the hypermutated JH2 to JH4 region in Peyer's patch B cells showed no effects as a result of Mbd4 deficiency. These data indicate that the Mbd4 glycosylase does not significantly contribute to mechanisms of Ab diversification.
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Affiliation(s)
- Philip D Bardwell
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Chanin 403, Bronx, NY 10461, USA
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29
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Kawane K, Fukuyama H, Yoshida H, Nagase H, Ohsawa Y, Uchiyama Y, Okada K, Iida T, Nagata S. Impaired thymic development in mouse embryos deficient in apoptotic DNA degradation. Nat Immunol 2003; 4:138-44. [PMID: 12524536 DOI: 10.1038/ni881] [Citation(s) in RCA: 191] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2002] [Accepted: 12/03/2002] [Indexed: 02/06/2023]
Abstract
Apoptosis is often accompanied by the degradation of chromosomal DNA. Caspase-activated DNase (CAD) is an endonuclease that is activated in dying cells, whereas DNase II is present in the lysosomes of macrophages. Here, we show that CAD(-/-) thymocytes did not undergo apoptotic DNA degradation. But, when apoptotic cells were phagocytosed by macrophages, their DNA was degraded by DNase II. The thymus of DNase II(-/-)CAD(-/-) embryos contained many foci carrying undigested DNA and the cellularity was severely reduced due to a block in T cell development. The interferon-beta gene was strongly up-regulated in the thymus of DNase II(-/-)CAD(-/-) embryos, suggesting that when the DNA of apoptotic cells is left undigested, it can activate innate immunity leading to defects in thymic development.
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Affiliation(s)
- Kohki Kawane
- Department of Genetics, Osaka University Medical School, Japan
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30
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Abstract
In mammalian cells, thymine glycols and other oxidized pyrimidines such as 5,6-dihydrouracil are removed from DNA by the NTH1 protein, a bifunctional DNA-N-glycosylase. However, mNTH1 knock-out mice in common with other DNA glycosylase-deficient mice do not show any severe abnormalities associated with accumulation of DNA damage and mutations. In the present study we used an in vitro repair system to investigate the mechanism for the removal of 5,6-dihydrouracil from DNA by mNTH1-deficient cell-free extracts derived from testes of mNTH1 knock-out mice. We found that these extracts are able to support the removal of 5,6-dihydrouracil from DNA at about 20% of the efficiency of normal extracts. Furthermore, we also found that single-nucleotide patch base excision repair is the major pathway for removal of 5,6-dihydrouracil in mNTH1-deficient cell extracts, suggesting the involvement of other DNA glycosylase(s) in the removal of oxidized pyrimidines.
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Affiliation(s)
- Rhoderick H Elder
- Medical Research Council Radiation and Genome Stability Unit, Harwell, Oxfordshire, OX11 0RD, United Kingdom
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31
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Wong E, Yang K, Kuraguchi M, Werling U, Avdievich E, Fan K, Fazzari M, Jin B, Brown AMC, Lipkin M, Edelmann W. Mbd4 inactivation increases Cright-arrowT transition mutations and promotes gastrointestinal tumor formation. Proc Natl Acad Sci U S A 2002; 99:14937-42. [PMID: 12417741 PMCID: PMC137523 DOI: 10.1073/pnas.232579299] [Citation(s) in RCA: 128] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Mbd4 (methyl-CpG binding domain 4) is a novel mammalian repair enzyme that has been implicated biochemically in the repair of mismatched G-T residues at methylated CpG sites. In addition, the human protein has been shown to interact with the DNA mismatch repair protein MLH1. To clarify the role of Mbd4 in DNA repair in vivo and to examine the impact of Mbd4 inactivation on gastrointestinal (GI) tumorigenesis, we introduced a null mutation into the murine Mbd4 gene by gene targeting. Heterozygous and homozygous Mbd4 mutant mice develop normally and do not show increased cancer susceptibility or reduced survival. Although Mbd4 inactivation did not increase microsatellite instability (MSI) in the mouse genome, it did result in a 2- to 3-fold increase in C-->T transition mutations at CpG sequences in splenocytes and epithelial cells of the small intestinal mucosa. The combination of Mbd4 deficiency with a germ line mutation in the adenomatous polyposis coli (Apc) gene increased the tumor number in the GI tract and accelerated tumor progression. The change in the GI cancer phenotype was associated with an increase in somatic C-->T mutations at CpG sites within the coding region of the wild-type Apc allele. These studies indicate that, although inactivation of Mbd4 does not by itself cause cancer predisposition in mice, it can alter the mutation spectrum in cancer cells and modify the cancer predisposition phenotype.
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Affiliation(s)
- Edmund Wong
- Department of Cell Biology, Biostatistics Core, Albert Einstein Cancer Center, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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32
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Ocampo MTA, Chaung W, Marenstein DR, Chan MK, Altamirano A, Basu AK, Boorstein RJ, Cunningham RP, Teebor GW. Targeted deletion of mNth1 reveals a novel DNA repair enzyme activity. Mol Cell Biol 2002; 22:6111-21. [PMID: 12167705 PMCID: PMC134015 DOI: 10.1128/mcb.22.17.6111-6121.2002] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
DNA N-glycosylase/AP (apurinic/apyrimidinic) lyase enzymes of the endonuclease III family (nth in Escherichia coli and Nth1 in mammalian organisms) initiate DNA base excision repair of oxidized ring saturated pyrimidine residues. We generated a null mouse (mNth1(-/-)) by gene targeting. After almost 2 years, such mice exhibited no overt abnormalities. Tissues of mNth1(-/-) mice contained an enzymatic activity which cleaved DNA at sites of oxidized thymine residues (thymine glycol [Tg]). The activity was greater when Tg was paired with G than with A. This is in contrast to Nth1, which is more active against Tg:A pairs than Tg:G pairs. We suggest that there is a back-up mammalian repair activity which attacks Tg:G pairs with much greater efficiency than Tg:A pairs. The significance of this activity may relate to repair of oxidized 5-methyl cytosine residues (5meCyt). It was shown previously (S. Zuo, R. J. Boorstein, and G. W. Teebor, Nucleic Acids Res. 23:3239-3243, 1995) that both ionizing radiation and chemical oxidation yielded Tg from 5meCyt residues in DNA. Thus, this previously undescribed, and hence novel, back-up enzyme activity may function to repair oxidized 5meCyt residues in DNA while also being sufficient to compensate for the loss of Nth1 in the mutant mice, thereby explaining the noninformative phenotype.
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Affiliation(s)
- Maria T A Ocampo
- Department of Pathology and Kaplan Comprehensive Cancer Center, New York University Medical Center, New York, New York 10016, USA
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33
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Krieser RJ, MacLea KS, Longnecker DS, Fields JL, Fiering S, Eastman A. Deoxyribonuclease IIalpha is required during the phagocytic phase of apoptosis and its loss causes perinatal lethality. Cell Death Differ 2002; 9:956-62. [PMID: 12181746 DOI: 10.1038/sj.cdd.4401056] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2001] [Revised: 02/12/2002] [Accepted: 03/18/2002] [Indexed: 11/10/2022] Open
Abstract
Deoxyribonuclease IIalpha (DNase IIalpha) is one of many endonucleases implicated in DNA digestion during apoptosis. We produced mice with targeted disruption of DNase IIalpha and defined its role in apoptosis. Mice deleted for DNase IIalpha die at birth with many tissues exhibiting large DNA-containing bodies that result from engulfed but undigested cell corpses. These DNA-containing bodies are pronounced in the liver where fetal definitive erythropoiesis occurs and extruded nuclei are degraded. They are found between the digits, where apoptosis occurs, and in many other regions of the embryo. Defects in the diaphragm appear to cause death of the mice due to asphyxiation. The DNA in these bodies contains 3'-hydroxyl ends and therefore stain positive in the TUNEL assay. In addition, numerous unengulfed TUNEL-positive cells are observed throughout the embryo. Apoptotic cells are normally cleared rapidly from a tissue; hence the persistence of the DNA-containing bodies and TUNEL-positive cells identifies sites where apoptosis occurs during development. These results demonstrate that DNase IIalpha is not required for the generation of the characteristic DNA fragmentation that occurs during apoptosis but is required for degrading DNA of dying cells and this function is necessary for proper fetal development.
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Affiliation(s)
- R J Krieser
- Department of Pharmacology and Toxicology, Dartmouth Medical School, Hanover, NH 03755, USA
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34
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Kucherlapati M, Yang K, Kuraguchi M, Zhao J, Lia M, Heyer J, Kane MF, Fan K, Russell R, Brown AMC, Kneitz B, Edelmann W, Kolodner RD, Lipkin M, Kucherlapati R. Haploinsufficiency of Flap endonuclease (Fen1) leads to rapid tumor progression. Proc Natl Acad Sci U S A 2002; 99:9924-9. [PMID: 12119409 PMCID: PMC126601 DOI: 10.1073/pnas.152321699] [Citation(s) in RCA: 199] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Flap endonuclease (Fen1) is required for DNA replication and repair, and defects in the gene encoding Fen1 cause increased accumulation of mutations and genome rearrangements. Because mutations in some genes involved in these processes cause cancer predisposition, we investigated the possibility that Fen1 may function in tumorigenesis of the gastrointestinal tract. Using gene knockout approaches, we introduced a null mutation into murine Fen1. Mice homozygous for the Fen1 mutation were not obtained, suggesting absence of Fen1 expression leads to embryonic lethality. Most Fen1 heterozygous animals appear normal. However, when combined with a mutation in the adenomatous polyposis coli (Apc) gene, double heterozygous animals have increased numbers of adenocarcinomas and decreased survival. The tumors from these mice show microsatellite instability. Because one copy of the Fen1 gene remained intact in tumors, Fen1 haploinsufficiency appears to lead to rapid progression of cancer.
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Affiliation(s)
- Melanie Kucherlapati
- Department of Medicine and Harvard Partners Center for Genetics and Genomics, Harvard Medical School, Boston, MA 02115, USA.
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35
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Dendouga N, Callebaut I, Tomavo S. A novel DNA repair enzyme containing RNA recognition, G-patch and specific splicing factor 45-like motifs in the protozoan parasite Toxoplasma gondii. Eur J Biochem 2002; 269:3393-401. [PMID: 12135477 DOI: 10.1046/j.1432-1033.2002.02993.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We report the cloning and functional characterization of the full-length cDNA and gene encoding a Toxoplasma gondii DNA repair enzyme designated TgDRE. The gene is composed of three exons separated by two introns of 780 and 630 bp, and encodes a protein with a predicted molecular mass of 49.6 kDa. The native TgDRE protein, with a molecular mass of 60 kDa, is only detected in the virulent tachyzoite stage of T. gondii. However, the transcript is present in both asexual parasite stages, virulent tachyzoite and avirulent encysted bradyzoite. When an Escherichia coli mutant lacking ruvC endonuclease and recG helicase was transformed with TgDRE cDNA, a significant increase in resistance to DNA-damaging agents, such as UV light and mitomycin C, was observed. Moreover, database searches revealed that TgDRE orthologues were present in the genome sequences of the related apicomplexa parasites Plasmodium falciparum and Plasmodium yoelii, as well as in those of Arabidopsis thaliana, Drosophila melanogaster, Caenorhabditis elegans and Homo sapiens. This novel family of proteins is characterized by the presence of human splicing factor SF45-like, RNA recognition (RRM) and glycine-rich (G-patch) motifs. The presence of these motifs suggests that T. gondii TgDRE might also be involved in other biological functions such as RNA metabolism in addition to DNA-repair.
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Affiliation(s)
- Najoua Dendouga
- Equipe de Parasitologie Moléculaire, Laboratoire de Chimie Biologique, CNRS UMR 8576, Université des Sciences et Technologies de Lille, France
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36
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Takao M, Kanno SI, Shiromoto T, Hasegawa R, Ide H, Ikeda S, Sarker AH, Seki S, Xing JZ, Le X, Weinfeld M, Kobayashi K, Miyazaki JI, Muijtjens M, Hoeijmakers JH, van der Horst G, Yasui A. Novel nuclear and mitochondrial glycosylases revealed by disruption of the mouse Nth1 gene encoding an endonuclease III homolog for repair of thymine glycols. EMBO J 2002; 21:3486-93. [PMID: 12093749 PMCID: PMC125395 DOI: 10.1093/emboj/cdf350] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Endonuclease III, encoded by nth in Escherichia coli, removes thymine glycols (Tg), a toxic oxidative DNA lesion. To determine the biological significance of this repair in mammals, we established a mouse model with mutated mNth1, a homolog of nth, by gene targeting. The homozygous mNth1 mutant mice showed no detectable phenotypical abnormality. Embryonic cells with or without wild-type mNth1 showed no difference in sensitivity to menadione or hydrogen peroxide. Tg produced in the mutant mouse liver DNA by X-ray irradiation disappeared with time, though more slowly than in the wild-type mouse. In extracts from mutant mouse liver, we found, instead of mNTH1 activity, at least two novel DNA glycosylase activities against Tg. One activity is significantly higher in the mutant than in wild-type mouse in mitochondria, while the other is another nuclear glycosylase for Tg. These results underscore the importance of base excision repair of Tg both in the nuclei and mitochondria in mammals.
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Affiliation(s)
| | | | - Tatsuya Shiromoto
- Department of Molecular Genetics, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575,
Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Department of Biochemistry, Faculty of Science, Okayama University of Science, Okayama 700-0005, Department of Molecular Biology, Institute of Cellular and Molecular Biology, Okayama University Medical School, Okayama 700-8558, Division of Stem Cell Regulation Research, Osaka University Medical School, Suita 565-0871, Japan, Department of Public Health Sciences, Faculty of Medicine, University of Alberta, Edmonton, Alberta T6G 2G3, Experimental Oncology, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada and MGC, Department of Cell Biology and Genetics, Erasmus University, PO Box 1738, 3000 DR Rotterdam, The Netherlands Present address: Department of Cell and Molecular Biology, Life Sciences Division, M.S. 74–157 Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA Present address: Department of Human Nutrition, Chugoku Junior College, Okayama, Japan Corresponding author e-mail: M.Takao and S.-i.Kanno contributed equally to this work
| | - Rei Hasegawa
- Department of Molecular Genetics, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575,
Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Department of Biochemistry, Faculty of Science, Okayama University of Science, Okayama 700-0005, Department of Molecular Biology, Institute of Cellular and Molecular Biology, Okayama University Medical School, Okayama 700-8558, Division of Stem Cell Regulation Research, Osaka University Medical School, Suita 565-0871, Japan, Department of Public Health Sciences, Faculty of Medicine, University of Alberta, Edmonton, Alberta T6G 2G3, Experimental Oncology, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada and MGC, Department of Cell Biology and Genetics, Erasmus University, PO Box 1738, 3000 DR Rotterdam, The Netherlands Present address: Department of Cell and Molecular Biology, Life Sciences Division, M.S. 74–157 Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA Present address: Department of Human Nutrition, Chugoku Junior College, Okayama, Japan Corresponding author e-mail: M.Takao and S.-i.Kanno contributed equally to this work
| | - Hiroshi Ide
- Department of Molecular Genetics, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575,
Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Department of Biochemistry, Faculty of Science, Okayama University of Science, Okayama 700-0005, Department of Molecular Biology, Institute of Cellular and Molecular Biology, Okayama University Medical School, Okayama 700-8558, Division of Stem Cell Regulation Research, Osaka University Medical School, Suita 565-0871, Japan, Department of Public Health Sciences, Faculty of Medicine, University of Alberta, Edmonton, Alberta T6G 2G3, Experimental Oncology, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada and MGC, Department of Cell Biology and Genetics, Erasmus University, PO Box 1738, 3000 DR Rotterdam, The Netherlands Present address: Department of Cell and Molecular Biology, Life Sciences Division, M.S. 74–157 Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA Present address: Department of Human Nutrition, Chugoku Junior College, Okayama, Japan Corresponding author e-mail: M.Takao and S.-i.Kanno contributed equally to this work
| | - Shogo Ikeda
- Department of Molecular Genetics, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575,
Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Department of Biochemistry, Faculty of Science, Okayama University of Science, Okayama 700-0005, Department of Molecular Biology, Institute of Cellular and Molecular Biology, Okayama University Medical School, Okayama 700-8558, Division of Stem Cell Regulation Research, Osaka University Medical School, Suita 565-0871, Japan, Department of Public Health Sciences, Faculty of Medicine, University of Alberta, Edmonton, Alberta T6G 2G3, Experimental Oncology, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada and MGC, Department of Cell Biology and Genetics, Erasmus University, PO Box 1738, 3000 DR Rotterdam, The Netherlands Present address: Department of Cell and Molecular Biology, Life Sciences Division, M.S. 74–157 Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA Present address: Department of Human Nutrition, Chugoku Junior College, Okayama, Japan Corresponding author e-mail: M.Takao and S.-i.Kanno contributed equally to this work
| | - Altraf H. Sarker
- Department of Molecular Genetics, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575,
Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Department of Biochemistry, Faculty of Science, Okayama University of Science, Okayama 700-0005, Department of Molecular Biology, Institute of Cellular and Molecular Biology, Okayama University Medical School, Okayama 700-8558, Division of Stem Cell Regulation Research, Osaka University Medical School, Suita 565-0871, Japan, Department of Public Health Sciences, Faculty of Medicine, University of Alberta, Edmonton, Alberta T6G 2G3, Experimental Oncology, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada and MGC, Department of Cell Biology and Genetics, Erasmus University, PO Box 1738, 3000 DR Rotterdam, The Netherlands Present address: Department of Cell and Molecular Biology, Life Sciences Division, M.S. 74–157 Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA Present address: Department of Human Nutrition, Chugoku Junior College, Okayama, Japan Corresponding author e-mail: M.Takao and S.-i.Kanno contributed equally to this work
| | - Shuji Seki
- Department of Molecular Genetics, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575,
Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Department of Biochemistry, Faculty of Science, Okayama University of Science, Okayama 700-0005, Department of Molecular Biology, Institute of Cellular and Molecular Biology, Okayama University Medical School, Okayama 700-8558, Division of Stem Cell Regulation Research, Osaka University Medical School, Suita 565-0871, Japan, Department of Public Health Sciences, Faculty of Medicine, University of Alberta, Edmonton, Alberta T6G 2G3, Experimental Oncology, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada and MGC, Department of Cell Biology and Genetics, Erasmus University, PO Box 1738, 3000 DR Rotterdam, The Netherlands Present address: Department of Cell and Molecular Biology, Life Sciences Division, M.S. 74–157 Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA Present address: Department of Human Nutrition, Chugoku Junior College, Okayama, Japan Corresponding author e-mail: M.Takao and S.-i.Kanno contributed equally to this work
| | - James Z. Xing
- Department of Molecular Genetics, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575,
Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Department of Biochemistry, Faculty of Science, Okayama University of Science, Okayama 700-0005, Department of Molecular Biology, Institute of Cellular and Molecular Biology, Okayama University Medical School, Okayama 700-8558, Division of Stem Cell Regulation Research, Osaka University Medical School, Suita 565-0871, Japan, Department of Public Health Sciences, Faculty of Medicine, University of Alberta, Edmonton, Alberta T6G 2G3, Experimental Oncology, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada and MGC, Department of Cell Biology and Genetics, Erasmus University, PO Box 1738, 3000 DR Rotterdam, The Netherlands Present address: Department of Cell and Molecular Biology, Life Sciences Division, M.S. 74–157 Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA Present address: Department of Human Nutrition, Chugoku Junior College, Okayama, Japan Corresponding author e-mail: M.Takao and S.-i.Kanno contributed equally to this work
| | - X.Chris Le
- Department of Molecular Genetics, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575,
Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Department of Biochemistry, Faculty of Science, Okayama University of Science, Okayama 700-0005, Department of Molecular Biology, Institute of Cellular and Molecular Biology, Okayama University Medical School, Okayama 700-8558, Division of Stem Cell Regulation Research, Osaka University Medical School, Suita 565-0871, Japan, Department of Public Health Sciences, Faculty of Medicine, University of Alberta, Edmonton, Alberta T6G 2G3, Experimental Oncology, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada and MGC, Department of Cell Biology and Genetics, Erasmus University, PO Box 1738, 3000 DR Rotterdam, The Netherlands Present address: Department of Cell and Molecular Biology, Life Sciences Division, M.S. 74–157 Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA Present address: Department of Human Nutrition, Chugoku Junior College, Okayama, Japan Corresponding author e-mail: M.Takao and S.-i.Kanno contributed equally to this work
| | - Michael Weinfeld
- Department of Molecular Genetics, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575,
Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Department of Biochemistry, Faculty of Science, Okayama University of Science, Okayama 700-0005, Department of Molecular Biology, Institute of Cellular and Molecular Biology, Okayama University Medical School, Okayama 700-8558, Division of Stem Cell Regulation Research, Osaka University Medical School, Suita 565-0871, Japan, Department of Public Health Sciences, Faculty of Medicine, University of Alberta, Edmonton, Alberta T6G 2G3, Experimental Oncology, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada and MGC, Department of Cell Biology and Genetics, Erasmus University, PO Box 1738, 3000 DR Rotterdam, The Netherlands Present address: Department of Cell and Molecular Biology, Life Sciences Division, M.S. 74–157 Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA Present address: Department of Human Nutrition, Chugoku Junior College, Okayama, Japan Corresponding author e-mail: M.Takao and S.-i.Kanno contributed equally to this work
| | | | - Jun-ichi Miyazaki
- Department of Molecular Genetics, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575,
Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Department of Biochemistry, Faculty of Science, Okayama University of Science, Okayama 700-0005, Department of Molecular Biology, Institute of Cellular and Molecular Biology, Okayama University Medical School, Okayama 700-8558, Division of Stem Cell Regulation Research, Osaka University Medical School, Suita 565-0871, Japan, Department of Public Health Sciences, Faculty of Medicine, University of Alberta, Edmonton, Alberta T6G 2G3, Experimental Oncology, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada and MGC, Department of Cell Biology and Genetics, Erasmus University, PO Box 1738, 3000 DR Rotterdam, The Netherlands Present address: Department of Cell and Molecular Biology, Life Sciences Division, M.S. 74–157 Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA Present address: Department of Human Nutrition, Chugoku Junior College, Okayama, Japan Corresponding author e-mail: M.Takao and S.-i.Kanno contributed equally to this work
| | - Manja Muijtjens
- Department of Molecular Genetics, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575,
Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Department of Biochemistry, Faculty of Science, Okayama University of Science, Okayama 700-0005, Department of Molecular Biology, Institute of Cellular and Molecular Biology, Okayama University Medical School, Okayama 700-8558, Division of Stem Cell Regulation Research, Osaka University Medical School, Suita 565-0871, Japan, Department of Public Health Sciences, Faculty of Medicine, University of Alberta, Edmonton, Alberta T6G 2G3, Experimental Oncology, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada and MGC, Department of Cell Biology and Genetics, Erasmus University, PO Box 1738, 3000 DR Rotterdam, The Netherlands Present address: Department of Cell and Molecular Biology, Life Sciences Division, M.S. 74–157 Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA Present address: Department of Human Nutrition, Chugoku Junior College, Okayama, Japan Corresponding author e-mail: M.Takao and S.-i.Kanno contributed equally to this work
| | - Jan H.J. Hoeijmakers
- Department of Molecular Genetics, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575,
Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Department of Biochemistry, Faculty of Science, Okayama University of Science, Okayama 700-0005, Department of Molecular Biology, Institute of Cellular and Molecular Biology, Okayama University Medical School, Okayama 700-8558, Division of Stem Cell Regulation Research, Osaka University Medical School, Suita 565-0871, Japan, Department of Public Health Sciences, Faculty of Medicine, University of Alberta, Edmonton, Alberta T6G 2G3, Experimental Oncology, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada and MGC, Department of Cell Biology and Genetics, Erasmus University, PO Box 1738, 3000 DR Rotterdam, The Netherlands Present address: Department of Cell and Molecular Biology, Life Sciences Division, M.S. 74–157 Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA Present address: Department of Human Nutrition, Chugoku Junior College, Okayama, Japan Corresponding author e-mail: M.Takao and S.-i.Kanno contributed equally to this work
| | - Gijsbertus van der Horst
- Department of Molecular Genetics, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575,
Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Department of Biochemistry, Faculty of Science, Okayama University of Science, Okayama 700-0005, Department of Molecular Biology, Institute of Cellular and Molecular Biology, Okayama University Medical School, Okayama 700-8558, Division of Stem Cell Regulation Research, Osaka University Medical School, Suita 565-0871, Japan, Department of Public Health Sciences, Faculty of Medicine, University of Alberta, Edmonton, Alberta T6G 2G3, Experimental Oncology, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada and MGC, Department of Cell Biology and Genetics, Erasmus University, PO Box 1738, 3000 DR Rotterdam, The Netherlands Present address: Department of Cell and Molecular Biology, Life Sciences Division, M.S. 74–157 Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA Present address: Department of Human Nutrition, Chugoku Junior College, Okayama, Japan Corresponding author e-mail: M.Takao and S.-i.Kanno contributed equally to this work
| | - Akira Yasui
- Department of Molecular Genetics, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575,
Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Department of Biochemistry, Faculty of Science, Okayama University of Science, Okayama 700-0005, Department of Molecular Biology, Institute of Cellular and Molecular Biology, Okayama University Medical School, Okayama 700-8558, Division of Stem Cell Regulation Research, Osaka University Medical School, Suita 565-0871, Japan, Department of Public Health Sciences, Faculty of Medicine, University of Alberta, Edmonton, Alberta T6G 2G3, Experimental Oncology, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada and MGC, Department of Cell Biology and Genetics, Erasmus University, PO Box 1738, 3000 DR Rotterdam, The Netherlands Present address: Department of Cell and Molecular Biology, Life Sciences Division, M.S. 74–157 Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA Present address: Department of Human Nutrition, Chugoku Junior College, Okayama, Japan Corresponding author e-mail: M.Takao and S.-i.Kanno contributed equally to this work
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37
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Abstract
The removal of oxidative base damage from the genome of Saccharomyces cerevisiae is thought to occur primarily via the base excision repair (BER) pathway in a process initiated by several DNA N-glycosylase/AP lyases. We have found that yeast strains containing simultaneous multiple disruptions of BER genes are not hypersensitive to killing by oxidizing agents, but exhibit a spontaneous hyperrecombinogenic (hyper-rec) and mutator phenotype. The hyper-rec and mutator phenotypes are further enhanced by elimination of the nucleotide excision repair (NER) pathway. Furthermore, elimination of either the lesion bypass (REV3-dependent) or recombination (RAD52-dependent) pathway results in a further, specific enhancement of the hyper-rec or mutator phenotypes, respectively. Sensitivity (cell killing) to oxidizing agents is not observed unless multiple pathways are eliminated simultaneously. These data suggest that the BER, NER, recombination, and lesion bypass pathways have overlapping specificities in the removal of, or tolerance to, exogenous or spontaneous oxidative DNA damage in S. cerevisiae. Our results also suggest a physiological role for the AP lyase activity of certain BER N-glycosylases in vivo.
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Affiliation(s)
- P W Doetsch
- Departments of Biochemistry and Radiation Oncology, Emory University, Atlanta, Georgia 30322, USA
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38
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Xiao W, Chow BL, Hanna M, Doetsch PW. Deletion of the MAG1 DNA glycosylase gene suppresses alkylation-induced killing and mutagenesis in yeast cells lacking AP endonucleases. Mutat Res 2001; 487:137-47. [PMID: 11738940 DOI: 10.1016/s0921-8777(01)00113-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
DNA base excision repair (BER) is initiated by DNA glycosylases that recognize and remove damaged bases. The phosphate backbone adjacent to the resulting apurinic/apyrimidinic (AP) site is then cleaved by an AP endonuclease or glycosylase-associated AP lyase to invoke subsequent BER steps. We have used a genetic approach in Saccharomyces cerevisiae to address whether AP sites are blocks to DNA replication and the biological consequences if AP sites persist in the genome. We found that yeast cells deficient in the two AP endonucleases (apn1 apn2 double mutant) are extremely sensitive to killing by methyl methanesulfonate (MMS), a model DNA alkylating agent. Interestingly, this sensitivity can be reduced up to 2500-fold by deleting the MAG1 3-methyladenine DNA glycosylase gene, suggesting that Mag1 not only removes lethal base lesions, but also benign lesions and possibly normal bases, and that the resulting AP sites are highly toxic to the cells. This rescuing effect appears to be specific for DNA alkylation damage, since the mag1 mutation reduces killing effects of two other DNA alkylating agents, but does not alter the sensitivity of apn cells to killing by UV, gamma-ray or H(2)O(2). Our mutagenesis assays indicate that nearly half of spontaneous and almost all MMS-induced mutations in the AP endonuclease-deficient cells are due to Mag1 DNA glycosylase activity. Although the DNA replication apparatus appears to be incapable of replicating past AP sites, Polzeta-mediated translesion synthesis is able to bypass AP sites, and accounts for all spontaneous and MMS-induced mutagenesis in the AP endonuclease-deficient cells. These results allow us to delineate base lesion flow within the BER pathway and link AP sites to other DNA damage repair and tolerance pathways.
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Affiliation(s)
- W Xiao
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5E5.
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39
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Tano K, Iwamatsu Y, Yasuhira S, Utsumi H, Takimoto K. Increased base change mutations at G:C pairs in Escherichia coli deficient in endonuclease III and VIII. J Radiat Res 2001; 42:409-413. [PMID: 11951664 DOI: 10.1269/jrr.42.409] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Various types of mutation induced by oxidative DNA damage, induced by hydrogen peroxide and riboflavin photosensitization, were determined in Escherichia coli (E. coli) mutants deficient in endonuclease III (endo III) and endonuclease VIII (endo VIII). The majority of hydrogen peroxide-induced and spontaneous mutations consisted of G:C to A:T and to T:A base changes, shown on the mutation assay system by a reversion at a specific site of the lacZ gene. Base changes were also localized at G:C pairs in the mutation of the supF gene, induced by riboflavin photosensitization, which specifically yields 7,8-dihydro-8-oxoguanine (8-oxoG). G:C to T:A and to C:G transversions dominated in both mutants. These results suggest that endo III and endo VIII are involved in the repair of oxidative lesions of guanine.
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Affiliation(s)
- K Tano
- Research Reactor Institute, Kyoto University, Noda, Kumatori, Sennan-gun, Osaka 590-0454, Japan.
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40
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Jin YH, Obert R, Burgers PM, Kunkel TA, Resnick MA, Gordenin DA. The 3'-->5' exonuclease of DNA polymerase delta can substitute for the 5' flap endonuclease Rad27/Fen1 in processing Okazaki fragments and preventing genome instability. Proc Natl Acad Sci U S A 2001; 98:5122-7. [PMID: 11309502 PMCID: PMC33174 DOI: 10.1073/pnas.091095198] [Citation(s) in RCA: 129] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many DNA polymerases (Pol) have an intrinsic 3'-->5' exonuclease (Exo) activity which corrects polymerase errors and prevents mutations. We describe a role of the 3'-->5' Exo of Pol delta as a supplement or backup for the Rad27/Fen1 5' flap endonuclease. A yeast rad27 null allele was lethal in combination with Pol delta mutations in Exo I, Exo II, and Exo III motifs that inactivate its exonuclease, but it was viable with mutations in other parts of Pol delta. The rad27-p allele, which has little phenotypic effect by itself, was also lethal in combination with mutations in the Pol delta Exo I and Exo II motifs. However, rad27-p Pol delta Exo III double mutants were viable. They exhibited strong synergistic increases in CAN1 duplication mutations, intrachromosomal and interchromosomal recombination, and required the wild-type double-strand break repair genes RAD50, RAD51, and RAD52 for viability. Observed effects were similar to those of the rad27-null mutant deficient in the removal of 5' flaps in the lagging strand. These results suggest that the 3'-->5' Exo activity of Pol delta is redundant with Rad27/Fen1 for creating ligatable nicks between adjacent Okazaki fragments, possibly by reducing the amount of strand-displacement in the lagging strand.
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Affiliation(s)
- Y H Jin
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, 111 TW Alexander Drive, Research Triangle Park, NC 27709, USA
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41
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Abstract
The Caenorhabditis elegans nuc-1 gene has previously been implicated in programmed cell death due to the presence of persistent undegraded apoptotic DNA in nuc-1 mutant animals. In this report, we describe the cloning and characterization of nuc-1, which encodes an acidic nuclease with significant sequence similarity to mammalian DNase II. Database searches performed with human DNase II protein sequence revealed a significant similarity with the predicted C. elegans C07B5.5 ORF. Subsequent analysis of crude C. elegans protein extracts revealed that wild-type animals contained a potent endonuclease activity with a cleavage preference similar to DNase II, while nuc-1 mutant worms demonstrated a marked reduction in this nuclease activity. Sequence analysis of C07B5.5 DNA and mRNA also revealed that nuc-1(e1392), but not wild-type animals contained a nonsense mutation within the CO7B5.5 coding region. Furthermore, nuc-1 transgenic lines carrying the wild-type C07B5.5 locus demonstrated a complete complementation of the nuc-1 mutant phenotype. Our results therefore provide compelling evidence that the C07B5.5 gene encodes the NUC-1 apoptotic nuclease and that this nuclease is related in sequence and activity to DNase II.
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Affiliation(s)
- C J Lyon
- Department of Molecular, Cell and Developmental Biology, University of California, 90995-1606, Los Angeles, CA, USA
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42
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Shimamura H, Akasaka S, Kubo K, Saito Y, Nakajima S, Tano K, Utsumi H, Yamamoto K. Mutational specificity of the ferrous ion in a supF gene of endonuclease III/VIII deficient Escherichia coli. J Radiat Res 1997; 38:165-171. [PMID: 9415748 DOI: 10.1269/jrr.38.165] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
When 125 microM Fe2+/EDTA treated plasmid pUB3 was used to transfect an Escherichia coli NKJ2004 (nth nei) host, which is totally defective in glycosylases for thymine glycol and 5-hydroxycytosine, a 3.7 fold increase in mutation frequency was observed. Among 46 supF mutants sequenced, 28 had base substitutions, with G:C-->C:G transversion predominant (14 cases), followed by G:C-->T:A transversion (6 cases) and G:C-->A:T transition (6 cases). The results are consistent with our previous Fe2+ mutagenesis results where, in the wild type host, 78% were base substitutions, with G:C-->C:G transversion (59%) predominant, followed by G:C-->T:A transversion (28%) and G:C-->A:T transition (11%). Treatment of pUB3 DNA with Fe2+/EDTA did not yield formation of Endonuclease III sensitive sites. The possibility of 5-hydroxycytosine as the causative lesion for Fe2+ induced G:C-->C:G transversion is discussed.
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Affiliation(s)
- H Shimamura
- Department of Applied Chemistry, Faculty of Science and Engineering, Kinki University, Osaka, Japan
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43
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Sander M, Ramotar D. Partial purification of Pde1 from Saccharomyces cerevisiae: enzymatic redundancy for the repair of 3'-terminal DNA lesions and abasic sites in yeast. Biochemistry 1997; 36:6100-6. [PMID: 9166780 DOI: 10.1021/bi970048y] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Earlier work indicates that the major DNA repair phosphodiesterase (PDE) in yeast cells is the well-characterized Apn1 protein. Apn1 demonstrates both Mg2+-independent PDE activity and Mg2+-independent class II apurinic/apyrimidinic (AP) endonuclease activity and represents greater than 90% of the activity detected in crude extracts from wild-type yeast cells. Apn1 is related to Echerichia coli endonuclease IV, both in its enzymatic properties and its amino acid sequence. In this work, we report the partial purification of a novel yeast protein, Pde1, present in Apn1-deficient cells. Pde1 is purified by sequential BioRex-70, PBE118, and MonoS chromatography steps using a sensitive and highly specific 3'-phosphoglycolate-terminated oligonucleotide-based assay as a measure of PDE activity. Mg2+-stimulated PDE and Mg2+-stimulated class II AP endonuclease copurify during this procedure. These results indicate that yeast, like many other organisms studied to date, has enzymatic redundancy for the repair of 3'-blocking groups and abasic sites.
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Affiliation(s)
- M Sander
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA.
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44
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Abstract
We have examined protein synthesis directed by bacteriophage T7 which had been alkylated with methyl methanesulfonate so as to produce apurinic sites in its DNA in vivo. Both repair-proficient and repair-deficient (xth nfo mutant) strains of Escherichia coli served as host cells. In repair-proficient cells, all three classes of phage proteins were synthesized, although with significant delays. In mutant cells, only class I proteins were produced and their synthesis was delayed and reduced, demonstrating a perturbation of protein synthesis and providing the first in vivo indication that transcription is inhibited by abasic sites. However, the proposed effects of abasic sites on transcription appear to be weaker than those on replication.
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Affiliation(s)
- G Sanchez
- Département de biochimie, Université de Montréal, Quebec, Canada
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45
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Davidson AR, Gold M. Mutations abolishing the endonuclease activity of bacteriophage lambda terminase lie in two distinct regions of the A gene, one of which may encode a "leucine zipper" DNA-binding domain. Virology 1992; 189:21-30. [PMID: 1534952 DOI: 10.1016/0042-6822(92)90677-h] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Bacteriophage lambda terminase is a multifunctional enzyme composed of two subunits which are the products of the phage-encoded Nu1 and A genes. The enzyme catalyzes the endonucleolytic cleavage of lambda DNA at a site known as cosN and mediates packaging of the phage DNA into empty heads. This work describes the characterization of mutations within the A gene which lead to the loss of terminase endonuclease activity without affecting the ability of the enzyme to package monomeric mature (cut) lambda DNA. The residues changed by these mutations lie in two distinct regions within the carboxy half of the A protein. One of these regions has sequence homology with a conserved region of DNA polymerases. The other region resembles the "leucine zipper" DNA binding domain (bZIP) found in eukaryotic transcription factors in that both a basic region and leucine heptad-repeat are present. This terminase domain may be involved in the recognition and/or cleavage of cosN.
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Affiliation(s)
- A R Davidson
- Department of Molecular and Medical Genetics, University of Toronto, Ontario, Canada
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46
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Abstract
Deficiency of apurinic/apyrimidinic (AP) DNA-repair enzymes in crude extracts of E. coli mutants was determined by following general and specific AP DNA-repair synthesis via nick translation in the presence of either all four dNTPs, or only one dNTP. We have shown that mutations either in DNA polymerase I or in AP endonucleases or in both, inhibit to different degrees the ability to repair AP DNA. The polA mutation totally abolishes the ability to perform both general and specific AP DNA repair, while the polAex mutation affects only general AP DNA repair. The xthA tight mutants, including the deletion mutant BW9101, can cope with small amounts of AP sites but hardly with high amounts of these lesions. In addition we have found that crude extracts of the xthA mutants degrade AP DNA by two modes: a nonspecific, and an AP-specific mode. These phenomena are common to all xth mutants and enabled us to discover this mutation. In contrast to the xth mutants so far isolated, BW2001 exhibits marked sensitivity to MMS and to X-ray irradiation. We found that this strain has a proficient DNA polymerase I but is absolutely deficient in AP endonucleases. We attribute its sensitivities to a secondary mutation at the structural gene of endonuclease IV.
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