DOCSLIB.ORG

Architecture of the Human XPC DNA Repair and Stem Cell Coactivator Complex

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Architecture of the Human XPC DNA Repair and Stem Cell Coactivator Complex Architecture of the human XPC DNA repair and stem cell coactivator complex Elisa T. Zhanga,b,c, Yuan Hed,1, Patricia Groba,b, Yick W. Fonga,b,2, Eva Nogalesa,b,d, and Robert Tjiana,b,c,e,3 aDepartment of Molecular and Cell Biology, University of California, Berkeley, CA 94720; bHoward Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720; cLi Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California Berkeley, CA 94720; dLife Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94710; and eHoward Hughes Medical Institute, Chevy Chase, MD 20815-6789 Contributed by Robert Tjian, October 16, 2015 (sent for review August 20, 2015; reviewed by Montserrat Samso and Ning Zheng) The Xeroderma pigmentosum complementation group C (XPC) involved in base excision repair (BER). BER is responsible for complex is a versatile factor involved in both nucleotide excision removing primarily non-helix-distorting lesions from the ge- repair and transcriptional coactivation as a critical component of nome (2). In BER, the XPC complex helps repair oxidative the NANOG, OCT4, and SOX2 pluripotency gene regulatory net- damage by stimulating the activities of DNA glycosylases such work. Here we present the structure of the human holo-XPC com- as OGG1 and TDG (3) to target lesions including 8-oxoguanine, plex determined by single-particle electron microscopy to reveal a independently of other downstream GG-NER factors (17). flexible, ear-shaped structure that undergoes localized loss of order More recently, the XPC complex has also been found to upon DNA binding. We also determined the structure of the complete perform crucial duties in the regulation of gene transcription, the yeast homolog Rad4 holo-complex to find a similar overall architec- second primary function of the genome. In embryonic stem cells ture to the human complex, consistent with their shared DNA repair (ESCs), the XPC complex acts as a coactivator to enhance the functions. Localized differences between these structures reflect an expression of OCT4- and SOX2-driven pluripotency genes, most intriguing phylogenetic divergence in transcriptional capabilities that notably NANOG (4), buttressing the gene regulatory network we present here. Having positioned the constituent subunits by tag- that establishes and maintains the unique self-renewal and plu- ging and deletion, we propose a model of key interaction interfaces ripotency properties of ESCs. The XPC complex performs its that reveals the structural basis for this difference in functional con- BIOCHEMISTRY servation. Together, our findings establish a framework for under- coactivator functions independently of DNA binding (4, 18), standing the structure-function relationships of the XPC complex in presumably by bridging interactions between the sequence-spe- the interplay between transcription and DNA repair. cific transcription factors OCT4 (octamer-binding transcrip- tion factor 4; also known as POU5F1) and SOX2 [SRY (sex- transcription | stem cells | DNA repair | structure | biochemistry determining region Y)-box 2] and the general transcriptional machinery, such as TFIID and RNA pol II, thus following a enomes of living organisms serve two primary functions: as mechanism reminiscent of that of other coactivator complexes Gvehicles for hereditary information and as the template for gene products involved in an organism’s development and re- Significance sponses to environmental stimuli. Vital to maintaining the health of genomes in the face of intrinsic and extrinsic sources of DNA Embryonic or pluripotent stem cells are unique in their ability to damage are a suite of DNA repair pathways, each dedicated to self-renew in culture and to generate all lineages of an adult or- handling specific lesions. Similarly, proper use and expression of ganism, making them valuable tools for modeling early de- this essential genomic information is regulated by a host of tran- velopmental processes and for developing regenerative medicine scription factors, chromatin remodelers, and epigenetic modifiers technologies. An important factor in controlling the expression of and readers (1). The Xeroderma pigmentosum complementation pluripotency genes is the Xeroderma pigmentosum complemen- group C (XPC) protein complex performs crucial roles in both tation group C (XPC) DNA repair complex. This study presents, to of these capacities by participating in nucleotide excision repair our knowledge, the first complete structures of different XPC complexes by electron microscopy to establish an important (NER) (2) and base excision repair (BER) (3), as well as transcrip- ’ tional regulation (4) and other processes (5). framework for a molecular understanding of XPC stwoprimary The XPC complex is one of seven XP complementation groups functions. In conjunction with our biochemical findings, we syn- thesize a model of how XPC performs both its evolutionarily A–G and is composed of the 125-kDa XPC, the 58-kDa RAD23B conserved DNA repair function and its evolutionarily noncon- (Rad23 homolog B; also known as HHR23B), and the 18-kDa served transcription function. CETN2 (Centrin2) subunits (2). RAD23B and CETN2 associate – tightly with XPC and stabilize both its DNA repair (6 10) and Author contributions: E.T.Z., E.N., and R.T. designed research; E.T.Z., Y.H., and Y.W.F. stem cell coactivator functions (4). The XPC complex is the ini- performed research; E.T.Z. and Y.W.F. contributed new reagents/analytic tools; E.T.Z., tiator and main DNA damage sensor in global genome nucleotide Y.H., P.G., and Y.W.F. analyzed data; and E.T.Z., E.N., and R.T. wrote the paper. excision repair (GG-NER), one of two branches of the nucleotide Reviewers: M.S., Virginia Commonwealth University; and N.Z., University of Washington. excision repair pathway that repairs a wide array of bulky, helix- The authors declare no conflict of interest. distorting lesions (2, 11); the second form of NER or transcrip- Data deposition: Atomic coordinates and structure factors have been deposited in the tion-coupled repair (TC-NER) targets lesions blocking tran- Electron Microscopy Data Bank (EMDB), https://www.ebi.ac.uk/pdbe/emdb/ (accession scription to reactivate proper gene expression (2, 12). Defects nos. EMD-6495–EMD-6498). 1 in GG-NER lead to photosensitivity and a predisposition to cer- Present address: Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208. tain cancers in animal models and in human patients with Xero- 2Present address: Brigham Regenerative Medicine Center, Cardiovascular Division, De- derma pigmentosum (13). In conjunction with the UV-damage partment of Medicine Brigham and Women’s Hospital, Harvard Medical School, Cam- DNA-binding protein (UV-DDB) (2, 12), the XPC complex bridge, MA 02139. recruits >30 downstream factors, such as XPA (14), TFIIH (15, 3To whom correspondence should be addressed. Email: [email protected]. 16), and the endonucleases XPF and XPG to remove these ad- This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. ducts (2, 11). In addition to its role in GG-NER, XPC is also 1073/pnas.1520104112/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1520104112 PNAS | December 1, 2015 | vol. 112 | no. 48 | 14817–14822 Downloaded by guest on September 28, 2021 such as Mediator and p300/CBP (19). In a separate study, XPC TFIIH-BD1 DNA-BD A 124 144 607 742 was found to localize to active but not to inactive RNA pol II- XPA- & OGG1-BD OCT4-BD SOX2-BD 1 154 331 511 808 940 dependent gene promoters in the absence of exogenous geno- XPC TGD TGD BH1 BH2 BH3 204 223 496 734 814 toxic stress (11, 20). RAD23B-BD2 TFIIH-BD2 RAD23B-BD1 847 863 Although both the DNA repair and transcriptional functions 1 276 334 419 CETN2-BD RAD23B UbL of mammalian XPC complexes have been characterized bio- UBA1 XPC-BD UBA2 chemically and genetically, 3D structural information of the 1 172 CETN2 EF EF holo-complex has been unavailable. The partial crystal structure 105 166 XPC-BD of Rad4, the yeast homolog of the human XPC subunit, in B D R C complex with the Rad4-interaction domain of yeast Rad23, has XPC provided information helpful toward an understanding of Rad4/ XPC’s biochemical behavior and of certain phenotypic outcomes 180° 180° ’ (18, 21). However, given XPC s low sequence homology with the 170 Å yeast homolog Rad4 (21, 22), the absence of key domains in the available crystal structure, and the divergence of requirements for transcriptional vs. repair activities (4, 15, 18, 23), structural in- 100 Å formation of the complete, three-subunit, native human XPC R MBP C C E complex is much needed for an understanding of the functional XPC versatility of the XPC complex. At present, no information has 180° been reported on the overall architecture of the XPC holo- 180° complex, the possible large-scale conformational rearrangements UbL in XPC upon DNA-binding, or the extent of structural conser- UBA1 vation of the human XPC complex with homolog complexes. UBA2 Here we address the lack of structural data on human XPC using 3D single-particle reconstruction by electron microscopy Fig. 1. 3D reconstruction of the human XPC complex and localization of (EM) to characterize the overall architecture of XPC, as well as subunits. (A) Schematic representation of the subunits and domains of the genetic tagging and computational docking to locate the relative human XPC complex. Transglutaminase homology domain (TGD), β-hairpin positions of its constituent subunits. We also assess the confor- domains 1–3 (BH), ubiquitin-like domain (UbL), ubiquitin-associated domains 1 mational changes to the complex upon binding to DNA. Given and 2 (UBA), EF-hand domains (EF), and protein- and DNA-binding domains the evolutionary conservation of GG-NER (24), we queried the (BD) are indicated accordingly. (B) Front and back views of the XPC complex extent of structural and functional conservation over evolution- reconstructed in EMAN2 (49).
Load more

Recommended publications
  • Deficiency in the DNA Repair Protein ERCC1 Triggers a Link Between Senescence and Apoptosis in Human Fibroblasts and Mouse Skin
    Lawrence Berkeley National Laboratory Recent Work Title Deficiency in the DNA repair protein ERCC1 triggers a link between senescence and apoptosis in human fibroblasts and mouse skin. Permalink https://escholarship.org/uc/item/73j1s4d1 Journal Aging cell, 19(3) ISSN 1474-9718 Authors Kim, Dong Eun Dollé, Martijn ET Vermeij, Wilbert P et al. Publication Date 2020-03-01 DOI 10.1111/acel.13072 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Received: 10 June 2019 | Revised: 7 October 2019 | Accepted: 30 October 2019 DOI: 10.1111/acel.13072 ORIGINAL ARTICLE Deficiency in the DNA repair protein ERCC1 triggers a link between senescence and apoptosis in human fibroblasts and mouse skin Dong Eun Kim1 | Martijn E. T. Dollé2 | Wilbert P. Vermeij3,4 | Akos Gyenis5 | Katharina Vogel5 | Jan H. J. Hoeijmakers3,4,5 | Christopher D. Wiley1 | Albert R. Davalos1 | Paul Hasty6 | Pierre-Yves Desprez1 | Judith Campisi1,7 1Buck Institute for Research on Aging, Novato, CA, USA Abstract 2Centre for Health Protection Research, ERCC1 (excision repair cross complementing-group 1) is a mammalian endonuclease National Institute of Public Health and that incises the damaged strand of DNA during nucleotide excision repair and inter- the Environment (RIVM), Bilthoven, The −/Δ Netherlands strand cross-link repair. Ercc1 mice, carrying one null and one hypomorphic Ercc1 3Department of Molecular Genetics, allele, have been widely used to study aging due to accelerated aging phenotypes Erasmus University Medical Center, −/Δ Rotterdam, The Netherlands in numerous organs and their shortened lifespan. Ercc1 mice display combined 4Princess Máxima Center for Pediatric features of human progeroid and cancer-prone syndromes.
    [Show full text]
  • Structure and Function of the Human Recq DNA Helicases
    Zurich Open Repository and Archive University of Zurich Main Library Strickhofstrasse 39 CH-8057 Zurich www.zora.uzh.ch Year: 2005 Structure and function of the human RecQ DNA helicases Garcia, P L Posted at the Zurich Open Repository and Archive, University of Zurich ZORA URL: https://doi.org/10.5167/uzh-34420 Dissertation Published Version Originally published at: Garcia, P L. Structure and function of the human RecQ DNA helicases. 2005, University of Zurich, Faculty of Science. Structure and Function of the Human RecQ DNA Helicases Dissertation zur Erlangung der naturwissenschaftlichen Doktorw¨urde (Dr. sc. nat.) vorgelegt der Mathematisch-naturwissenschaftlichen Fakultat¨ der Universitat¨ Z ¨urich von Patrick L. Garcia aus Unterseen BE Promotionskomitee Prof. Dr. Josef Jiricny (Vorsitz) Prof. Dr. Ulrich H ¨ubscher Dr. Pavel Janscak (Leitung der Dissertation) Z ¨urich, 2005 For my parents ii Summary The RecQ DNA helicases are highly conserved from bacteria to man and are required for the maintenance of genomic stability. All unicellular organisms contain a single RecQ helicase, whereas the number of RecQ homologues in higher organisms can vary. Mu- tations in the genes encoding three of the five human members of the RecQ family give rise to autosomal recessive disorders called Bloom syndrome, Werner syndrome and Rothmund-Thomson syndrome. These diseases manifest commonly with genomic in- stability and a high predisposition to cancer. However, the genetic alterations vary as well as the types of tumours in these syndromes. Furthermore, distinct clinical features are observed, like short stature and immunodeficiency in Bloom syndrome patients or premature ageing in Werner Syndrome patients. Also, the biochemical features of the human RecQ-like DNA helicases are diverse, pointing to different roles in the mainte- nance of genomic stability.
    [Show full text]
  • Evolutionary Origins of DNA Repair Pathways: Role of Oxygen Catastrophe in the Emergence of DNA Glycosylases
    cells Review Evolutionary Origins of DNA Repair Pathways: Role of Oxygen Catastrophe in the Emergence of DNA Glycosylases Paulina Prorok 1 , Inga R. Grin 2,3, Bakhyt T. Matkarimov 4, Alexander A. Ishchenko 5 , Jacques Laval 5, Dmitry O. Zharkov 2,3,* and Murat Saparbaev 5,* 1 Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany; [email protected] 2 SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; [email protected] 3 Center for Advanced Biomedical Research, Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia 4 National Laboratory Astana, Nazarbayev University, Nur-Sultan 010000, Kazakhstan; [email protected] 5 Groupe «Mechanisms of DNA Repair and Carcinogenesis», Equipe Labellisée LIGUE 2016, CNRS UMR9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, F-94805 Villejuif, France; [email protected] (A.A.I.); [email protected] (J.L.) * Correspondence: [email protected] (D.O.Z.); [email protected] (M.S.); Tel.: +7-(383)-3635187 (D.O.Z.); +33-(1)-42115404 (M.S.) Abstract: It was proposed that the last universal common ancestor (LUCA) evolved under high temperatures in an oxygen-free environment, similar to those found in deep-sea vents and on volcanic slopes. Therefore, spontaneous DNA decay, such as base loss and cytosine deamination, was the Citation: Prorok, P.; Grin, I.R.; major factor affecting LUCA’s genome integrity. Cosmic radiation due to Earth’s weak magnetic field Matkarimov, B.T.; Ishchenko, A.A.; and alkylating metabolic radicals added to these threats.
    [Show full text]
  • Paul Modrich Howard Hughes Medical Institute and Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, USA
    Mechanisms in E. coli and Human Mismatch Repair Nobel Lecture, December 8, 2015 by Paul Modrich Howard Hughes Medical Institute and Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, USA. he idea that mismatched base pairs occur in cells and that such lesions trig- T ger their own repair was suggested 50 years ago by Robin Holliday in the context of genetic recombination [1]. Breakage and rejoining of DNA helices was known to occur during this process [2], with precision of rejoining attributed to formation of a heteroduplex joint, a region of helix where the two strands are derived from the diferent recombining partners. Holliday pointed out that if this heteroduplex region should span a genetic diference between the two DNAs, then it will contain one or more mismatched base pairs. He invoked processing of such mismatches to explain the recombination-associated phenomenon of gene conversion [1], noting that “If there are enzymes which can repair points of damage in DNA, it would seem possible that the same enzymes could recognize the abnormality of base pairing, and by exchange reactions rectify this.” Direct evidence that mismatches provoke a repair reaction was provided by bacterial transformation experiments [3–5], and our interest in this efect was prompted by the Escherichia coli (E. coli) work done in Matt Meselson’s lab at Harvard. Using artifcially constructed heteroduplex DNAs containing multiple mismatched base pairs, Wagner and Meselson [6] demonstrated that mismatches elicit a repair reaction upon introduction into the E. coli cell. Tey also showed that closely spaced mismatches, mismatches separated by a 1000 base pairs or so, are usually repaired on the same DNA strand.
    [Show full text]
  • Open Full Page
    CCR PEDIATRIC ONCOLOGY SERIES CCR Pediatric Oncology Series Recommendations for Childhood Cancer Screening and Surveillance in DNA Repair Disorders Michael F. Walsh1, Vivian Y. Chang2, Wendy K. Kohlmann3, Hamish S. Scott4, Christopher Cunniff5, Franck Bourdeaut6, Jan J. Molenaar7, Christopher C. Porter8, John T. Sandlund9, Sharon E. Plon10, Lisa L. Wang10, and Sharon A. Savage11 Abstract DNA repair syndromes are heterogeneous disorders caused by around the world to discuss and develop cancer surveillance pathogenic variants in genes encoding proteins key in DNA guidelines for children with cancer-prone disorders. Herein, replication and/or the cellular response to DNA damage. The we focus on the more common of the rare DNA repair dis- majority of these syndromes are inherited in an autosomal- orders: ataxia telangiectasia, Bloom syndrome, Fanconi ane- recessive manner, but autosomal-dominant and X-linked reces- mia, dyskeratosis congenita, Nijmegen breakage syndrome, sive disorders also exist. The clinical features of patients with DNA Rothmund–Thomson syndrome, and Xeroderma pigmento- repair syndromes are highly varied and dependent on the under- sum. Dedicated syndrome registries and a combination of lying genetic cause. Notably, all patients have elevated risks of basic science and clinical research have led to important in- syndrome-associated cancers, and many of these cancers present sights into the underlying biology of these disorders. Given the in childhood. Although it is clear that the risk of cancer is rarity of these disorders, it is recommended that centralized increased, there are limited data defining the true incidence of centers of excellence be involved directly or through consulta- cancer and almost no evidence-based approaches to cancer tion in caring for patients with heritable DNA repair syn- surveillance in patients with DNA repair disorders.
    [Show full text]
  • Identification of Novel Pathogenic MSH2 Mutation and New DNA Repair Genes Variants: Investigation of a Tunisian Lynch Syndrome F
    Jaballah‑Gabteni et al. J Transl Med (2019) 17:212 https://doi.org/10.1186/s12967‑019‑1961‑9 Journal of Translational Medicine RESEARCH Open Access Identifcation of novel pathogenic MSH2 mutation and new DNA repair genes variants: investigation of a Tunisian Lynch syndrome family with discordant twins Amira Jaballah‑Gabteni1,3* , Haifa Tounsi1,3, Maria Kabbage1,3, Yosr Hamdi3, Sahar Elouej3,4, Ines Ben Ayed1,3, Mouna Medhioub2, Moufda Mahmoudi2, Hamza Dallali3, Hamza Yaiche1,3, Nadia Ben Jemii1,3, Affa Maaloul1, Najla Mezghani1,3, Sonia Abdelhak3, Lamine Hamzaoui2, Mousaddak Azzouz2 and Samir Boubaker1,3 Abstract Background: Lynch syndrome (LS) is a highly penetrant inherited cancer predisposition syndrome, characterized by autosomal dominant inheritance and germline mutations in DNA mismatch repair genes. Despite several genetic variations that have been identifed in various populations, the penetrance is highly variable and the reasons for this have not been fully elucidated. This study investigates whether, besides pathogenic mutations, environment and low penetrance genetic risk factors may result in phenotype modifcation in a Tunisian LS family. Patients and methods: A Tunisian family with strong colorectal cancer (CRC) history that fulfll the Amsterdam I criteria for the diagnosis of Lynch syndrome was proposed for oncogenetic counseling. The index case was a man, diagnosed at the age of 33 years with CRC. He has a monozygotic twin diagnosed at the age of 35 years with crohn disease. Forty‑seven years‑old was the onset age of his paternal uncle withCRC. An immunohistochemical (IHC) labe‑ ling for the four proteins (MLH1, MSH2, MSH6 and PMS2) of the MisMatchRepair (MMR) system was performed for the index case.
    [Show full text]
  • Mechanism and Regulation of DNA Damage Recognition in Nucleotide Excision Repair
    Kusakabe et al. Genes and Environment (2019) 41:2 https://doi.org/10.1186/s41021-019-0119-6 REVIEW Open Access Mechanism and regulation of DNA damage recognition in nucleotide excision repair Masayuki Kusakabe1, Yuki Onishi1,2, Haruto Tada1,2, Fumika Kurihara1,2, Kanako Kusao1,3, Mari Furukawa1, Shigenori Iwai4, Masayuki Yokoi1,2,3, Wataru Sakai1,2,3 and Kaoru Sugasawa1,2,3* Abstract Nucleotide excision repair (NER) is a versatile DNA repair pathway, which can remove an extremely broad range of base lesions from the genome. In mammalian global genomic NER, the XPC protein complex initiates the repair reaction by recognizing sites of DNA damage, and this depends on detection of disrupted/destabilized base pairs within the DNA duplex. A model has been proposed that XPC first interacts with unpaired bases and then the XPD ATPase/helicase in concert with XPA verifies the presence of a relevant lesion by scanning a DNA strand in 5′-3′ direction. Such multi-step strategy for damage recognition would contribute to achieve both versatility and accuracy of the NER system at substantially high levels. In addition, recognition of ultraviolet light (UV)-induced DNA photolesions is facilitated by the UV-damaged DNA-binding protein complex (UV-DDB), which not only promotes recruitment of XPC to the damage sites, but also may contribute to remodeling of chromatin structures such that the DNA lesions gain access to XPC and the following repair proteins. Even in the absence of UV-DDB, however, certain types of histone modifications and/or chromatin remodeling could occur, which eventually enable XPC to find sites with DNA lesions.
    [Show full text]
  • Role of Apurinic/Apyrimidinic Nucleases in the Regulation of Homologous Recombination in Myeloma: Mechanisms and Translational S
    Kumar et al. Blood Cancer Journal (2018) 8:92 DOI 10.1038/s41408-018-0129-9 Blood Cancer Journal ARTICLE Open Access Role of apurinic/apyrimidinic nucleases in the regulation of homologous recombination in myeloma: mechanisms and translational significance Subodh Kumar1,2, Srikanth Talluri1,2, Jagannath Pal1,2,3,XiaoliYuan1,2, Renquan Lu1,2,PuruNanjappa1,2, Mehmet K. Samur1,4,NikhilC.Munshi1,2,4 and Masood A. Shammas1,2 Abstract We have previously reported that homologous recombination (HR) is dysregulated in multiple myeloma (MM) and contributes to genomic instability and development of drug resistance. We now demonstrate that base excision repair (BER) associated apurinic/apyrimidinic (AP) nucleases (APEX1 and APEX2) contribute to regulation of HR in MM cells. Transgenic as well as chemical inhibition of APEX1 and/or APEX2 inhibits HR activity in MM cells, whereas the overexpression of either nuclease in normal human cells, increases HR activity. Regulation of HR by AP nucleases could be attributed, at least in part, to their ability to regulate recombinase (RAD51) expression. We also show that both nucleases interact with major HR regulators and that APEX1 is involved in P73-mediated regulation of RAD51 expression in MM cells. Consistent with the role in HR, we also show that AP-knockdown or treatment with inhibitor of AP nuclease activity increases sensitivity of MM cells to melphalan and PARP inhibitor. Importantly, although inhibition 1234567890():,; 1234567890():,; 1234567890():,; 1234567890():,; of AP nuclease activity increases cytotoxicity, it reduces genomic instability caused by melphalan. In summary, we show that APEX1 and APEX2, major BER proteins, also contribute to regulation of HR in MM.
    [Show full text]
  • DNA Repair with Its Consequences (E.G
    Cell Science at a Glance 515 DNA repair with its consequences (e.g. tolerance and pathways each require a number of apoptosis) as well as direct correction of proteins. By contrast, O-alkylated bases, Oliver Fleck* and Olaf Nielsen* the damage by DNA repair mechanisms, such as O6-methylguanine can be Department of Genetics, Institute of Molecular which may require activation of repaired by the action of a single protein, Biology, University of Copenhagen, Øster checkpoint pathways. There are various O6-methylguanine-DNA Farimagsgade 2A, DK-1353 Copenhagen K, Denmark forms of DNA damage, such as base methyltransferase (MGMT). MGMT *Authors for correspondence (e-mail: modifications, strand breaks, crosslinks removes the alkyl group in a suicide fl[email protected]; [email protected]) and mismatches. There are also reaction by transfer to one of its cysteine numerous DNA repair pathways. Each residues. Photolyases are able to split Journal of Cell Science 117, 515-517 repair pathway is directed to specific Published by The Company of Biologists 2004 covalent bonds of pyrimidine dimers doi:10.1242/jcs.00952 types of damage, and a given type of produced by UV radiation. They bind to damage can be targeted by several a UV lesion in a light-independent Organisms are permanently exposed to pathways. Major DNA repair pathways process, but require light (350-450 nm) endogenous and exogenous agents that are mismatch repair (MMR), nucleotide as an energy source for repair. Another damage DNA. If not repaired, such excision repair (NER), base excision NER-independent pathway that can damage can result in mutations, diseases repair (BER), homologous recombi- remove UV-induced damage, UVER, is and cell death.
    [Show full text]
  • DNA Replication, Repair and Recombination
    DNA replication, repair and recombination Asst. Prof. Dr. Altijana Hromic-Jahjefendic SS2020 DNA Genetic material Eukaryotes: in nucleus Prokaryotes: as plasmid Mitosis Division and duplication of somatic cells Production of two identical daughter cells from a single parent cell 4 stages: Prophase: The chromatin condenses into chromosomes. Each chromosome has duplicated to tow sister chromatids. The nuclear envelope breaks down. Metaphase: The chromosomes align at the equatorial plate and are held by microtubules attached to the mitotic spindle and to part of the centromere Anaphase: Centromeres divide and sister chromatids separate and move to corresponding poles Telophase: Daughter chromosomes arrive at the poles and the microtubules disappear. The nuclear envelope reappears DNA replication & recombination Reproduction (Replication) of a DNA-double helix - semiconservative fashion demonstrated by Meselson & Stahl by using 15N-labeled ammonium chloride in the growth medium heavy nitrogen label was incorporated in the DNA of the bacteria shifted to normal 14N-medium giving rise to density band between the “heavy” and the “light” band in the 1st generation In the 2nd generation, in addition to the hybrid band a light band appears which contains only 14N- DNA Synthesis of a new DNA strand nucleoside triphosphates are selected ability to form Watson-Crick base pairs to the corresponding position in the template strand DNA replication occurs at replication forks For replication - two parental DNA-strands must separate from
    [Show full text]
  • Distribution of DNA Repair-Related Ests in Sugarcane
    Genetics and Molecular Biology, 24 (1-4), 141-146 (2001) Distribution of DNA repair-related ESTs in sugarcane W.C. Lima, R. Medina-Silva, R.S. Galhardo and C.F.M. Menck* Abstract DNA repair pathways are necessary to maintain the proper genomic stability and ensure the survival of the organism, protecting it against the damaging effects of endogenous and exogenous agents. In this work, we made an analysis of the expression patterns of DNA repair-related genes in sugarcane, by determining the EST (expressed sequence tags) distribution in the different cDNA libraries of the SUCEST transcriptome project. Three different pathways - photoreactivation, base excision repair and nucleotide excision repair - were investigated by employing known DNA repair proteins as probes to identify homologous ESTs in sugarcane, by means of computer similarity search. The results showed that DNA repair genes may have differential expressions in tissues, depending on the pathway studied. These in silico data provide important clues on the potential variation of gene expression, to be confirmed by direct biochemical analysis. INTRODUCTION (The Arabidopsis Genome Initiative, 2000), have provided huge amounts of data that still need to be processed, in or- The genome of all living beings is constantly subject der to enable us to understand the physiological mecha- to damage generated by exogenous and endogenous fac- nisms of these organisms. This is the case of the DNA tors, reducing DNA stability and leading to an increase of repair pathways. Although repair and damage tolerance mutagenesis, cancer, cell death, senescence and other dele- mechanisms have been well described in bacteria, yeast, terious effects to organisms (de Laat et al., 1999).
    [Show full text]
  • Arsenic Disruption of DNA Damage Responses—Potential Role in Carcinogenesis and Chemotherapy
    Biomolecules 2015, 5, 2184-2193; doi:10.3390/biom5042184 OPEN ACCESS biomolecules ISSN 2218-273X www.mdpi.com/journal/biomolecules/ Review Arsenic Disruption of DNA Damage Responses—Potential Role in Carcinogenesis and Chemotherapy Clarisse S. Muenyi 1, Mats Ljungman 2 and J. Christopher States 3,* 1 Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, KY 40292, USA; E-Mail: [email protected] 2 Departments of Radiation Oncology and Environmental Health Sciences, University of Michigan, Ann Arbor, MI 48109-2800, USA; E-Mail: [email protected] 3 Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, KY 40292, USA * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +1-502-852-5347; Fax: +1-502-852-3123. Academic Editors: Wolf-Dietrich Heyer, Thomas Helleday and Fumio Hanaoka Received: 14 August 2015 / Accepted: 9 September 2015 / Published: 24 September 2015 Abstract: Arsenic is a Class I human carcinogen and is widespread in the environment. Chronic arsenic exposure causes cancer in skin, lung and bladder, as well as in other organs. Paradoxically, arsenic also is a potent chemotherapeutic against acute promyelocytic leukemia and can potentiate the cytotoxic effects of DNA damaging chemotherapeutics, such as cisplatin, in vitro. Arsenic has long been implicated in DNA repair inhibition, cell cycle disruption, and ubiquitination dysregulation, all negatively impacting the DNA damage response and potentially contributing to both the carcinogenic and chemotherapeutic potential of arsenic. Recent studies have provided mechanistic insights into how arsenic interferes with these processes including disruption of zinc fingers and suppression of gene expression.
    [Show full text]