DOCSLIB.ORG

University of Florida Thesis Or Dissertation Formatting

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
University of Florida Thesis Or Dissertation Formatting AAA ATPASE CDC48A AND ITS ASSOCIATION WITH UBIQUITIN-LIKE SAMP1 AND DNA REPAIR IN ARCHAEA By SWATHI DANTULURI A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2018 © 2018 Swathi Dantuluri I dedicate this to my family and friends for their endless love, support and company.Everybody who has taken the time and energy to teach me everything small or big. ACKNOWLEDGMENTS During my graduate career at the University of Florida, there are many people to whom I will be eternally indebted to for supporting and advising me along the way. Firstly, I would like to thank my advisor, Dr. Julie A. Maupin-Furlow for providing me the opportunity to work under her guidance as well as for all her help, advice, support, and encouragement throughout my time in her lab. I would also like to thank my committee members Dr. Sixue Chen, Dr.Tony Romeo and Dr. Nemat.O.Keyhani for their constructive advice and guidance. I must also express my gratitude to all the past and current Maupin lab members with whom I developed a warm and friendly working relationship over time, especially Dr. Nathaniel Hepowit who patiently taught me all the lab techniques, Dr. Xian Fu, Dr. Lana J. McMillan, Dr. Shiyun Cao, Dr. Sungmin Hwang, Zachary Adams, Cuper Ramirez, Paula Mondragon, and Jou Chin Chan. I also would like to thank all the undergraduate researchers in our lab for their dedication: Shae Marguiles, Sonam Parag, Gayathri Srinivasan, and Whinkie Leung. I am grateful to our collaborator, Dr. Thorsten Allers, for his generous contribution of strains to our lab and the field in general. I express deep gratitude to my family, especially to my parents, Dantuluri Satya Chandra Subrahmanya Varma, Dantuluri Kamala Devi and sister Dantuluri Sanjana Varma, for their unconditional love and support. Last but not the least I would like to thank Rahul Babu Koneru for his time, company and feeding me while I wrote my dissertation. 4 TABLE OF CONTENTS ACKNOWLEDGMENTS .................................................................................................. 4 LIST OF TABLES ............................................................................................................ 8 LIST OF FIGURES .......................................................................................................... 9 LIST OF ABBREVIATIONS ........................................................................................... 11 ABSTRACT ................................................................................................................... 13 CHAPTER 1 LITERATURE REVIEW .......................................................................................... 15 Introduction ............................................................................................................. 15 Cdc48 ..................................................................................................................... 16 Structure Of Cdc48 ........................................................................................... 17 Cdc48 Mediated Nucleotide Hydrolysis ............................................................ 18 Surface only model .................................................................................... 19 D2 in-D2 out model .................................................................................... 20 Cdc48 Interacting Proteins ............................................................................... 21 Cdc48 Role In Cellular Processes .......................................................................... 22 Cdc48 In Protein Quality Control ...................................................................... 22 Other Cellular Processes.................................................................................. 22 RecJ Exonucleases ................................................................................................ 23 RecJ Characterized So Far .............................................................................. 24 E. coli RecJ ................................................................................................ 24 Thermus thermophilus RecJ ...................................................................... 25 Deinococcus radiodurans RecJ ................................................................. 26 Archaeal RecJ ............................................................................................ 27 RNase J .................................................................................................................. 27 Objectives ............................................................................................................... 31 2 MATERIALS AND METHODS ................................................................................ 34 Chemicals, Strains and Growth Conditions ............................................................. 34 Chemicals and Reagents ................................................................................. 34 Strains, Media and Conditions For Growth Assay ............................................ 34 DNA Manipulation ................................................................................................... 34 Cloning ............................................................................................................. 34 DNA Electrophoresis ........................................................................................ 35 Site-Directed Mutagenesis ............................................................................... 35 SDS-PAGE ............................................................................................................. 35 3 ROLE OF CDC48A IN ARCHAEAL DNA REPAIR ................................................. 39 5 Introduction ............................................................................................................. 39 Materials and Methods Used In This Study ............................................................ 40 Purification Of SAMP1 ...................................................................................... 40 Cell Lysate For SAMP1 Pull-Down Assay ........................................................ 41 Coupling Of SAMP1 To Amine Reactive Beads ............................................... 42 SAMP1 Pull-Down Assay ................................................................................. 43 Mass Spectrometry .......................................................................................... 43 Partner Protein Pull-Down Assays ................................................................... 45 RNase J1 pull down assay ......................................................................... 45 RecJ 4 pull-down assay ............................................................................. 46 Cdc48A Pulldown Assay for Identification Of Protein Partners......................... 46 Strep resin enrichment of Cdc48A ............................................................. 46 Nickel column enrichment of Cdc48A ........................................................ 47 Construction Of Substrate Trap Mutant Of Cdc48A ......................................... 47 qRT-PCR Analysis ........................................................................................... 48 Growth Curves ................................................................................................. 49 Results .................................................................................................................... 49 Cdc48A Forms An Apparent Complex With DNA Repair/Replication Proteins That Binds Ubiquitin-Like SAMP1 ................................................... 49 Partner Proteins Of Cdc48A, RecJ4 and RNase J1 ......................................... 50 The (QQ) Mutant Of Cdc48A Potentially Traps Protein Partners Due To Its Decreased Ability To Hydrolyze ATP ............................................................ 51 DBeQ, A Cdc48-Specific Chemical Inhibitor, Slightly Impairs The Growth and Considerably Impairs The Pigmentation Of H. volcanii .......................... 51 Mutation of cdc48a Renders H. volcanii Cells Sensitive To DNA Damage and Mutation of samp1 Renders Cells Resistant To DNA damage ............... 52 Transcript Levels Of cdc48a , recj and rnj1 Are Increased During Conditions Of DNA Damage ........................................................................................... 53 4 BIOCHEMICAL CHARACTERIZATION OF CDC48 IN ARCHAEA ........................ 75 Introduction ............................................................................................................. 75 Materials and Methods............................................................................................ 76 Modelling and Alignment Of Cdc48A ................................................................ 76 Cloning, Culture and Purification Of Cdc48A From H. volcanii ......................... 76 Construction and Purification Of Substrate Trap Mutant Of Cdc48A ................ 78 ATPase Hydrolysis Activity Assay .................................................................... 79 Peptide Hydrolysis Assay ................................................................................. 80 Results .................................................................................................................... 82 Cdc48A Is A Structural Homolog Of Eukaryotic
Load more

Recommended publications
  • XPB Induces C1D Expression to Counteract UV-Induced Apoptosis
    Published OnlineFirst June 8, 2010; DOI: 10.1158/1541-7786.MCR-09-0467 Molecular DNA Damage and Cellular Stress Responses Cancer Research XPB Induces C1D Expression to Counteract UV-Induced Apoptosis Guang Li1, Juhong Liu2, Mones Abu-Asab1, Shibuya Masabumi3, and Yoshiro Maru4 Abstract Although C1D has been shown to be involved in DNA double-strand break repair, how C1D expression was induced and the mechanism(s) by which C1D facilitates DNA repair in mammalian cells remain poorly understood. We and others have previously shown that expression of xeroderma pigmentosum B (XPB) pro- tein efficiently compensated the UV irradiation–sensitive phenotype of 27-1 cells, which lack functional XPB. To further explore XPB-regulated genes that could be involved in UV-induced DNA repair, differential dis- play analysis of mRNA levels from CHO-9, 27-1, and 27-1 complemented with wild-type XPB was done and C1D gene was identified as one of the major genes whose expression was significantly upregulated by restoring XPB function. We found that XPB is essential to induce C1D transcription after UV irradiation. The increase in C1D expression effectively compensates for the UV-induced proteolysis of C1D and thus maintains cellular C1D level to cope with DNA damage inflicted by UV irradiation. We further showed that although insufficient to rescue 27-1 cells from UV-induced apoptosis by itself, C1D facilitates XPB DNA repair through direct interaction with XPB. Our findings provided direct evidence that C1D is associated with DNA repair complex and may promote repair of UV-induced DNA damage. Mol Cancer Res; 8(6); 885–95.
    [Show full text]
  • Oncogenic H-Ras Up-Regulates Expression of ERCC1 to Protect Cells from Platinum-Based Anticancer Agents
    [CANCER RESEARCH 64, 4849–4857, July 15, 2004] Oncogenic H-Ras Up-Regulates Expression of ERCC1 to Protect Cells from Platinum-Based Anticancer Agents Cha-Kyung Youn,1 Mi-Hwa Kim,1 Hyun-Ju Cho,1 Hong-Beum Kim,1 In-Youb Chang,1 Myung-Hee Chung,3 and Ho Jin You1,2 1Research Center for Proteineous Materials and 2Department of Pharmacology, School of Medicine, Chosun University, Gwangju, and 3Department of Pharmacology, School of Medicine, Seoul National University, Seoul, Korea ABSTRACT elucidated, evidence suggests that the activated Ras may contribute to cisplatin resistance by stimulating the DNA repair activity (9, 12, 13). Tumors frequently contain mutations in the ras genes, resulting in the Hence, there has been considerable interest in determining which constitutive activation of the Ras-activated signaling pathway. The acti- vation of Ras is involved not only in tumor progression but also in the proteins mediate the altered DNA repair capacity in activated Ras- development of resistance of the tumor cells to platinum-based chemo- containing cells. However, the downstream target genes of the onco- therapeutic agents. To investigate the potential mechanisms underlying genic Ras, which are involved in the enhancement of the DNA repair this resistance, we analyzed the effect of activated H-Ras on the expression activity, are unclear. of the nucleotide excision repair genes. Here we identified ERCC1, which Cisplatin is one of the most effective and widely used anticancer is one of the key enzymes involved in nucleotide excision repair, as being drugs for treating human solid tumors (14). However, its therapeutic markedly up-regulated by the activated H-Ras.
    [Show full text]
  • P38 MAPK-Mediated Activation of NF-Kb by the Rhogef Domain of Bcr
    Oncogene (2002) 21, 4601 – 4612 ª 2002 Nature Publishing Group All rights reserved 0950 – 9232/02 $25.00 www.nature.com/onc p38 MAPK-mediated activation of NF-kB by the RhoGEF domain of Bcr Malgorzata Korus1,2, Gwendolyn M Mahon1,2, Li Cheng1 and Ian P Whitehead*,1 1Department of Microbiology and Molecular Genetics, UMDNJ – New Jersey Medical School, Newark, New Jersey, NJ 07103, USA The oncogenic fusion protein p210 Bcr-Abl is causally et al., 1988; Fainstein et al., 1987; Konopka et al., associated with virtually all cases of chronic myelogenous 1984; Kurzrock et al., 1987; Walker et al., 1987). leukemia. The wild-type Bcr product has several Although animal models suggest that elevated levels of recognizable structural and functional motifs including Abl tyrosine kinase activity contribute to Bcr-Abl a domain that contains guanine nucleotide exchange mediated leukemogenesis (Lugo et al., 1990), the activity for Rho family GTPases (DH/PH domain). residues that distinguish the rearrangements associated Although this domain is retained within p210 Bcr-Abl, it with ALL (p185 Bcr-Abl) from the rearrangements has no known signaling activities in vivo. Here we report associated with CML (p210 Bcr-Abl) reside within the that a fragment of Bcr that encodes the isolated DH/PH Bcr protein. Thus, a complete understanding of the domain is a potent activator of the NF-kB transcription biological mechanisms that distinguish ALL from factor. Within the context of full length Bcr, this activity CML may depend upon the characterization of the is regulated by proximal flanking sequences that suppress signaling activities that reside within Bcr.
    [Show full text]
  • Ras/Raf/MEK/ERK and PI3K/PTEN/Akt/Mtor Cascade Inhibitors: How Mutations Can Result in Therapy Resistance and How to Overcome Resistance
    www.impactjournals.com/oncotarget/ Oncotarget, October, Vol.3, No 10 Ras/Raf/MEK/ERK and PI3K/PTEN/Akt/mTOR Cascade Inhibitors: How Mutations Can Result in Therapy Resistance and How to Overcome Resistance James A. McCubrey1, Linda S. Steelman1, William H. Chappell1, Stephen L. Abrams1, Richard A. Franklin1, Giuseppe Montalto2, Melchiorre Cervello3, Massimo Libra4, Saverio Candido4, Grazia Malaponte4, Maria C. Mazzarino4, Paolo Fagone4, Ferdinando Nicoletti4, Jörg Bäsecke5, Sanja Mijatovic6, Danijela Maksimovic- Ivanic6, Michele Milella7, Agostino Tafuri8, Francesca Chiarini9, Camilla Evangelisti9, Lucio Cocco10, Alberto M. Martelli9,10 1 Department of Microbiology and Immunology, Brody School of Medicine at East Carolina University, Greenville, NC, USA 2 Department of Internal Medicine and Specialties, University of Palermo, Palermo, Italy 3 Consiglio Nazionale delle Ricerche, Istituto di Biomedicina e Immunologia Molecolare “Alberto Monroy”, Palermo, Italy 4 Department of Bio-Medical Sciences, University of Catania, Catania, Italy 5 Department of Medicine, University of Göttingen, Göttingen, Germany 6 Department of Immunology, Instititue for Biological Research “Sinisa Stankovic”, University of Belgrade, Belgrade, Serbia 7 Regina Elena National Cancer Institute, Rome, Italy 8 Sapienza, University of Rome, Department of Cellular Biotechnology and Hematology, Rome, Italy 9 Institute of Molecular Genetics, National Research Council-Rizzoli Orthopedic Institute, Bologna, Italy. 10 Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy Correspondence to: James A. McCubrey, email: [email protected] Keywords: Targeted Therapy, Therapy Resistance, Cancer Stem Cells, Raf, Akt, PI3K, mTOR Received: September 12, 2012, Accepted: October 18, 2012, Published: October 20, 2012 Copyright: © McCubrey et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
    [Show full text]
  • Discovery of the Essential Roles of CRK9 in Gene Expression and Of
    University of Connecticut OpenCommons@UConn Doctoral Dissertations University of Connecticut Graduate School 5-27-2015 Lessons from Trypanosome TFIIH: Discovery of the Essential Roles of CRK9 in Gene Expression and of the Divergent Helicase Paralog XPB-R in Nucleotide Excision Repair Nitika Badjatia University of Connecticut - Storrs, [email protected] Follow this and additional works at: https://opencommons.uconn.edu/dissertations Recommended Citation Badjatia, Nitika, "Lessons from Trypanosome TFIIH: Discovery of the Essential Roles of CRK9 in Gene Expression and of the Divergent Helicase Paralog XPB-R in Nucleotide Excision Repair" (2015). Doctoral Dissertations. 866. https://opencommons.uconn.edu/dissertations/866 Lessons from Trypanosome TFIIH: Discovery of the Essential Roles of CRK9 in Gene Expression and of the Divergent Helicase Paralog XPB-R in Nucleotide Excision Repair Nitika Badjatia University of Connecticut, [2015] Eukaryotic TFIIH consists of a core of seven subunits, including the DNA helicase Xeroderma Pigmentosum B (XPB), and a cyclin-dependent kinase (CDK)-activating complex (CAK) that contains CDK7. XPB is crucial for DNA unwinding during transcription and nucleotide excision repair (NER) while the CAK complex phosphorylates RNA polymerase II (RNAPII) carboxy terminal domain (CTD), enabling the enzyme’s promoter clearance. Trypanosoma brucei, Trypanosoma cruzi and Leishmania spp. are lethal human parasites, belonging to the early-diverged order Kinetoplastida. They transcribe genes polycistronically and require spliced leader (SL) trans splicing for the maturation of mRNAs from polycistronic precursors. SL RNA gene (SLRNA) transcription by RNAPII depends on trypanosome TFIIH complex which contains orthologs of all core subunits but lacks the CAK complex. Despite this, the trypanosome CTD is phosphorylated and essential for SLRNA transcription.
    [Show full text]
  • Melanomas Are Comprised of Multiple Biologically Distinct Categories
    Melanomas are comprised of multiple biologically distinct categories, which differ in cell of origin, age of onset, clinical and histologic presentation, pattern of metastasis, ethnic distribution, causative role of UV radiation, predisposing germ line alterations, mutational processes, and patterns of somatic mutations. Neoplasms are initiated by gain of function mutations in one of several primary oncogenes, typically leading to benign melanocytic nevi with characteristic histologic features. The progression of nevi is restrained by multiple tumor suppressive mechanisms. Secondary genetic alterations override these barriers and promote intermediate or overtly malignant tumors along distinct progression trajectories. The current knowledge about pathogenesis, clinical, histological and genetic features of primary melanocytic neoplasms is reviewed and integrated into a taxonomic framework. THE MOLECULAR PATHOLOGY OF MELANOMA: AN INTEGRATED TAXONOMY OF MELANOCYTIC NEOPLASIA Boris C. Bastian Corresponding Author: Boris C. Bastian, M.D. Ph.D. Gerson & Barbara Bass Bakar Distinguished Professor of Cancer Biology Departments of Dermatology and Pathology University of California, San Francisco UCSF Cardiovascular Research Institute 555 Mission Bay Blvd South Box 3118, Room 252K San Francisco, CA 94158-9001 [email protected] Key words: Genetics Pathogenesis Classification Mutation Nevi Table of Contents Molecular pathogenesis of melanocytic neoplasia .................................................... 1 Classification of melanocytic neoplasms
    [Show full text]
  • Genome-Wide Discovery of G-Quadruplexes in Barley
    www.nature.com/scientificreports OPEN Genome‑wide discovery of G‑quadruplexes in barley H. Busra Cagirici1, Hikmet Budak2,3 & Taner Z. Sen1* G‑quadruplexes (G4s) are four‑stranded nucleic acid structures with closely spaced guanine bases forming square planar G‑quartets. Aberrant formation of G4 structures has been associated with genomic instability. However, most plant species are lacking comprehensive studies of G4 motifs. In this study, genome‑wide identifcation of G4 motifs in barley was performed, followed by a comparison of genomic distribution and molecular functions to other monocot species, such as wheat, maize, and rice. Similar to the reports on human and some plants like wheat, G4 motifs peaked around the 5′ untranslated region (5′ UTR), the frst coding domain sequence, and the frst intron start sites on antisense strands. Our comparative analyses in human, Arabidopsis, maize, rice, and sorghum demonstrated that the peak points could be erroneously merged into a single peak when large window sizes are used. We also showed that the G4 distributions around genic regions are relatively similar in the species studied, except in the case of Arabidopsis. G4 containing genes in monocots showed conserved molecular functions for transcription initiation and hydrolase activity. Additionally, we provided examples of imperfect G4 motifs. DNA and RNA sequences ofen form functional secondary structures, such as loops, hairpins, duplexes, triplexes, and quadruplexes1,2. G-quadruplexes (G4) are four-stranded nucleic acid structures formed within guanine (G) rich sequences. Consecutive G bases form G-stems (also called G-islands3 or G-runs4), which make up one strand of a G4 structure.
    [Show full text]
  • Nucleotide Excision Repair of DNA with Recombinant Human Proteins: Definition of the Minimal Set of Factors, Active Forms of TFIIH, and Modulation by CAK
    Downloaded from genesdev.cshlp.org on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press Nucleotide excision repair of DNA with recombinant human proteins: definition of the minimal set of factors, active forms of TFIIH, and modulation by CAK Sofia J. Arau´jo,1 Franck Tirode,2 Frederic Coin,2 Helmut Pospiech,3 Juhani E. Syva¨oja,3 Manuel Stucki,4 Ulrich Hu¨bscher,4 Jean-Marc Egly,2 and Richard D. Wood1,5 1Imperial Cancer Research Fund (ICRF), Clare Hall Laboratories, South Mimms, Hertfordshire EN6 3LD, UK; 2Institut de Ge´ne´tique et de Biologie Mole´culaire et Cellulaire (IGBMC), BP163 67404 Illkirch Cedex, C.U. de Strasbourg, France; 3Biocenter Oulu and Department of Biochemistry, University of Oulu, FIN-90570 Oulu and Department of Biology, University of Joensuu, FIN-80100 Joensuu, Finland; 4Department of Veterinary Biochemistry, University of Zurich-Irchel, CH-8057 Zu¨rich, Switzerland During human nucleotide excision repair, damage is recognized, two incisions are made flanking a DNA lesion, and residues are replaced by repair synthesis. A set of proteins required for repair of most lesions is RPA, XPA, TFIIH, XPC–hHR23B, XPG, and ERCC1–XPF, but additional components have not been excluded. The most complex and difficult to analyze factor is TFIIH, which has a 6-subunit core (XPB, XPD, p44, p34, p52, p62) and a 3-subunit kinase (CAK). TFIIH has roles both in basal transcription initiation and in DNA repair, and several inherited human disorders are associated with mutations in TFIIH subunits. To identify the forms of TFIIH that can function in repair, recombinant XPA, RPA, XPC–hHR23B, XPG, and ERCC1–XPF were combined with TFIIH fractions purified from HeLa cells.
    [Show full text]
  • The General Transcription Factors of RNA Polymerase II
    Downloaded from genesdev.cshlp.org on October 7, 2021 - Published by Cold Spring Harbor Laboratory Press REVIEW The general transcription factors of RNA polymerase II George Orphanides, Thierry Lagrange, and Danny Reinberg 1 Howard Hughes Medical Institute, Department of Biochemistry, Division of Nucleic Acid Enzymology, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854-5635 USA Messenger RNA (mRNA) synthesis occurs in distinct unique functions and the observation that they can as- mechanistic phases, beginning with the binding of a semble at a promoter in a specific order in vitro sug- DNA-dependent RNA polymerase to the promoter re- gested that a preinitiation complex must be built in a gion of a gene and culminating in the formation of an stepwise fashion, with the binding of each factor promot- RNA transcript. The initiation of mRNA transcription is ing association of the next. The concept of ordered as- a key stage in the regulation of gene expression. In eu- sembly recently has been challenged, however, with the karyotes, genes encoding mRNAs and certain small nu- discovery that a subset of the GTFs exists in a large com- clear RNAs are transcribed by RNA polymerase II (pol II). plex with pol II and other novel transcription factors. However, early attempts to reproduce mRNA transcrip- The existence of this pol II holoenzyme suggests an al- tion in vitro established that purified pol II alone was not ternative to the paradigm of sequential GTF assembly capable of specific initiation (Roeder 1976; Weil et al. (for review, see Koleske and Young 1995).
    [Show full text]
  • Covalent Modification of a Cysteine Residue in the XPB Subunit of The
    Angewandte Chemie DOI: 10.1002/anie.201408817 Covalent Inhibitors Covalent Modification of a Cysteine Residue in the XPB Subunit of the General Transcription Factor TFIIH Through Single Epoxide Cleavage of the Transcription Inhibitor Triptolide** Qing-Li He, Denis V. Titov, Jing Li, Minjia Tan, Zhaohui Ye, Yingming Zhao, Daniel Romo, and Jun O. Liu* Abstract: Triptolide is a key component of the traditional Chinese medicinal plant Thunder God Vine and has potent anticancer and immunosuppressive activities. It is an irrever- sible inhibitor of eukaryotic transcription through covalent modification of XPB, a subunit of the general transcription factor TFIIH. Cys342 of XPB was identified as the residue that undergoes covalent modification by the 12,13-epoxide group of triptolide. Mutation of Cys342 of XPB to threonine conferred resistance to triptolide on the mutant protein. Replacement of the endogenous wild-type XPB with the Cys342Thr mutant in a HEK293T cell line rendered it completely resistant to Figure 1. Structures of triptolide and triptolide analogues under clinical triptolide, thus validating XPB as the physiologically relevant development. Potential sites of attack by a nucleophile from a protein target of triptolide. Together, these results deepen our under- are marked with red arrows. Sections for which the analogues differ in standing of the interaction between triptolide and XPB and structure from triptolide are highlighted in blue. have implications for the future development of new analogues of triptolide as leads for anticancer and immunosuppressive drugs. (XPB)/ERCC3 subunit of TFIIH as a new molecular target of triptolide.[4] We showed that triptolide forms a covalent Triptolide (1, TPL), a diterpene triepoxide (Figure 1), was complex with XPB and inhibits its DNA-dependent ATPase isolated from Trypterygium Wilfordii Hook F (Lei Gong Teng activity without affecting its DNA helicase activity.
    [Show full text]
  • WO 2015/048577 A2 April 2015 (02.04.2015) W P O P C T
    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2015/048577 A2 April 2015 (02.04.2015) W P O P C T (51) International Patent Classification: (81) Designated States (unless otherwise indicated, for every A61K 48/00 (2006.01) kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, (21) International Application Number: BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, PCT/US20 14/057905 DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, (22) International Filing Date: HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, 26 September 2014 (26.09.2014) KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, (25) Filing Language: English PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, (26) Publication Language: English SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (30) Priority Data: 61/883,925 27 September 2013 (27.09.2013) US (84) Designated States (unless otherwise indicated, for every 61/898,043 31 October 2013 (3 1. 10.2013) US kind of regional protection available): ARIPO (BW, GH, GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, (71) Applicant: EDITAS MEDICINE, INC.
    [Show full text]
  • Molecular Mechanism of Nucleotide Excision Repair
    Downloaded from genesdev.cshlp.org on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press REVIEW Molecular mechanism of nucleotide excision repair Wouter L. de Laat, Nicolaas G.J. Jaspers, and Jan H.J. Hoeijmakers1 Medical Genetic Center, Department of Cell Biology and Genetics, Erasmus University, 3000 DR Rotterdam, The Netherlands From its very beginning, life has faced the fundamental Two modes of NER can be distinguished: repair of le- problem that the form in which genetic information is sions over the entire genome, referred to as global ge- stored is not chemically inert. DNA integrity is chal- nome NER (GG–NER), and repair of transcription-block- lenged by the damaging effect of numerous chemical and ing lesions present in transcribed DNA strands, hence physical agents, compromizing its function. To protect called transcription-coupled NER (TC–NER). Most XP this Achilles heel, an intricate network of DNA repair groups harbor defects in a common component of both systems has evolved early in evolution. One of these is NER subpathways. GG–NER is dependent on the activ- nucleotide excision repair (NER), a highly versatile and ity of all factors mentioned above, including the GG– sophisticated DNA damage removal pathway that coun- NER-specific complex XPC–hHR23B. The rate of repair teracts the deleterious effects of a multitude of DNA for GG–NER strongly depends on the type of lesion. For lesions, including major types of damage induced by en- instance, 6-4PPs are removed much faster from the ge- vironmental sources. The most relevant lesions subject nome than CPDs, probably because of differences in af- to NER are cyclobutane pyrimidine dimers (CPDs) and finity of the damage sensor XPC–hHR23B.
    [Show full text]