DNA damage recognition w siede, y kow, p doetsch (taylor francis, 2006)

DNA Damage Recognition edited by Wolfram Siede University of North Texas Health Science Center Fort Worth, Texas, U.S.A Yoke Wah Kow Emory University School of Medicine Atlanta, Georgia, U.S.A Paul W Doetsch Emory University School of Medicine Atlanta, Georgia, U.S.A New York London Published in 2006 by Taylor & Francis Group 270 Madison Avenue New York, NY 10016 © 2006 by Taylor & Francis Group, LLC No claim to original U.S Government works Printed in the United States of America on acid-free paper 10 International Standard Book Number-10: 0-8247-5961-3 (Hardcover) International Standard Book Number-13: 978-0-8247-5961-2 (Hardcover) This book contains information obtained from authentic and highly regarded sources Reprinted material is quoted with permission, and sources are indicated A wide variety of references are listed Reasonable efforts have been made to publish reliable data and information, but the author and the publisher cannot assume responsibility for the validity of all materials or for the consequences of their use No part of this book may be reprinted, reproduced, transmitted, or utilized in any form by any electronic, mechanical, or other means, now known or hereafter invented, including photocopying, microfilming, and recording, or in any information storage or retrieval system, without written permission from the publishers For permission to photocopy or use material electronically from this work, please access www.copyright.com (http://www.copyright.com/) or contact the Copyright Clearance Center, Inc (CCC) 222 Rosewood Drive, Danvers, MA 01923, 978-750-8400 CCC is a not-for-profit organization that provides licenses and registration for a variety of users For organizations that have been granted a photocopy license by the CCC, a separate system of payment has been arranged Trademark Notice: Product or corporate names may be trademarks or registered trademarks, and are used only for identification and explanation without intent to infringe Library of Congress Cataloging-in-Publication Data Catalog record is available from the Library of Congress Taylor & Francis Group is the Academic Division of T&F Informa plc Visit the Taylor & Francis Web site at http://www.taylorandfrancis.com Preface The topics of this book are the various molecular mechanisms that are involved in the process of DNA damage recognition as the initial step of DNA damage repair and of other related responses, such as damage tolerance and cell cycle checkpoint regulation The authors were asked to provide review-type articles designed with the researcher in the field in mind But sufficient introductory comments were requested so that a non-expert or an interested advanced student with some background knowledge can follow While we did not have a narrow definition of damage recognition in mind, a complete description of cellular DNA repair mechanisms was certainly not our goal However, looking at the scope of this impressive collection of in-depth reviews, it almost happened In the beginning of the book, certain theoretical aspects of damage recognition that are common themes throughout the book have been addressed How can one imagine that recognition proteins find their rare targets? How can we envisage protein movement—by random diffusion or ‘‘patrolling’’ along DNA? Another equally important topic addresses protein cooperation that enhances recognition specificity There is clearly an emphasis on structural aspects of DNA damage recognition throughout the book Wherever such information is available, it is explained in detail how protein/DNA damage contacts are being accomplished and which types of structural features or consequences of DNA damage are being probed by the recognition apparatus in order to permit a distinction from undamaged DNA In this fashion, damage recognition is addressed within the major pathways of DNA repair, i.e., simple damage reversal, nucleotide excision repair, base excision repair, mismatch repair, recombinational repair, and DNA endjoining We interpret the pathways of damage tolerance as a consequence of a combined recognition/accommodation process and thus we have also included chapters on translesion synthesis DNA recognition steps occur at several levels within a single repair pathway and this complexity has been considered How are repair intermediates being recognized? How is a repair intermediate handed over to the next player? If there is a competition between different mechanisms: how is a pathway choice accomplished? While we not emphasize downstream reactions, the strategy of originating a transmissible downstream signal will be addressed wherever appropriate, especially in the context of regulatory responses We were equally interested in putting specific aspects of DNA damage recognition in the cellular context Certain chapters provide the necessary backdrop by giving up-to-date reviews of certain pathways However, also chromosome structure, iii iv Preface DNA structure, and sequence context, which may affect DNA damage recognition positively or negatively, are being addressed The interference with cellular processes such as replication and transcription is discussed for several examples since such interference as a consequence of DNA damage may influence, aide, or even initiate a recognition process All that is left is to thank our authors for their hard work and superb contributions We would like to acknowledge the help of Stacy Harman Holloway We are also indebted to Anita Lekhwani, Moraima Suarez, Joseph Stubenrauch, and their colleagues at Taylor & Francis Books for pursuing the idea and providing such excellent editorial support We also thank the National Institute of Environmental Health Sciences for supporting a research collaboration amongst the three editors as well as two other authors of individual chapters that made this book possible (‘‘Cellular Responses to Genotoxic Stress’’ Program Project ES11163) Wolfram Siede Yoke Wah Kow Paul W Doetsch Contents Preface iii Contributors xvii PART I MECHANISMS OF DAMAGE RECOGNITION: THEORETICAL CONSIDERATIONS 1 Dynamics of DNA Damage Recognition Eleanore Seibert, Roman Osman, and J B Alexander Ross Introduction Role of DNA Flexibility in Sequence-Dependent Activity of UDG Opening and Bending Dynamics of GU Mismatches in DNA Conclusions 13 References 15 In Search of Damaged Bases 21 R Stephen Lloyd, A K McCullough, and M L Dodson Introduction 21 Mechanism for an Increased Rate of Target Site Location 21 In Vitro Evidence for Processive Nicking Activity of DNA Glycosylases 23 Discovery and Significance of In Vivo Processive Nicking Activity by T4-pdg 26 DNA Bending as a Potential Prerequisite for Nucleotide Flipping 27 Mechanisms of Nucleotide Flipping 29 Specificity of Glycosylase Binding Sites and Catalytic Activities 30 References 31 v vi Contents Increased Specificity and Efficiency of Base Excision Repair Through Complex Formation 33 Karen H Almeida and Robert W Sobol Introduction 33 DNA Lesion Recognition and Removal 36 Strand Incision 42 Gap Filling and Religation 46 XRCC1 Coordination 49 Long-Patch Repair 52 Emerging Subpathways 54 Conclusions 54 References 55 PART II UV DAMAGE AND OTHER BULKY DNA-ADDUCTS 65 Structure and Properties of DNA Photoproducts 67 John-Stephen Taylor Introduction 67 Cyclobutane Pyrimidine Dimers 69 Other Dimer-Related Products 79 (6–4) Products 81 Dewar Photoproduct 86 Spore Photoproduct 88 TAÃ Product 89 Conclusions 90 References 90 Damage Recognition by DNA Photolyases 95 Gwendolyn B Sancar Overview of Photolyases 95 The Nature of the Substrates 96 Characterization of Substrate Binding and Discrimination by Photolyases 97 Interactions at the Photolyase–Photoproduct Interface: The Molecular Basis for Substrate Binding and Discrimination 98 Substrate Binding In Vivo 105 Summary and Future Directions 107 References 107 Damage Recognition by the Bacterial Nucleotide Excision Repair Machinery 111 Deborah L Croteau, Matthew J DellaVecchia, Milan Skorvaga, and Bennett Van Houten Introduction 111 Diversity of DNA Lesions Recognized 113 The Proteins and Their Structural Domains 114 Contents vii Reaction Pathway for Damage Detection and Processing 123 DNA Damage Recognition within the Biological Context of the Cell 130 Similarities in Damage Recognition and Verification Between Bacterial and Eukaryotic Nucleotide Excision Repair Systems 133 References 133 Recognition of DNA Damage During Eukaryotic Nucleotide Excision Repair 139 Hanspeter Naegeli Introduction 139 Nucleotide Excision Repair Substrates 139 Eukaryotic NER Reaction 140 Subunits of the Eukaryotic NER Machinery 142 Stepwise Assembly of the Mammalian NER Recognition Complex 143 A Preassembled Repairosome in Yeast? 144 Role of Damaged DNA Binding in Damage Recognition 146 Recognition of Bulky Lesions During Transcription-Coupled DNA Repair 147 Bipartite Substrate Discrimination in the GGR Pathway 148 10 XPC–hHR23B as a Sensor of Defective Base Pairing 149 11 Transcription Factor IIH as a Sensor of Defective Deoxyribonucleotide Chemistry 151 12 Role of XPA–RPA in Integrating Different Recognition Signals 153 13 Damage-Specific Recruitment of XPG and XPF–ERCC1 155 14 Regulation of the Damage Recognition Process 155 15 Conclusions 158 References 159 Interactions of the Transcription Machinery with DNA Damage in Prokaryotes 165 Isabel Mellon General Overview 165 The Behavior of RNA Polymerase Complexes with Different Types of DNA Damage 168 The Behavior of RNA Polymerase Complexes at Lesions and NER 170 The Behavior of RNA Polymerase Complexes at Lesions and BER 173 Summary and Future Directions 175 References 175 viii Contents DNA Repair in Actively Transcribed Genes in Eukaryotic Cells 181 Moon-shong Tang Introduction 181 Heterogeneity of DNA Repair 182 Methods for Detecting TCR and GGR 185 DNA Repair in Transcriptionally Active Genes in Different Organisms 188 Models of TCR in Eukaryotic Cells 193 Effect of Different Kinds of DNA Damage on TCR 194 References 195 10 Chromatin Structure and the Repair of UV Light-Induced DNA Damage 201 Fritz Thoma Introduction 201 Nucleosomes: Heterogeneity in a Conserved Structure 202 Dynamic Properties of Nucleosomes Regulate DNA Accessibility 203 Damage Tolerance of Nucleosomes 208 Repair of Nucleosomes by Photolyase 209 Repair of Nucleosomes by NER 211 Site-Specific Repair in Nucleosome and Damage Recognition 214 Chromatin Remodeling and DNA Repair 214 Conclusions 216 References 216 11 The Ultraviolet Damage Endonuclease (UVDE) Protein and Alternative Excision Repair: A Highly Diverse System for Damage Recognition and Processing 223 Paul W Doetsch, Vladimir Beljanski, and Binwei Song Introduction 223 Discovery and Initial Characterization of S pombe UVDE 224 Recognition and Processing of UV Photoproducts 226 Recognition and Processing of Platinum G-G Diadducts 227 Recognition and Processing of Abasic Sites 227 Modified Bases not Recognized by UVDE 229 Recognition and Processing of Base–Base Mismatches 230 Recognition and Processing of Insertion–Deletion Loops 231 Subsequent Steps Following UVDE-Initiated Alternative Excision Repair 232 10 Schizosaccharomyces pombe UVDE Homologs 233 11 Conclusions 234 References 234 Contents ix 12 Structural Aspects of Pt-DNA Adduct Recognition by Proteins 239 Uta-Maria Ohndorf and Stephen J Lippard Background 239 Introduction 239 Structural Consequences of Platinum-Binding to Double-Stranded DNA 240 Recognition of cis-DDP-1,2 Intrastrand Cross-Link by Cellular Proteins 245 Summary and Outlook 254 References 255 13 Structural Aspects of Polycyclic Aromatic Carcinogen-Damaged DNA and Its Recognition by NER Proteins 263 Nicholas E Geacintov, Hanspeter Naegeli, Dinshaw J Patel, and Suse Broyde Introduction 263 Metabolism of PAH to Diol Epoxides and Formation of Stereoisomeric DNA Adducts 265 Methods 267 PAH–DNA Adducts: Conformational Motifs 269 Insights into the Structural Motifs at the Nucleoside Adduct Level Derived from Computational Approaches 273 PAH–DNA Adduct Conformational Motifs and NER 274 Structural Differences Between Bay and Fjord Stereoisomeric PAH-N6–Adenine Adducts and Correlations with NER Susceptibilities 276 Computational Analysis 279 Conclusions 289 References 290 PART III NON-BULKY BASE DAMAGE 297 14 Structural Features of DNA Glycosylases and AP Endonucleases 299 Joy L Huffman, Ottar Sundheim, and John A Tainer The Base Excision Repair Pathway 299 DNA Glycosylase Structural Families 300 Specific Mechanisms for Recognition of Damage 303 AP Endonucleases 313 Emerging Questions 315 References 315 15 Repair of Oxidized Bases 323 Yoke Wah Kow Biological Consequences of Oxidative Damage 323 ... retrieval system, without written permission from the publishers For permission to photocopy or use material electronically from this work, please access www.copyright.com (http://www.copyright.com/)... excision repair process by which DNA damage is repaired The recognition of DNA damage by repair enzymes is a dynamic process that involves the initial non-targeted binding to DNA repair enzymes, then... Recruitment of Y- Family DNA Polymerases 543 Lesion Specificity of the Y- Family DNA Polymerases 545 References 546 26 Regulation of Damage Tolerance by the RAD6 Pathway 549 Helle