DNA REPAIR Edited by Inna Kruman DNA Repair Edited by Inna Kruman Published by InTech Janeza Trdine 9, 51000 Rijeka, Croatia Copyright © 2011 InTech All chapters are Open Access distributed under the Creative Commons Attribution 3.0 license, which permits to copy, distribute, transmit, and adapt the work in any medium, so long as the original work is properly cited. After this work has been published by InTech, authors have the right to republish it, in whole or part, in any publication of which they are the author, and to make other personal use of the work. Any republication, referencing or personal use of the work must explicitly identify the original source. As for readers, this license allows users to download, copy and build upon published chapters even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. Notice Statements and opinions expressed in the chapters are these of the individual contributors and not necessarily those of the editors or publisher. No responsibility is accepted for the accuracy of information contained in the published chapters. The publisher assumes no responsibility for any damage or injury to persons or property arising out of the use of any materials, instructions, methods or ideas contained in the book. Publishing Process Manager Alenka Urbancic Technical Editor Teodora Smiljanic Cover Designer Jan Hyrat Image Copyright ZF, 2011. Used under license from Shutterstock.com First published October, 2011 Printed in Croatia A free online edition of this book is available at www.intechopen.com Additional hard copies can be obtained from orders@intechweb.org DNA Repair, Edited by Inna Kruman p. cm. ISBN 978-953-307-697-3 free online editions of InTech Books and Journals can be found at www.intechopen.com Contents Preface XI Part 1 DNA Damage Response 1 Chapter 1 A Recombination Puzzle Solved: Role for New DNA Repair Systems in Helicobacter pylori Diversity/Persistence 3 Ge Wang and Robert J. Maier Chapter 2 RloC: A Translation-Disabling tRNase Implicated in Phage Exclusion During Recovery from DNA Damage 21 Gabriel Kaufmann, Elena Davidov, Emmanuelle Steinfels-Kohn, Ekaterina Krutkina, Daniel Klaiman, Tamar Margalit, Michal Chai-Danino and Alexander Kotlyar Chapter 3 The Role of DDB2 in Regulating Cell Survival and Apoptosis Following DNA Damage - A Mini-Review 45 Chuck C K. Chao Chapter 4 The Potential Roles of DNA-Repair Proteins in Centrosome Maintenance 57 Mikio Shimada, Akihiro Kato and Junya Kobayashi Chapter 5 Shared Regulatory Motifs in Promoters of Human DNA Repair Genes 67 Lonnie R. Welch, Laura M. Koehly and Laura Elnitski Chapter 6 Mitochondrial DNA Damage: Role of Ogg1 and Aconitase 85 Gang Liu and David W. Kamp Chapter 7 Structure-Function Relationship of DNA Repair Proteins: Lessons from BRCA1 and RAD51 Studies 103 Effrossyni Boutou, Vassiliki Pappa, Horst-Werner Stuerzbecher and Constantinos E. Vorgias VI Contents Chapter 8 The Involvement of E2F1 in the Regulation of XRCC1-Dependent Base Excision DNA Repair 127 Yulin Zhang and Dexi Chen Chapter 9 Posttranslational Modifications of Rad51 Protein and Its Direct Partners: Role and Effect on Homologous Recombination – Mediated DNA Repair 143 Milena Popova, Sébastien Henry and Fabrice Fleury Chapter 10 Post-Transcriptional Regulation of E2F Transcription Factors: Fine-Tuning DNA Repair, Cell Cycle Progression and Survival in Development & Disease 161 Lina Dagnino, Randeep Kaur Singh and David Judah Chapter 11 Eidetic Analysis of the Premature Chromosome Condensation Process 185 Dorota Rybaczek Chapter 12 A DNA Repair Protein BRCA1 as a Potentially Molecular Target for the Anticancer Platinum Drug Cisplatin 205 Adisorn Ratanaphan Chapter 13 Saccharomyces cerevisiae as a Model System to Study the Role of Human DDB2 in Chromatin Repair 231 Kristi L. Jones, Ling Zhang and Feng Gong Chapter 14 Cell Cycle and DNA Damage Response in Postmitotic Neurons 241 Inna I. Kruman Chapter 15 TopBP1 in DNA Damage Response 281 Ewa Forma, Magdalena Brys and Wanda M. Krajewska Chapter 16 Post-Meiotic DNA Damage and Response in Male Germ Cells 305 Guylain Boissonneault, Frédéric Leduc, Geneviève Acteau, Marie-Chantal Grégoire, Olivier Simard, Jessica Leroux, Audrey Carrier-Leclerc and Mélina Arguin Chapter 17 BRCA2 Mutations and Consequences for DNA Repair 327 Erika T. Brown Chapter 18 Roles of MicroRNA in DNA Damage and Repair 341 Xinrong Chen and Tao Chen Part 2 Evolution of DNA Repair 355 Chapter 19 Meiosis as an Evolutionary Adaptation for DNA Repair 357 Harris Bernstein, Carol Bernstein and Richard E. Michod Contents VII Chapter 20 From Seed to Tree: The Functioning and Evolution of DNA Repair in Plants 383 Jaana Vuosku, Marko Suokas, Johanna Kestilä, Tytti Sarjala and Hely Häggman Part 3 Mechanisms of DNA Repair 399 Chapter 21 The Gratuitous Repair on Undamaged DNA Misfold 401 Xuefeng Pan, Peng Xiao, Hongqun Li, Dongxu Zhao and Fei Duan Chapter 22 ATP-Binding Cassette Properties of Recombination Mediator Protein RecF 431 Sergey Korolev Chapter 23 DNA Damage Recognition for Mammalian Global Genome Nucleotide Excision Repair 453 Kaoru Sugasawa Chapter 24 DNA Double-Strand Break Repair Through Non-Homologous End-Joining: Recruitment and Assembly of the Players 477 Radhika Pankaj Kamdar and Yoshihisa Matsumoto Part 4 Polymorphism of DNA Repair Genes 503 Chapter 25 DNA Repair Capacity-Related to Genetic Polymorphisms of DNA Repair Genes and Aflatoxin B1-Related Hepatocellular Carcinoma Among Chinese Population 505 Xi-Dai Long, Jin-Guang Yao, Zhi Zeng, Cen-Han Huang, Pinhu Liao, Zan-Song Huang, Yong-Zhi Huang, Fu-Zhi Ban, Xiao-Yin Huang, Li-Min Yao, Lu-Dan Fan and Guo-Hui Fu Chapter 26 Low Penetrance Genetic Variations in DNA Repair Genes and Cancer Susceptibility 525 Ravindran Ankathil Chapter 27 Polymorphisms in Nucleotide Excision Repair Genes and Risk of Colorectal Cancer: A Systematic Review 539 Rikke Dalgaard Hansen and Ulla Vogel Chapter 28 Variants and Polymorphisms of DNA Repair Genes and Neurodegenerative Diseases 567 Fabio Coppedè Part 5 Telomeres and DNA Repair 583 Chapter 29 Characterization of 5’-Flanking Regions of Various Human Telomere Maintenance Factor-Encoding Genes 585 Fumiaki Uchiumi, Takahiro Oyama, Kensuke Ozaki and Sei-ichi Tanuma VIII Contents Chapter 30 Roles of DNA Repair Proteins in Telomere Maintenance 597 Masaru Ueno Part 6 Measuring DNA Repair Capacity 613 Chapter 31 DNA Repair Measured by the Comet Assay 615 Amaya Azqueta, Sergey Shaposhnikov and Andrew R. Collins [...]... evolutionary adaptation for DNA Repair (Bernstein et al.) and evolution of DNA repair in plants (Vuosku et al.) The third part discusses the mechanisms of DNA repair, particularly non-homologous end-joining (Kamdar and Matsumoto), homologous recombination (Korolev), global genome nucleotide excision repair (Sugasawa) and the gratuitous repair on undamaged DNA formed by unusual DNA structures generating... (homeologous) that may be used for recombinational DNA repair 3 Mechanisms of DNA recombinational repair known in model bacteria Although the bulk of DNA damage affects one strand of a duplex DNA segment, occasionally both DNA strands opposite each other are damaged; the latter situation necessitates recombinational repair using an intact homologous DNA sequence [56, 57] DNA double-strand breaks (DSB) occur as... mechanisms (mainly urease) [43], efficient DNA repair systems are required for H pylori to survive in the host 2.1 DNA repair systems in H pylori The whole genome sequences of H pylori revealed it contains several DNA repair pathways that are common to many bacterial species, while it lacks other repair pathways or contains A Recombination Puzzle Solved: Role for New DNA Repair Systems in Helicobacter pylori... book reviews a number of important DNA repairrelated topics The book consists of 31 chapters, divided into six parts Each chapter is written by one or several experts in the corresponding area The scope of the book ranges from the DNA damage response and DNA repair mechanisms, to evolutionary aspects of DNA repair, providing a snapshot of current understanding of DNA repair processes A collection of... pylori genome also has extensive repetitive DNA sequences that are targets for intragenomic recombination [35] 2 Overview of DNA repair in H pylori Oxidative DNA damage represents a major form of DNA damage Among the many oxidized bases in DNA, 8-oxo-guanine is a ubiquitous biomarker of DNA oxidation [36] In addition, acid (low pH) conditions may result in DNA damage via depurination [37] H pylori survives... cell cycle machinery in DNA damage response of postmitotic cells (Kruman), the involvement of DNA- repair proteins in centrosome maintenance (Mikio), transcriptional regulatory networks controlling DNA repair pathways (Welch et al.) and on the function of microRNA in DNA damage response (Chen and Chen) XII Preface The second part of the book deals with an evolutionary view of DNA repair, focusing on meiosis... fifth parts cover roles of DNA repair gene mutations in carcinogenesis and neurodegeneration (Long et al.; Ankathil; Hansen and Vogel; Coppede), and the role of DNA repair machinery in telomere maintenance (Uchiumi et al., Ueno) In the last part, Dr Azqueta and colleagues review various applications of the comet assay for quantification of DNA repair capacity, including DNA repair analysis at the level... frequency, suggesting that RecN is a critical factor in DNA recombinational repair [83] In contrast, loss of UvrD or MutS2 in H pylori resulted in an increase of DNA recombination frequency [46, 48] Suppression of DNA recombination by UvrD or MutS2, and facilitation of DNA recombination by RecN, may play a role in coordinating DNA repair pathways Recombinational repair could be mutagenic due to homeologous recombination... Whereas the RecO protein can displace ssDNA-binding protein (SSB) and 12 DNA Repair bind to ssDNA, RecR is the key component for loading RecA onto ssDNA [95, 97] Likely, the RecRO pathway (with no RecF) is present in H pylori The recR and recO mutants showed marked sensitivity to DNA damaging agents metronidazole and UV light, indicating roles of RecR and RecO in DNA repair Unlike the addA (recB) mutant,... which are major components of DNA recombination machinery, RecN is a protein specific for repairing DSBs by linking DSB recognition and DNA recombination initiation It was proposed that the attenuated ability to colonize mouse stomachs by recN cells was mainly due to the strain’s failure to repair DSBs through a DNA recombinational repair pathway 4.4 AddAB helicase-nuclease DNA helicases play key roles . the book ranges from the DNA damage response and DNA repair mechanisms, to evolutionary aspects of DNA repair, providing a snapshot of current understanding of DNA repair processes. A collection. recombinational DNA repair. 3. Mechanisms of DNA recombinational repair known in model bacteria Although the bulk of DNA damage affects one strand of a duplex DNA segment, occasionally both DNA strands. VIII Contents Chapter 30 Roles of DNA Repair Proteins in Telomere Maintenance 597 Masaru Ueno Part 6 Measuring DNA Repair Capacity 613 Chapter 31 DNA Repair Measured by the Comet Assay 615