DNA Repair and Replication (eBook)

Cover 1
DNA Repair and Replication 4
Copyright Page 5
CONTENTS 6
PREFACE 10
Chapter 1. Base Excision Repair 13
I. Introduction 13
II. Types of Damage Repaired by BER 17
III. DNA Glycosylases 19
IV. Downstream BER Enzymes 30
V. Mammalian BER 35
VI. Roles of BER Enzymes in Other Processes 39
References 40
Chapter 2. Nucleotide Excision Repair in E. Coli and Man 55
I. Introduction 55
II. Damage Recognition 57
III. Mechanism of Excision Repair 60
IV. Transcription-Coupled Repair 68
V. Repair of Chromatin 71
VI. Conclusion 75
References 77
Chapter 3. Photolyase and Cryptochrome Blue-Light Photoreceptors 85
I. Introduction 85
II. Phylogenetics 86
III. Structure of Photolyase 89
IV. Reaction Mechanism of Photolyase 91
V. (6–4) Photolyase 98
VI. Cryptochrome 102
VII. Conclusion 108
References 108
Chapter 4. Coordination of Repair, Checkpoint, and Cell Death Responses to DNA Damage 113
I. Introduction 113
II. Overview of Biological Responses to DNA Damage 116
III. Molecular Components for the Initiation of DNA Damage Responses 121
IV. Apoptotic Effectors in DNA Damage Response 127
V. DNA Repair Proteins in Damage Signaling 132
VI. Alternative Models for the Temporal Coordination of DNA Damage Responses 135
VII. Future Prospects 139
References 140
Chapter 5. Functions of DNA Polymerases 149
I. DNA Polymerase Families 149
II. Structures and Compositions of DNA Polymerases 151
III. Functions of DNA Polymerases 153
IV. Polymerases for DNA Repair 153
V. Polymerases for Replicating Undamaged DNA 162
VI. Polymerases for Sister Chromatid Cohesion 163
VII. Mitochondrial DNA Replication. 164
VIII. Polymerases for Replicating Damaged DNA. 164
IX. Polymerases and Cell-Cycle Checkpoints 167
X. Polymerases for Replication Restart and Homologous Recombination 167
XI. Polymerases for DNA Mismatch Repair 168
XII. Polymerases in the Development of the Immune System 168
XIII. Biological Consequences of Polymerase Dysfunction 169
XIV. Closing Comments 170
References 171
Chapter 6. Cellular Functions of DNA Polymerase and Rev1 Protein 179
I. Introduction 179
II. Enzymological Studies With Pol. and Rev1p 184
III. Genetic Analysis 190
IV. Processes Other than General Translesion Replication that Employ Pol and Rev1p 194
V. Regulation of Pol. and Rev1p and Interactions with other Proteins 198
VI. Conclusions and Speculations 202
References 207
Chapter 7. DNA Polymerases. and . 217
I. Historical Perspective 217
II. Identification of RAD30 and its Orthologs 218
III. Biochemical Properties of Pol. and Pol. 219
IV. Translesion Synthesis by Pol. and Pol. 222
V. Structure of the Catalytic Core of S. cerevisiae Pol. 224
VI. Regulation and Localization of Pol. and Pol. 227
VII. Mutations in Polc. in XP Variants 229
VIII. Pols. and . and the Polymerase Switch: Interactions with PCNA and Rev1 231
IX. Protection from Cellular Effects of DNA Damage 232
X. Roles of Pol. and Pol. in Somatic Hypermutation 233
References 234
Chapter 8. Properties and Functions of Escherichia Coli : Pol IV and Pol V 241
I. DNA Pol IV, the dinB Gene Product 242
II. DNA Polymerase V, the umuDC Gene Product 260
References 269
Chapter 9. Mammalian Pol .: Regulation of Its Expression and Lesion Substrates 277
I. Structures of the Genes and Proteins 277
II. Enzymatic Properties of Pol. 283
III. Possible Mechanisms of TLS by Pol. In Vivo 286
References 287
Chapter 10. DNA Postreplication Repair Modulated by Ubiquitination and Sumoylation 291
I. Introduction 291
II. DNA Postreplication Repair Prokaryotes 292
III. DNA Postreplication Repair in Eukaryotes 293
IV. Ubiquitination 295
V. Protein Conjugation in PRR 298
VI. Postreplication Repair via Covalent Modifications of PCNA 304
VII. Functional Conservation of Eukaryotic Postreplication Repair 307
VIII. Future Directions 309
IX. Conclusions 312
References 313
Chapter 11. Somatic Hypermutation: A Mutational Panacea 319
I. Generation of Antibody Diversity 319
II. Somatic Hypermutation 325
III. Apobec Protein Family 335
IV. Biochemical Perspective 338
References 339
Author Index 349
Subject Index 381