DNA Repair and Mutagenesis

, by Friedberg, Errol C.; Walker, Graham C.; Siede, Wolfram

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ISBN: 9781555810887 | 1555810888
Cover: Paperback
Copyright: 5/1/1995

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This is a major revision and updating of the classic work in the field of DNA repair by Errol Friedberg published in 1985. The authors have extensively revised the original text and provided more than 4000 references to current primary research literature. In addition, there are four new chapters on mutagenesis. The book will serve as an important reference resource for all courses in DNA repair and mutagenesis, and for molecular biologists working in many areas of cancer research

Preface

DNA Damage

(58)

Spontaneous Alterations of and Damage to DNA

(17)

Mismatches

(4)

Spontaneous Alterations in the Chemistry of DNA Bases

(7)

Loss of Bases---Depurination and Depyrimidination

(1)

Oxidative Damage to DNA

(5)

Environmental Damage to DNA

(23)

Physical Agents That Damage DNA

(12)

Chemical Agents That Damage DNA

(11)

DNA Damage and Chromatin Structure

(3)

Detection and Measurement of Base Damage in DNA

(2)

Enzyme Probes for Measuring DNA Damage

(1)

Postlabeling Methods for Detecting Base Damage

(1)

Specific Antibodies for Measuring DNA Damage

(1)

Summary and Conclusions

(12)

Introduction to Mutagenesis

(32)

Mutations and Mutants: Some Definitions

(6)

Point Mutations and Other Classes of Mutations

(1)

Base Substitution Mutations

(2)

Mutations Resulting from the Addition or Deletion of Small Numbers of Base Pairs

(1)

Systems Used To Detect and Analyze Mutations

(6)

The First Systems for Analysis of Mutagenesis

(1)

The Ames Salmonella Test: a Widely Used Reversion System

(2)

Other Examples of Forward Mutational Systems

(2)

Special Systems To Detect Frameshift or Deletion Mutations

(1)

Analyses of Mutagenesis in Mammalian Cells

(6)

Shuttle Vectors

(2)

Sequencing of Mutated Target Genes in Mammalian Cells by Use of PCR

(2)

Chemical and Physical Methods for Identifying DNA Fragments Carrying a Mutation

(1)

Analyses of Mutagenesis in Whole Animals

(1)

Use of Site-Specific Adducts

(1)

Insights into the Molecular Basis of Mutagenesis from the Study of Purified Polymerases

(5)

Error Discrimination by DNA Polymerases: Mechanisms Responsible for Polymerase Fidelity

(4)

Mechanisms Contributing to Spontaneous Mutagenesis

(8)

Base Substitution Mutations Resulting from Misincorporation during DNA Synthesis

(1)

Mutations Resulting from Misalignments during DNA Synthesis

(8)

DNA Repair by Reversal of Damage

(44)

Photoreactivation of DNA

(15)

DNA Photolyase (Photoreactivating Enzyme)

(1)

Properties and Mechanism of Action of DNA Photolyases

(12)

Light-Dependent ``Repair'' of (6-4) Photoproducts in DNA

107

(1)

Photoreactivation of RNA

107

(1)

Repair of Spore Photoproduct

107

(1)

Formation of Spore Photoproduct

108

(1)

Repair of O6-Guanine and O4-Thymine Alkylations and Phosphotriesters in DNA

108

(18)

Adaptation to Alkylation Damage in E. coli

109

(1)

Repair of O6-Alkylguanine and O4-Alkylthymine in DNA

110

(1)

O6-Methylguanine-DNA Methyltransferase I of E. coli

110

(4)

Role of Ada Protein in the Adaptive Response to Mutagenesis

114

(5)

Termination of the Adaptive Response

119

(1)

DNA Alkyltransferase II

120

(1)

DNA Alkyltransferases in Other Organisms

121

(5)

Repair of Single-Strand Breaks by Direct Rejoining

126

(1)

Summary and Conclusions

126

(9)

Base Excision Repair

135

(56)

Excision Repair of DNA---General Considerations

135

(4)

DNA Glycosylases

139

(15)

3-Methyladenine-DNA Glycosylase

140

(7)

Uracil-DNA Glycosylase

147

(6)

Hydroxymethyluracil-DNA Glycosylase

153

(1)

Hypoxanthine-DNA Glycosylase

153

(1)

5-Methylcytosine-DNA Glycosylase

154

(1)

Thymine Mismatch-DNA Glycosylase

154

(1)

DNA Glycosylases with Associated AP Lyase Activity

154

(15)

MutY-DNA Glycosylase

157

(1)

Formamidopyrimidine-DNA Glycosylase

158

(3)

Thymine Glycol-DNA Glycosylase

161

(1)

Endonucleases VIII and IX

162

(1)

Pyrimidine Dimer-DNA Glycosylase

163

(1)

Bacteriophage T4 PD-DNA Glycosylase

164

(2)

M. luteus PD-DNA Glycosylase

166

(1)

A PD-DNA Glycosylase Activity in S. cerevisiae

167

(1)

Biological Significance of the AP Lyase Activity Associated with DNA Glycosylases

167

(2)

Conclusing Comments on DNA Glycosylases

169

(1)

AP Endonucleases

169

(8)

AP Endonucleases in E. coli

169

(4)

AP Endonucleases in Eukaryotes

173

(2)

BAPI, APEX, and HAPI AP Endonucleases

175

(2)

Relevance of Base Excision Repair to Oxidative Damage---General Considerations

177

(1)

Postincision Events during Base Excision Repair

177

(14)

DNA Deoxyribophosphodiesterase of E. coli

177

(1)

Completion of Base Excision Repair Initiated by the Phage T4 and M. luteus PD-DNA Glycosylases

178

(1)

Repair Synthesis during Base Excision Repair

178

(3)

DNA Ligation

181

(10)

Nucleotide Excision Repair in Prokaryotes

191

(42)

UvrABC Damage-Specific Endonuclease of E. coli

192

(18)

The uvrA+ Gene and UvrA Protein

194

(3)

The uvrB+ Gene and UvrB Protein

197

(7)

The uvrC+ Gene and UvrC Protein

204

(3)

Substrate Specificity of the UvrABC Endonuclease

207

(2)

Roles of ATP in Damage-Specific Incision

209

(1)

Role of Proteolysis in the Regulation of DNA Incision by the UvrABC Endonuclease

209

(1)

Summary of Damage-Specific Incision during Nucleotide Excision Repair in E. coli

209

(1)

Postincisional Events---Excision of Damaged Nucleotides, Repair Synthesis, and DNA Ligation

210

(4)

Role of UvrD Protein (DNA Helicase II) and Pol I in Excision and Repair Synthesis

210

(4)

Repair Synthesis

214

(1)

DNA Ligation

214

(1)

Nucleotide Excision Repair of Cross-Links in DNA---a Special Situation

214

(2)

A Uvr Protein-Independent Pathway for the Repair of Cross-Links in DNA?

216

(1)

Coupling of Transcription and Nucleotide Excision Repair in E. coli

216

(2)

Miscellaneous Functions Possibly Associated with Nucleotide Excision Repair

218

(1)

Are Uvr Proteins Involved in Other Cellular Processes in E. coli?

218

(1)

Detection and Measurement of Nucleotide Excision Repair

219

(4)

Nucleotide Excision Repair in Other Prokaryotes

223

(2)

Other Damage-Specific DNA-Incising Activities?

225

(1)

Summary and Conclusions

225

(8)

Nucleotide Excision Repair in Lower Eukaryotes

233

(50)

Eukaryotic Models for Nucleotide Excision Repair

234

(1)

Nucleotide Excision Repair in the Yeast Saccharomyces cerevisiae

234

(38)

Overview of the Genetics of Nucleotide Excision Repair

234

(2)

Some Nucleotide Excision Repair Genes Were Discovered Incidentally

236

(2)

Potential Roles of RAD7, RAD16, and RAD23 in Perturbing Chromatin Structure

238

(2)

Possible Presence of More Genes for Nucleotide Excision Repair

240

(1)

Genes That Are Indispensable for Nucleotide Excision Repair

241

(23)

Other Genes Involved in Nucleotide Excision Repair

264

(2)

Summary of Nucleotide Excision Repair in Yeast Cells

266

(1)

Other Members of the RAD3 Epistasis Group

267

(1)

Enzymes Involved in Postincision Events during Nucleotide Excision Repair in Yeast Cells

268

(4)

Nucleotide Excision Repair in Other Lower Eukaryotes

272

(3)

Schizosaccharomyces pombe

272

(1)

Drosophila melanogaster

273

(1)

Other Lower Eukaryotes

274

(1)

Conclusions

275

(8)

Nucleotide Excision Repair in Mammalian Cells: General Considerations and Chromatin Dynamics

283

(34)

Biology of Nucleotide Excision Repair in Mammalian Cells

283

(2)

Damage-Specific Incision of DNA

284

(1)

Loss of Radiolabeled Thymine-Containing Pyrimidine Dimers from DNA

284

(1)

Loss of Sites in DNA Sensitive to Pyrimidine Dimer-Specific Enzymes

284

(1)

Ligation-Mediated PCR

284

(1)

Measurement of Repair Synthesis in DNA

285

(1)

Kinetics of Nucleotide Excision Repair in Mammalian Cells

285

(3)

Repair Patch Sizes in Mammalian Cells

288

(1)

Influence of Chromatin and Higher-Order Structure on Nucleotide Excision Repair in Mammalian Cells

289

(5)

Nucleotide Excision Repair in Chromatin

291

(3)

Heterogeneity of Nucleotide Excision Repair in the Mammalian Genome

294

(10)

Intragenomic Heterogeneity

294

(2)

Intragenic Heterogeneity of Repair: Preferential Repair of Actively Transcribed DNA

296

(2)

Transcription-Dependent Nucleotide Excision Repair

298

(6)

Other Aspects of Genomic Organization during Excision Repair

304

(6)

Methylation of DNA during Excision Repair

304

(2)

ADP-Ribosylation and DNA Repair in Mammalian Cells

306

(4)

The Poly(ADP-Ribose) Polymerase Gene

310

(1)

Conclusions

310

(7)

Nucleotide Excision Repair: Mammalian Genes and Proteins

317

(50)

Genes Involved in Nucleotide Excision Repair

317

(23)

Excision Repair Mutants from Rodent Cells

317

(1)

Rodent Genetic Complementation Groups

318

(2)

Cloning Human ERCC Genes

320

(11)

Use of Rodent Cell Lines for Cloning Human Repair Genes: Concluding Comments

331

(1)

Mutant Cell Lines from Patients with XP

332

(8)

Nucleotide Excision Repair in Cell-Free Systems

340

(17)

Requirements for Nucleotide Excision Repair in a Cell-Free System

343

(1)

Permeabilized Cell Systems for Identifying Factors Required for Nucleotide Excision Repair

344

(1)

Mammalian DNA Polymerases

345

(6)

Use of Permeabilized Cell Systems To Study Repair Synthesis

351

(1)

Mammalian DNA Ligases

352

(4)

Mammalian DNA Topoisomerases and DNA Repair

356

(1)

Nucleotide Excision Repair of Mitochondrial DNA

357

(1)

Conclusions

357

(10)

Mismatch Repair

367

(40)

Early Biological Evidence for the Existence of Mismatch Repair

368

(1)

Genetic Phenomena Suggesting the Existence of Mismatch Repair

368

(1)

Long-Patch Mismatch Repair in Prokaryotes

369

(19)

Mismatch Repair after Transformation of S. pneumoniae

369

(7)

Biochemistry of Methyl-Directed Mismatch Repair in E. coli

376

(12)

Long-Patch Mismatch Repair in Eukaryotes

388

(8)

In Vivo Evidence for Mismatch Repair in Yeasts and Fungi

388

(1)

Homologs of mutL+ and mutS+ in Eukaryotic Cells

389

(2)

In Vitro Analyses of Mismatch Repair in Eukaryotic Cells: Human Cells Have a Bidirectional Mismatch Repair System

391

(2)

An Alkylation-Tolerant Mutator Human Cell Line Is Deficient in Strand-Specific Repair

393

(1)

Destabilization of Tracts of Simple Repetitive DNA by Mutations Affecting Mismatch Repair: Implications for Human Diseases

393

(3)

Short-Patch Mismatch Repair in Prokaryotes and Eukaryotes

396

(11)

Very Short Patch Mismatch Correction in E. coli

396

(2)

MutY-Dependent Mismatch Repair in E. coli

398

(1)

Short-Patch Mismatch Repair in Mammalian Cells

399

(8)

SOS Responses and DNA Damage Tolerance in Prokaryotes

407

(58)

The SOS Responses

408

(1)

Current Model for SOS Regulation

408

(27)

Development of the Model for SOS Regulation

411

(16)

Differential Regulation of SOS-Controlled Genes

427

(1)

What Is the SOS-Inducing Signal?

428

(4)

Physiological Considerations of the SOS Regulatory Circuit

432

(2)

SOS Responses in Other Bacteria

434

(1)

RecA Protein: a Protein with Mechanistic Roles in Homologous Recombination and DNA Repair

435

(5)

Recombination Reactions of RecA Protein

436

(4)

DNA Replication and Damage Tolerance in Cells Exposed to DNA-Damaging Agents

440

(25)

Transient Inhibition of DNA Synthesis after DNA Damage

440

(1)

Recovery of DNA Replication after DNA Damage

441

(12)

Repair of Double-Strand Breaks

453

(12)

Mutagenesis in Prokaryotes

465

(58)

SOS-Dependent Mutagenesis: Requirements for Particular Gene Products

465

(21)

SOS Mutagenesis by UV Radiation and Most Chemicals Is Not a Passive Process

465

(2)

The UmuD and UmuC Proteins Are Important for UV Radiation and Chemical Mutagenesis

467

(5)

Posttranslational Activation of UmuD Protein: a New Dimension to SOS Regulation

472

(7)

umuD+C+ Homologs in Other Organisms

479

(2)

Genetic and Physiological Evidence for the Involvement of RecA Protein, DNA Polymerase III, and GroEL/GroES Proteins in SOS Mutagenesis

481

(5)

Inferences about the Mechanism of SOS Mutagenesis Based on Mutational Spectra and Site-Directed Adduct Studies

486

(17)

The Original lacI System: a Purely Genetic Means of Determining Mutational Spectra

487

(2)

Mutational Spectra Obtained by Direct DNA Sequencing

489

(1)

Factors Influencing the Mutational Spectrum for a Given Mutagen

489

(1)

Influence of Transcription-Coupled Excision Repair on Mutational Spectra

490

(2)

Identification of Pramutagenic Lesions

492

(8)

The Predominance of C → T Transitions in UV Radiation Mutagenesis

500

(2)

More-Complex Lesions as Premutagenic Lesions

502

(1)

Model for the Molecular Mechanism of SOS Mutagenesis

503

(4)

Experiments Involving UV Irradiation plus Photoreversal

503

(2)

Premutagenic Lesions on the Lagging versus the Leading Strand May Influence the Probability of a Mutation

505

(1)

Biochemical Mechanism of SOS Mutagenesis

505

(2)

SOS-Dependent Mutagenesis in Cells Not Exposed to Exogenous DNA-Damaging Agents

507

(3)

The SOS Mutator Effect on Chromosomal Loci or on an F' Plasmid

508

(1)

The SOS Mutator Effect on Single- and Double-Stranded Phages

509

(1)

What Is the Biological Purpose of SOS Mutagenesis?

510

(1)

SOS-Independent Mutagenesis

510

(2)

Mutations Arising in Cell Populations That Are Not Actively Dividing

512

(11)

DNA Damage Tolerance and Mutagenesis in Eukaryotic Cells

523

(72)

DNA Damage-Induced Mutagenesis in the Yeast Saccharomyces cerevisiae

524

(12)

The Genetic Framework

524

(5)

Timing and Regulation of UV Radiation-Induced Mutagenesis

529

(3)

Contributions from Mutational Spectra

532

(2)

Untargeted Mutagenesis in Yeast Cells Exposed to DNA Damage

534

(1)

Summary and Conclusions

535

(1)

DNA Damage-Induced Mutagenesis in Mammalian Cells

536

(19)

Genetic Control

536

(1)

Replicational Bypass of UV Radiation Lesions

537

(4)

Inducibility of Mutagenic Processes in Mammalian Cells?

541

(3)

Mutational Specificity of UV-Induced Lesions

544

(10)

Summary and Conclusions

554

(1)

DNA Strand Break Repair and Recombination in S. cerevisiae

555

(12)

DNA Strand Breaks and Their Repair after Treatment with Ionizing Radiation

555

(2)

The Genetic Framework

557

(5)

Strand Exchange Proteins

562

(1)

Intrachromosomal Recombination and the Role of the RAD1/RAD10 Nuclease

562

(3)

Illegitimate Recombination

565

(1)

Recombination in the Cellular Context

566

(1)

DNA Strand Break Repair and Recombination in Mammalian Cells

567

(28)

The Genetic Framework

567

(2)

Repair of Localized Double-Strand Breaks: V(D)J Recombination

569

(4)

Mammalian Proteins Possibly Involved in Recombination

573

(1)

Illegitimate Recombination and DNA End Joining

574

(1)

UV Radiation-Stimulated Recombination

575

(1)

Summary and Conclusions

576

(19)

Regulatory Responses to DNA-Damaging Agents in Eukaryotic Cells

595

(38)

Gene Activation following Exposure to DNA-Damaging Agents

595

(12)

Induction of Genes in Saccharomyces cerevisiae

595

(6)

Gene Activation in Mammalian Cells following Exposure to DNA-Damaging Agents

601

(6)

Cell Cycle Arrest as a Response to DNA Damage

607

(11)

Regulation of Cell Cycle Progression

607

(1)

G2 Arrest in the Presence of DNA Damage: the S. cerevisiae RAD9 Gene as a Paradigm

608

(1)

G2 Checkpoint Control in S. pombe

609

(2)

G2 Checkpoint Control in Mammalian Cells

611

(1)

G1 and G1/S Arrest

611

(2)

The p53 Gene and Its Role in the Cell Cycle

613

(5)

Programmed Cell Death (Apoptosis)

618

(1)

Potential Signaling Enzymes

619

(2)

Summary and Conclusions

621

(12)

Human Hereditary Diseases with Defective Processing of DNA Damage

633

(54)

Hereditary Diseases Characterized by Defective DNA Repair

634

(28)

Xeroderma Pigmentosum

634

(15)

Trichothiodystrophy

649

(6)

Cockayne's Syndrome

655

(3)

Fanconi's Anemia

658

(4)

Hereditary Diseases Characterized by Defective Cellular Responses to DNA Damage

662

(9)

Ataxia Telangiectasia (Louis-Bar Syndrome)

662

(6)

Bloom's Syndrome

668

(2)

A Clinical Syndrome That Yielded the 46BR Cell Line

670

(1)

Miscellaneous Diseases with Possible Defects in the Processing of Damaged DNA

671

(16)

Index

687

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DNA Repair and Mutagenesis

Summary

Table of Contents

Supplemental Materials

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Summary

Table of Contents

Supplemental Materials

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