DNA Damage Recognition

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ISBN: 9780824759612 | 0824759613
Cover: Hardcover
Copyright: 9/19/2005

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Covering an array of topics, this authoritative work summarizes recent developments, while providing timely reviews on the molecular mechanisms employed by cells to distinguish between damaged and undamaged sites and stimulate the appropriate repair pathways. Richly illustrated, this guide discusses the theoretical aspects of DNA damage recognition, exploring those that are relevant for various regulatory responses, such as transcriptional regulation or checkpoint arrest. It also details key concepts in the recognition of bulky DNA base damage, reviews the excision repair of non-bulky base damage, covers short-patch repair and the recognition and repair of single- and double-strand breaks. br clear=all

Preface

iii

Contributors

xvii

PART I. MECHANISMS OF DAMAGE RECOGNITION: THEORETICAL CONSIDERATIONS

(64)

Dynamics of DNA Damage Recognition

(18)

Eleanore Seibert

Roman Osman

J. B. Alexander Ross

Introduction

(1)

Role of DNA Flexibility in Sequence-Dependent Activity of UDG

(4)

Opening and Bending Dynamics of G•U Mismatches in DNA

(5)

Conclusions

(8)

References

(6)

In Search of Damaged Bases

(12)

R. Stephen Lloyd

A. K. McCullough

M. L. Dodson

Introduction

(1)

Mechanism for an Increased Rate of Target Site Location

(2)

In Vitro Evidence for Processive Nicking Activity of DNA Glycosylases

(3)

Discovery and Significance of In Vivo Processive Nicking Activity by T4-pdg

(1)

DNA Bending as a Potential Prerequisite for Nucleotide Flipping

(2)

Mechanisms of Nucleotide Flipping

(1)

Specificity of Glycosylase Binding Sites and Catalytic Activities

(3)

References

(2)

Increased Specificity and Efficiency of Base Excision Repair Through Complex Formation

(32)

Karen H. Almeida

Robert W. Sobol

Introduction

(3)

DNA Lesion Recognition and Removal

(6)

Strand Incision

(4)

Gap Filling and Religation

(3)

XRCC1 Coordination

(3)

Long-Patch Repair

(2)

Emerging Subpathways

(1)

Conclusions

(11)

References

(10)

PART II. UV DAMAGE AND OTHER BULKY DNA-ADDUCTS

(232)

Structure and Properties of DNA Photoproducts

(28)

John-Stephen Taylor

Introduction

(2)

Cyclobutane Pyrimidine Dimers

(10)

Other Dimer-Related Products

(2)

(6-4) Products

(5)

Dewar Photoproduct

(2)

Spore Photoproduct

(1)

TA* Product

(1)

Conclusions

(5)

References

(5)

Damage Recognition by DNA Photolyases

(16)

Gwendolyn B. Sancar

Overview of Photolyases

(1)

The Nature of the Substrates

(1)

Characterization of Substrate Binding and Discrimination by Photolyases

(1)

Interactions at the Photolyase-Photoproduct Interface: The Molecular Basis for Substrate Binding and Discrimination

(7)

Substrate Binding In Vivo

105

(2)

Summary and Future Directions

107

(4)

References

107

(4)

Damage Recognition by the Bacterial Nucleotide Excision Repair Machinery

111

(28)

Deborah L. Croteau

Matthew J. Della Vecchia

Milan Skorvaga

Bennett Van Houten

Introduction

111

(2)

Diversity of DNA Lesions Recognized

113

(1)

The Proteins and Their Structural Domains

114

(9)

Reaction Pathway for Damage Detection and Processing

123

(7)

DNA Damage Recognition within the Biological Context of the Cell

130

(3)

Similarities in Damage Recognition and Verification Between Bacterial and Eukaryotic Nucleotide Excision Repair Systems

133

(6)

References

133

(6)

Recognition of DNA Damage During Eukaryotic Nucleotide Excision Repair

139

(26)

Hanspeter Naegeli

Introduction

139

(1)

Nucleotide Excision Repair Substrates

139

(1)

Eukaryotic NER Reaction

140

(2)

Subunits of the Eukaryotic NER Machinery

142

(1)

Stepwise Assembly of the Mammalian NER Recognition Complex

143

(1)

A Preassembled Repairosome in Yeast?

144

(2)

Role of Damaged DNA Binding in Damage Recognition

146

(1)

Recognition of Bulky Lesions During Transcription-Coupled DNA Repair

147

(1)

Bipartite Substrate Discrimination in the GGR Pathway

148

(1)

XPC-hHR23B as a Sensor of Defective Base Pairing

149

(2)

Transcription Factor IIH as a Sensor of Defective Deoxyribonucleotide Chemistry

151

(2)

Role of XPA-RPA in Integrating Different Recognition Signals

153

(2)

Damage-Specific Recruitment of XPG and XPF-ERCC1

155

(1)

Regulation of the Damage Recognition Process

155

(3)

Conclusions

158

(7)

References

159

(6)

Interactions of the Transcription Machinery with DNA Damage in Prokaryotes

165

(16)

Isabel Mellon

General Overview

165

(3)

The Behavior of RNA Polymerase Complexes with Different Types of DNA Damage

168

(2)

The Behavior of RNA Polymerase Complexes at Lesions and NER

170

(3)

The Behavior of RNA Polymerase Complexes at Lesions and BER

173

(2)

Summary and Future Directions

175

(6)

References

175

(6)

DNA Repair in Actively Transcribed Genes in Eukaryotic Cells

181

(20)

Moon-shong Tang

Introduction

181

(1)

Heterogeneity of DNA Repair

182

(3)

Methods for Detecting TCR and GGR

185

(3)

DNA Repair in Transcriptionally Active Genes in Different Organisms

188

(5)

Models of TCR in Eukaryotic Cells

193

(1)

Effect of Different Kinds of DNA Damage on TCR

194

(7)

References

195

(6)

Chromatin Structure and the Repair of UV Light-Induced DNA Damage

201

(22)

Fritz Thoma

Introduction

201

(1)

Nucleosomes: Heterogeneity in a Conserved Structure

202

(1)

Dynamic Properties of Nucleosomes Regulate DNA Accessibility

203

(5)

Damage Tolerance of Nucleosomes

208

(1)

Repair of Nucleosomes by Photolyase

209

(2)

Repair of Nucleosomes by NER

211

(3)

Site-Specific Repair in Nucleosome and Damage Recognition

214

(1)

Chromatin Remodeling and DNA Repair

214

(2)

Conclusions

216

(7)

References

216

(7)

The Ultraviolet Damage Endonuclease (UVDE) Protein and Alternative Excision Repair: A Highly Diverse System for Damage Recognition and Processing

223

(16)

Paul W. Doetsch

Vladimir Beljanski

Binwei Song

Introduction

223

(1)

Discovery and Initial Characterization of S. pombe UVDE

224

(2)

Recognition and Processing of UV Photoproducts

226

(1)

Recognition and Processing of Platinum G-G Diadducts

227

(1)

Recognition and Processing of Abasic Sites

227

(2)

Modified Bases not Recognized by UVDE

229

(1)

Recognition and Processing of Base-Base Mismatches

230

(1)

Recognition and Processing of Insertion-Deletion Loops

231

(1)

Subsequent Steps Following UVDE-Initiated Alternative Excision Repair

232

(1)

Schizosaccharomyces pombe UVDE Homologs

233

(1)

Conclusions

234

(5)

References

234

(5)

Structural Aspects of Pt-DNA Adduct Recognition by Proteins

239

(24)

Uta-Maria Ohndorf

Stephen J. Lippard

Background

239

(1)

Introduction

239

(1)

Structural Consequences of Platinum-Binding to Double-Stranded DNA

240

(5)

Recognition of cis-DDP-1,2 Intrastrand Cross-Link by Cellular Proteins

245

(9)

Summary and Outlook

254

(9)

References

255

(8)

Structural Aspects of Polycyclic Aromatic Carcinogen-Damaged DNA and Its Recognition by NER Proteins

263

(34)

Nicholas E. Geacintov

Hanspeter Naegeli

Dinshaw J. Patel

Suse Broyde

Introduction

263

(2)

Metabolism of PAH to Diol Epoxides and Formation of Stereoisomeric DNA Adducts

265

(2)

Methods

267

(2)

PAH-DNA Adducts: Conformational Motifs

269

(4)

Insights into the Structural Motifs at the Nucleoside Adduct Level Derived from Computational Approaches

273

(1)

PAH-DNA Adduct Conformational Motifs and NER

274

(2)

Structural Differences Between Bay and Fjord Stereoisomeric PAH-N6-Adenine Adducts and Correlations with NER Susceptibilities

276

(3)

Computational Analysis

279

(10)

Conclusions

289

(8)

References

290

(7)

PART III. NON-BULKY BASE DAMAGE

297

(164)

Structural Features of DNA Glycosylases and AP Endonucleases

299

(24)

Joy L. Huffman

Ottar Sundheim

John A. Tainer

The Base Excision Repair Pathway

299

(1)

DNA Glycosylase Structural Families

300

(3)

Specific Mechanisms for Recognition of Damage

303

(10)

AP Endonucleases

313

(2)

Emerging Questions

315

(8)

References

315

(8)

Repair of Oxidized Bases

323

(16)

Yoke Wah Kow

Biological Consequences of Oxidative Damage

323

(3)

Major Repair Enzymes that Recognize Oxidative Base Damage

326

(7)

Repair Pathways for Oxidative DNA Damage

333

(2)

Conclusions

335

(4)

References

335

(4)

Recognition of Alkylating Agent Damage in DNA

339

(50)

Timothy R. O'Connor

Modification of DNA by Small Alkylating Agents

339

(2)

DNA Repair Systems for Removal of Alkylating Agent Damage

341

(1)

O6-Alkylguanine DNA Methyltransferases---AGTs

342

(13)

AlkB---2-oxoglutarate-Dependent Fe(II)-Dependent Oxygenases

355

(7)

DNA Glycosylases---Base Excision Repair

362

(15)

Nucleotide Excision Repair

377

(12)

References

382

(7)

Deaminated Bases in DNA

389

(14)

Bernard Weiss

Introduction

389

(1)

Lesions and Their Consequences

389

(1)

Deaminating Agents

390

(3)

Endonuclease V, An Enzyme Specific for Deaminated Purines

393

(3)

Hypoxanthine/Alkylpurine DNA Glycosylases

396

(3)

Endonuclease VIII of E. coli

399

(1)

Conclusions

399

(4)

References

399

(4)

New Paradigms for DNA Base Excision Repair in Mammals

403

(18)

Sankar Mitra

Lee R. Wiederhold

Hong Dou

Tadahide Izumi

Tapas K. Hazra

Introduction

403

(1)

Oxidized Base-Specific Glycosylases in E. coli and Mammals

404

(12)

Conclusions

416

(5)

References

417

(4)

Recognition and Repair of Abasic Sites

421

(24)

David M. Wilson III

David F. Lowry

AP Site Formation and Biological Impact

421

(2)

AP-DNA Dynamics and Structure

423

(2)

AP Endonucleases

425

(1)

AP Site Recognition and Processing

426

(6)

AP Site Repair in General

432

(13)

References

436

(9)

Oxidative Mitochondrial DNA Damage Resistance and Repair

445

(16)

Gerald S. Shadel

Introduction

445

(1)

General Features of Human mtDNA

446

(3)

Oxidative mtDNA Damage Resistance and Repair

449

(3)

New Lessons About Oxidative mtDNA Damage from the Budding Yeast, S. cerevisiae, Genetic Model System

452

(3)

Conclusions and New Horizons

455

(6)

References

456

(5)

PART IV. MISMATCH REPAIR

461

(32)

Mechanism of DNA Mismatch Repair from Bacteria to Human

463

(20)

Samir Acharya

Richard Fishel

Introduction

463

(3)

Biochemistry of Mismatch Repair Proteins

466

(3)

Mechanism of Mismatch Repair

469

(5)

Implications

474

(9)

References

475

(8)

Interaction of the Escherichia coli Vsr with DNA and Mismatch Repair Proteins

483

(10)

Ashok S. Bhagwat

Bernard Connolly

Introduction

483

(2)

Structure of Vsr

485

(5)

Summary and Concluding Remarks

490

(3)

References

490

(3)

PART V. REPLICATION AND BYPASS OF DNA LESIONS

493

(86)

Mechanism of Translesion DNA Synthesis in Escherichia coli

495

(12)

Zvi Livneh

Ayelet Maor-Shoshani

Moshe Goldsmith

Gali Arad

Ayal Hendel

Lior Izhar

Introduction

495

(1)

Translesion DNA Synthesis and the SOS Response

496

(1)

Overview on Pol V

497

(1)

Fidelity of Pol V

497

(1)

Lesion Bypass By Pol V

498

(1)

Accessory Proteins Are Required for Lesion Bypass By Pol V

499

(2)

Other DNA Polymerases Involved in TLS in E. coli

501

(1)

In Vivo Role of TLS

502

(5)

References

503

(4)

Mechanism of Bypass Polymerases in Eukaryotes

507

(22)

Zhigang Wang

Introduction

507

(2)

Concepts of Translesion Synthesis

509

(1)

Translesion Polymerases

510

(3)

Mechanistic Models of Translesion Synthesis

513

(2)

Translesion Synthesis of Various DNA Damage in Eukaryotes

515

(5)

Importance of Translesion Synthesis in Eukaryotic Biology

520

(9)

References

521

(8)

Structural Features of Bypass Polymerases

529

(20)

Caroline Kisker

Introduction

529

(6)

DNA Synthesis by the DINB Family Members from the Sulfolobus Genus

535

(6)

DNA Binding and Lesion Bypass in Polη

541

(2)

Recruitment of Y-Family DNA Polymerases

543

(2)

Lesion Specificity of the Y-Family DNA Polymerases

545

(4)

References

546

(3)

Regulation of Damage Tolerance by the RAD6 Pathway

549

(30)

Helle D. Ulrich

Introduction

549

(1)

Mechanisms of Damage Bypass

550

(4)

The RAD6 Pathway

554

(12)

Proliferating Cell Nuclear Antigen Modification by the Ubiquitin-Like Protein Sumo

566

(1)

Mechanistic Considerations

567

(3)

Interactions of the RAD6 Pathway with Other Factors

570

(3)

Summary and Outlook

573

(6)

References

574

(5)

PART VI. DNA STRAND BREAKS

579

(176)

Biochemical and Cellular Aspects of Homologous Recombination

581

(28)

Lieneke van Veelen

Joanna Wesoly

Roland Kanaar

Introduction

581

(1)

DNA Double-Strand Break Repair Through Homologous Recombination

582

(1)

Biochemical Properties of Homologous Recombination Proteins

582

(4)

Cellular Properties of Homologous Recombination Proteins

586

(23)

References

602

(7)

The Mechanism of Vertebrate Nonhomologous DNA End Joining and Its Role in Immune System Gene Rearrangements

609

(20)

Michael R. Lieber

Yunmei Ma

Kefei Yu

Ulrich Pannicke

Klaus Schwarz

Introduction

609

(1)

Essential Aspects of Vertebrate Nonhomologous DNA End Joining (NHEJ)

609

(4)

Overview of V(D)J Recombination and its Utilization of NHEJ in the Rejoining Process

613

(2)

Overview of Immunoglobulin Class Switch Recombination and its Utilization of NHEJ in the Rejoining Process

615

(4)

Points of Biochemical Detail in the NHEJ Pathway

619

(3)

Special Aspects of NHEJ as it Relates to V(D)J Recombination

622

(1)

Are There Multiple NHEJ Pathways?

622

(2)

NHEJ and Human Disease

624

(1)

Future Avenues of Study of the NHEJ Pathway

624

(5)

References

624

(5)

Structural Aspects of Ku and the DNA-Dependent Protein Kinase Complex

629

(56)

Eric A. Hendrickson

Joy L. Huffman

John A. Tainer

Introduction

629

(5)

The Ku Autoantigen

634

(14)

DNA-PKcs

648

(7)

DNA-PK, Telomeres and Genomic Stability

655

(7)

Summary

662

(23)

References

663

(22)

Cellular Functions of Mammalian DNA Ligases

685

(20)

John B. Leppard

Julie Della-Maria Goetz

Teresa A. Motycka

Zhiwan Dong

Wei Song

Hui-Min Tseng

Sangeetha Vijayakumar

Alan E. Tomkinson

Introduction

685

(1)

Reaction Mechanism

686

(1)

DNA Ligase Structure

686

(1)

Mammalian DNA Ligases

687

(6)

Cellular Functions of DNA Ligase

693

(12)

References

697

(8)

The Mre11/Rad50/Nbs1 Complex

705

(18)

Karl-Peter Hopfner

Introduction

705

(1)

The Mre11 Complex

706

(4)

Cellular Biochemistry of the Mre11 Complex

710

(4)

Structural Biochemistry of the Mre11 Complex

714

(3)

Unified Model, Conclusions, and Outlook

717

(6)

References

718

(5)

Histone γ-H2AX Involvement in DNA Double-Strand Break Repair Pathways

723

(14)

Nikolaos A.A. Balatsos

Emmy P. Rogakou

Introduction

723

(1)

Formation and Detection of γ-Phosphorylation

724

(2)

γ-Phosphorylation of H2A(X) Spans Megabase-Long Domains in Chromatin

726

(1)

Kinases Involved in γ-Phosphorylation of H2A(X) Histone Family

727

(1)

Recruitment of Repair Factors to γ-Phosphorylated Chromatin

728

(1)

Models and Speculations About the Biological Role of γ-H2AX Foci

729

(8)

References

732

(5)

DNA Strand-Break Recognition, Signaling, and Resolution: The Role of Poly(ADP-Ribose) Polymerases-1 and -2

737

(18)

Emmanuelle Pion

Catherine Spenlehauer

Laurence Tartier

Jean-Christophe Ame

Francoise Dantzer

Valerie Schreiber

Gerard Gradwohl

Josiane Menissier-de Murcia

Gilbert de Murcia

Background

737

(1)

Introduction

737

(2)

Nick Sensor Function of PARP-1

739

(4)

Dual Role of DNA-Damage Induced PAR Synthesis: Break Signaling and Recruitment of XRCC1

743

(4)

No Cross-Talk Between PAR Synthesis and γ-H2AX Formation in Response to DNA-Strand Break Injury

747

(2)

Conclusions and Future Prospects

749

(6)

References

750

(5)

PART VII. PERCEPTION OF DNA DAMAGE FOR INITIATING REGULATORY RESPONSES

755

(86)

Cellular and Molecular Responses to Alkylation Damage in DNA

757

(24)

James M. Bugni

Leona D. Samson

Introduction

757

(3)

The E. coli Adaptive Response: Translating Methyl DNA Adducts into a Transcriptional Signal

760

(6)

Cellular Responses to O6MeG

766

(5)

Cellular Responses to 3MeA

771

(4)

Genome-Wide Analysis of Responses to Alkylating Agents

775

(1)

Conclusions

776

(5)

References

776

(5)

Damage Signals Triggering the Escherichia coli SOS Response

781

(22)

Mark D. Sutton

Introduction

781

(1)

The E. coli SOS Response

781

(3)

Structure-Function of the LexA Protein Family

784

(2)

RecA Protein-DNA Interactions and LexA Self-Cleavage

786

(3)

Role of DNA Damage in Inducing the E. coli SOS Response

789

(2)

Upregulation of DNA Repair and DNA Damage Tolerance Under the SOS Response

791

(4)

After the Damage is Repaired: Turning off the SOS Response and the Return to Normalcy

795

(2)

Concluding Remarks and Future Perspectives

797

(6)

References

798

(5)

Recognition of DNA Damage as the Initial Step of Eukaryotic Checkpoint Arrest

803

(24)

Wolfram Siede

Introduction

803

(1)

Early Studies Characterizing Checkpoint Triggering Damage and Sensor Proteins

804

(1)

The ATM Protein is a Kinase and a Putative Damage Sensor

805

(2)

The ATR Protein and its Targeting Subunit

807

(1)

PCNA- and RFC-like Clamp and Clamp Loader Complexes Function as Damage Sensors

808

(2)

Crosstalk Between Sensors

810

(1)

The MRN Complex Plays a Role in Checkpoint Arrests

811

(1)

Synopsis: Independent But Communicating Sensors Are Linked By Common Requirements

812

(1)

The Generation of a Transducible Signal

812

(2)

Other Sensor Candidates

814

(1)

Sensing UV Damage

815

(1)

Adaptation and Cell Cycle Restart

816

(11)

References

818

(9)

Responses to Replication of DNA Damage

827

(14)

Maria Pia Longhese

Marco Foiani

Introduction

827

(1)

How do Cells Deal with a Damaged Template During DNA Replication?

828

(2)

The S-Phase Checkpoint

830

(7)

Replication-Related Genome Instability

837

(4)

References

837

(4)

Index

841

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DNA Damage Recognition

Summary

Table of Contents

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