DNA damage recognition:
Gespeichert in:
| Format: | Buch |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
New York, NY [u.a.]
Taylor & Francis
2006
|
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XXII, 845 S. Ill., graph. Darst. 26 cm |
| ISBN: | 0824759613 9780824759612 |
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| 245 | 1 | 0 | |a DNA damage recognition |c ed. by Wolfram Siede ... |
| 264 | 1 | |a New York, NY [u.a.] |b Taylor & Francis |c 2006 | |
| 300 | |a XXII, 845 S. |b Ill., graph. Darst. |c 26 cm | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 650 | 4 | |a DNA repair | |
| 650 | 4 | |a DNA Damage |x physiology | |
| 650 | 4 | |a DNA Damage |x genetics | |
| 650 | 4 | |a DNA Repair |x genetics | |
| 650 | 4 | |a DNA Repair |x physiology | |
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| 700 | 1 | |a Siede, Wolfram |e Sonstige |4 oth | |
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Datensatz im Suchindex
| _version_ | 1804135309092323328 |
|---|---|
| adam_text | Contents
Preface .... Hi
Contributors .... xvii
PART I. MECHANISMS OF DAMAGE RECOGNITION: THEORETICAL
CONSIDERATIONS 1
1. Dynamics of DNA Damage Recognition 3
Eleanore Seibert, Roman Osman, and J. B. Alexander Ross
1. Introduction .... 3
2. Role of DNA Flexibility in Sequence Dependent Activity
of UDG .... 4
3. Opening and Bending Dynamics of G«U Mismatches
in DNA .... 8
4. Conclusions .... 13
References .... 15
2. In Search of Damaged Bases 21
R Stephen Lloyd, A. K. McCullough, and M. L. Dodson
1. Introduction .... 21
2. Mechanism for an Increased Rate of Target Site Location .... 21
3. In Vitro Evidence for Processive Nicking Activity of DNA
Glycosylases .... 23
4. Discovery and Significance of In Vivo Processive Nicking
Activity by T4 pdg .... 26
5. DNA Bending as a Potential Prerequisite for Nucleotide
Flipping .... 27
6. Mechanisms of Nucleotide Flipping .... 29
7. Specificity of Glycosylase Binding Sites and Catalytic
Activities .... 30
References .... 31
vi Contents
3. Increased Specificity and Efficiency of Base Excision Repair
Through Complex Formation 33
Karen H. Almeida and Robert W. Sobol
1. Introduction .... 33
2. DNA Lesion Recognition and Removal .... 36
3. Strand Incision .... 42
4. Gap Filling and Religation .... 46
5. XRCC1 Coordination .... 49
6. Long Patch Repair .... 52
7. Emerging Subpathways .... 54
8. Conclusions .... 54
References .... 55
PART II. UV DAMAGE AND OTHER BULKY DNA ADDUCTS 65
4. Structure and Properties of DNA Photoproducts 67
John Stephen Taylor
1. Introduction .... 67
2. Cyclobutane Pyrimidine Dimers .... 69
3. Other Dimer Related Products .... 79
4. (6 4) Products .... 81
5. Dewar Photoproduct .... 86
6. Spore Photoproduct .... 88
7. TA* Product .... 89
8. Conclusions .... 90
References .... 90
5. Damage Recognition by DNA Photolyases 95
Gwendolyn B. Sancar
1. Overview of Photolyases .... 95
2. The Nature of the Substrates .... 96
3. Characterization of Substrate Binding and Discrimination
by Photolyases .... 97
4. Interactions at the Photolyase Photoproduct Interface: The
Molecular Basis for Substrate Binding and
Discrimination .... 98
5. Substrate Binding In Vivo .... 105
6. Summary and Future Directions .... 107
References .... 107
6. Damage Recognition by the Bacterial Nucleotide Excision
Repair Machinery HI
Deborah L. Croteau, Matthew J. DellaVecchia, Milan Skorvaga,
and Bennett Van Houten
1. Introduction .... Ill
2. Diversity of DNA Lesions Recognized .... 113
3. The Proteins and Their Structural Domains .... 114
Contents vii
4. Reaction Pathway for Damage Detection and Processing .... 123
5. DNA Damage Recognition within the Biological
Context of the Cell .... 130
6. Similarities in Damage Recognition and Verification
Between Bacterial and Eukaryotic Nucleotide
Excision Repair Systems .... 133
References .... 133
7. Recognition of DNA Damage During Eukaryotic
Nucleotide Excision Repair 139
Hanspeter Naegeli
1. Introduction .... 139
2. Nucleotide Excision Repair Substrates .... 139
3. Eukaryotic NER Reaction .... 140
4. Subunits of the Eukaryotic NER Machinery .... 142
5. Stepwise Assembly of the Mammalian NER Recognition
Complex .... 143
6. A Preassembled Repairosome in Yeast? .... 144
7. Role of Damaged DNA Binding in Damage Recognition .... 146
8. Recognition of Bulky Lesions During Transcription Coupled
DNA Repair .... 147
9. 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
8. Interactions of the Transcription Machinery with DNA
Damage in Prokaryotes 165
Isabel Mellon
1. General Overview .... 165
2. The Behavior of RNA Polymerase Complexes with Different
Types of DNA Damage .... 168
3. The Behavior of RNA Polymerase Complexes
at Lesions and NER .... 170
4. The Behavior of RNA Polymerase Complexes
at Lesions and BER .... 173
5. Summary and Future Directions .... 175
References .... 175
viii Contents
9. DNA Repair in Actively Transcribed Genes
in Eukaryotic Cells 181
Moon shong Tang
1. Introduction .... 181
2. Heterogeneity of DNA Repair .... 182
3. Methods for Detecting TCR and GGR .... 185
4. DNA Repair in Transcriptionally Active Genes in Different
Organisms .... 188
5. Models of TCR in Eukaryotic Cells... ... 193
6. 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
1. Introduction .... 201
2. Nucleosomes: Heterogeneity in a Conserved Structure .... 202
3. Dynamic Properties of Nucleosomes Regulate
DNA Accessibility .... 203
4. Damage Tolerance of Nucleosomes .... 208
5. Repair of Nucleosomes by Photolyase .... 209
6. Repair of Nucleosomes by NER .... 211
7. Site Specific Repair in Nucleosome and Damage
Recognition .... 214
8. Chromatin Remodeling and DNA Repair .... 214
9. 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
1. Introduction .... 223
2. Discovery and Initial Characterization of S. pombe
UVDE .... 224
3. Recognition and Processing of UV Photoproducts .... 226
4. Recognition and Processing of Platinum
G G Diadducts .... 227
5. Recognition and Processing of Abasic Sites .... 227
6. Modified Bases not Recognized by UVDE .... 229
7. Recognition and Processing of Base Base Mismatches .... 230
8. Recognition and Processing of Insertion Deletion Loops .... 231
9. 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
1. Background .... 239
2. Introduction .... 239
3. Structural Consequences of Platinum Binding to Double Stranded
DNA .... 240
4. Recognition of cis DDP 1,2 Intrastrand Cross Link by Cellular
Proteins .... 245
5. 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
1. Introduction .... 263
2. Metabolism of PAH to Diol Epoxides and Formation
of Stereoisomeric DNA Adducts .... 265
3. Methods .... 267
4. PAH DNA Adducts: Conformational Motifs .... 269
5. Insights into the Structural Motifs at the Nucleoside Adduct
Level Derived from Computational Approaches .... 273
6. PAH DNA Adduct Conformational Motifs and NER .... 274
7. Structural Differences Between Bay and Fjord Stereoisomeric
PAH iV^ Adenine Adducts and Correlations with NER
Susceptibilities .... 276
8. Computational Analysis .... 279
9. 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
1. The Base Excision Repair Pathway .... 299
2. DNA Glycosylase Structural Families .... 300
3. Specific Mechanisms for Recognition of Damage .... 303
4. AP Endonucleases .... 313
5. Emerging Questions .... 315
References .... 315
15. Repair of Oxidized Bases 323
Yoke Wah Kow
1. Biological Consequences of Oxidative Damage .... 323
x Contents
2. Major Repair Enzymes that Recognize Oxidative Base
Damage .... 326
3. Repair Pathways for Oxidative DNA Damage .... 333
4. Conclusions .... 335
References .... 335
16. Recognition of Alkylating Agent Damage in DNA 339
Timothy R. O Connor
1. Modification of DNA by Small Alkylating Agents .... 339
2. DNA Repair Systems for Removal of Alkylating Agent
Damage .... 341
3. O6 Alkylguanine DNA Methyltransferases—AGTs .... 342
4. AlkB—2 oxoglutarate Dependent Fe(II) Dependent
Oxygenases .... 355
5. DNA Glycosylases—Base Excision Repair .... 362
6. Nucleotide Excision Repair .... 377
References .... 382
17. Deaminated Bases in DNA 389
Bernard Weiss
1. Introduction .... 389
2. Lesions and Their Consequences .... 389
3. Deaminating Agents .... 390
4. Endonuclease V, An Enzyme Specific for Deaminated
Purines .... 393
5. Hypoxanthine/Alkylpurine DNA Glycosylases .... 396
6. Endonuclease VIII of E. coli .... 399
7. Conclusions .... 399
References .... 399
18. New Paradigms for DNA Base Excision Repair
in Mammals . . 403
Sankar Mitra, Lee R. Wiederhold, Hong Don, Tadahide Izumi,
and Tapas K. Hazra
1. Introduction .... 403
2. Oxidized Base Specific Glycosylases in E. coli
and Mammals .... 404
3. Conclusions .... 416
References .... 417
19. Recognition and Repair of Abasic Sites 421
David M. Wilson III and David F. Lowry
1. AP Site Formation and Biological Impact .... 421
2. AP DNA Dynamics and Structure .... 423
Contents xi
3. AP Endonucleases .... 425
4. AP Site Recognition and Processing .... 426
5. AP Site Repair in General .... 432
References .... 436
20. Oxidative Mitochondrial DNA Damage Resistance and Repair . . . 445
GeraldS. Shadel
1. Introduction .... 445
2. General Features of Human mtDNA .... 446
3. Oxidative mtDNA Damage Resistance and Repair .... 449
4. New Lessons About Oxidative mtDNA Damage from the Budding
Yeast, S. cerevisiae, Genetic Model System .... 452
5. Conclusions and New Horizons .... 455
References .... 456
PART IV. MISMATCH REPAIR 461
21. Mechanism of DNA Mismatch Repair from
Bacteria to Human 463
Samir Acharya and Richard Fishel
1. Introduction .... 463
2. Biochemistry of Mismatch Repair Proteins .... 466
3. Mechanism of Mismatch Repair .... 469
4. Implications .... 474
References .... 475
22. Interaction of the Escherichia coli Vsr with DNA and Mismatch
Repair Proteins 483
Ashok S. Bhagwat and Bernard Connolly
1. Introduction .... 483
2. Structure of Vsr .... 485
3. Summary and Concluding Remarks .... 490
References .... 490
PART V. REPLICATION AND BYPASS OF DNA LESIONS 493
23. Mechanism of Translesion DNA Synthesis in Escherichia coli .... 495
Zvi Livneh, Ayelet Maor Shoshani, Moshe Goldsmith, Gali Arad,
Ayal Hendel, and Lior Izhar
1. Introduction .... 495
2. Translesion DNA Synthesis and the SOS Response .... 496
3. Overview on Pol V .... 497
4. Fidelity of Pol V .... 497
5. Lesion Bypass By Pol V .... 498
6. Accessory Proteins Are Required for Lesion Bypass
By Pol V .... 499
xii Contents
7. Other DNA Polymerases Involved in TLS in E. coli .... 501
8. In Vivo Role of TLS .... 502
References .... 503
24. Mechanism of Bypass Polymerases in Eukaryotes 507
Zhigang Wang
1. Introduction .... 507
2. Concepts of Translesion Synthesis .... 509
3. Translesion Polymerases .... 510
4. Mechanistic Models of Translesion Synthesis .... 513
5. Translesion Synthesis of Various DNA Damage
in Eukaryotes .... 515
6. Importance of Translesion Synthesis in Eukaryotic
Biology .... 520
References .... 521
25. Structural Features of Bypass Polymerases 529
Caroline Kisker
1. Introduction .... 529
2. DNA Synthesis by the DINB Family Members from
the Sulfolobus Genus .... 535
3. DNA Binding and Lesion Bypass in Polr) .... 541
4. Recruitment of Y Family DNA Polymerases .... 543
5. Lesion Specificity of the Y Family DNA Polymerases .... 545
References .... 546
26. Regulation of Damage Tolerance by the RAD6 Pathway 549
Helle D. Ulrich
1. Introduction .... 549
2. Mechanisms of Damage Bypass .... 550
3. The RAD6 Pathway .... 554
4. Proliferating Cell Nuclear Antigen Modification
by the Ubiquitin Like Protein Sumo .... 566
5. Mechanistic Considerations .... 567
6. Interactions of the RAD6 Pathway with Other Factors .... 570
7. Summary and Outlook .... 573
References .... 574
PART VI. DNA STRAND BREAKS 579
27. Biochemical and Cellular Aspects of Homologous
Recombination 581
Lieneke van Veelen, Joanna Wesoly, and Roland Kanaar
1. Introduction .... 581
2. DNA Double Strand Break Repair Through Homologous
Recombination .... 582
Contents xiii
3. Biochemical Properties of Homologous Recombination
Proteins .... 582
4. Cellular Properties of Homologous Recombination
Proteins .... 586
References .... 602
28. The Mechanism of Vertebrate Nonhomologous DNA End Joining and Its
Role in Immune System Gene Rearrangements 609
Michael R. Lieber, Yunmei Ma, Kefei Yu, Ulrich Pannicke,
and Klaus Schwarz
1. Introduction .... 609
2. Essential Aspects of Vertebrate Nonhomologous DNA
End Joining (NHEJ) .... 609
3. Overview of V(D)J Recombination and its Utilization of NHEJ
in the Rejoining Process .... 613
4. Overview of Immunoglobulin Class Switch Recombination and its
Utilization of NHEJ in the Rejoining Process .... 615
5. Points of Biochemical Detail in the NHEJ Pathway .... 619
6. Special Aspects of NHEJ as it Relates to V(D)J
Recombination .... 622
7. Are There Multiple NHEJ Pathways? .... 622
8. NHEJ and Human Disease .... 624
9. Future Avenues of Study of the NHEJ Pathway .... 624
References .... 624
29. Structural Aspects of Ku and the DNA Dependent Protein
Kinase Complex 629
Eric A. Hendrickson, Joy L. Huffman, and John A. Tainer
1. Introduction .... 629
2. The Ku Autoantigen .... 634
3. DNA PKcs .... 648
4. DNA PK, Telomeres and Genomic Stability .... 655
5. Summary .... 662
References .... 663
30. Cellular Functions of Mammalian DNA Ligases 685
John B. Leppard, Julie Delia Maria Goetz, Teresa A. Motycka,
Zhiwan Dong, Wei Song, Hui Min Tseng, Sangeetha Vijayakumar,
and Alan E. Tomkinson
1. Introduction .... 685
2. Reaction Mechanism .... 686
3. DNA Ligase Structure .... 686
4. Mammalian DNA Ligases .... 687
5. Cellular Functions of DNA Ligase .... 693
References .... 697
xiv Contents
31. The Mrell/Rad50/Nbsl Complex 705
Karl Peter Hopfner
1. Introduction .... 705
2. The Mrell Complex .... 706
3. Cellular Biochemistry of the Mrell Complex .... 710
4. Structural Biochemistry of the Mrell Complex .... 714
5. Unified Model, Conclusions, and Outlook .... 717
References .... 718
32. Histone y H2AX Involvement in DNA Double Strand Break
Repair Pathways 723
Nikolaos A. A. Balatsos and Emmy P. Rogakou
1. Introduction .... 723
2. Formation and Detection of y Phosphorylation .... 724
3. y Phosphorylation of H2A(X) Spans Megabase Long
Domains in Chromatin .... 726
4. Kinases Involved in y Phosphorylation of H2A(X)
Histone Family .... 727
5. Recruitment of Repair Factors to y Phosphorylated
Chromatin .... 728
6. Models and Speculations About the Biological Role of
Y H2AX Foci .... 729
References .... 732
33. DNA Strand Break Recognition, Signaling, and Resolution: The Role of
Poly(ADP Ribose) Polymerases 1 and 2 737
Emmanuelle Pion, Catherine Spenlehauer, Laurence Tartier,
Jean Christophe Ame, Francoise Dantzer, Valerie Schreiber,
Gerard Gradwohl, Josiane Menissier de Murcia, and Gilbert de Murcia
1. Background .... 737
2. Introduction .... 737
3. Nick Sensor Function of PARP 1 .... 739
4. Dual Role of DNA Damage Induced PAR Synthesis: Break Signaling
and Recruitment of XRCC1 .... 743
5. No Cross Talk Between PAR Synthesis and y H2AX Formation in
Response to DNA Strand Break Injury .... 747
6. Conclusions and Future Prospects .... 749
References .... 750
PART VII. PERCEPTION OF DNA DAMAGE FOR INITIATING
REGULATORY RESPONSES 755
34. Cellular and Molecular Responses to Alkylation Damage
in DNA 757
James M. Bugni and Leona D. Samson
1. Introduction .... 757
Contents xv
2. The E. coli Adaptive Response: Translating Methyl DNA Adducts
into a Transcriptional Signal .... 760
3. Cellular Responses to 06MeG .... 766
4. Cellular Responses to 3MeA .... 771
5. Genome Wide Analysis of Responses to Alkylating
Agents .... 775
6. Conclusions .... 776
References .... 776
35. Damage Signals Triggering the Escherichia coli SOS Response . . . 781
Mark D. Sutton
1. Introduction .... 781
2. The E. coli SOS Response .... 781
3. Structure Function of the LexA Protein Family .... 784
4. RecA Protein DNA Interactions and LexA
Self Cleavage .... 786
5. Role of DNA Damage in Inducing the E. coli SOS
Response .... 789
6. Upregulation of DNA Repair and DNA Damage Tolerance Under
the SOS Response .... 791
7. After the Damage is Repaired: Turning off the SOS Response and the
Return to Normalcy .... 795
8. Concluding Remarks and Future Perspectives .... 797
References .... 798
36. Recognition of DNA Damage as the Initial Step of Eukaryotic
Checkpoint Arrest 803
Wolfram Siede
1. Introduction .... 803
2. Early Studies Characterizing Checkpoint Triggering Damage
and Sensor Proteins .... 804
3. The ATM Protein is a Kinase and a Putative Damage
Sensor .... 805
4. The ATR Protein and its Targeting Subunit .... 807
5. PCNA and RFC like Clamp and Clamp Loader Complexes
Function as Damage Sensors .... 808
6. Crosstalk Between Sensors .... 810
7. The MRN Complex Plays a Role in Checkpoint Arrests .... 811
8. Synopsis: Independent But Communicating Sensors Are Linked By
Common Requirements .... 812
9. The Generation of a Transducible Signal .... 812
10. Other Sensor Candidates .... 814
11. Sensing UV Damage .... 815
12. Adaptation and Cell Cycle Restart .... 816
References .... 818
xvi Contents
37. Responses to Replication of DNA Damage 827
Maria Pia Longhese and Marco Foiani
1. Introduction .... 827
2. How do Cells Deal with a Damaged Template During
DNA Replication? .... 828
3. The S Phase Checkpoint .... 830
4. Replication Related Genome Instability .... 837
References .... 837
Index .... 841
|
| adam_txt |
Contents
Preface . Hi
Contributors . xvii
PART I. MECHANISMS OF DAMAGE RECOGNITION: THEORETICAL
CONSIDERATIONS 1
1. Dynamics of DNA Damage Recognition 3
Eleanore Seibert, Roman Osman, and J. B. Alexander Ross
1. Introduction . 3
2. Role of DNA Flexibility in Sequence Dependent Activity
of UDG . 4
3. Opening and Bending Dynamics of G«U Mismatches
in DNA . 8
4. Conclusions . 13
References . 15
2. In Search of Damaged Bases 21
R Stephen Lloyd, A. K. McCullough, and M. L. Dodson
1. Introduction . 21
2. Mechanism for an Increased Rate of Target Site Location . 21
3. In Vitro Evidence for Processive Nicking Activity of DNA
Glycosylases . 23
4. Discovery and Significance of In Vivo Processive Nicking
Activity by T4 pdg . 26
5. DNA Bending as a Potential Prerequisite for Nucleotide
Flipping . 27
6. Mechanisms of Nucleotide Flipping . 29
7. Specificity of Glycosylase Binding Sites and Catalytic
Activities . 30
References . 31
vi Contents
3. Increased Specificity and Efficiency of Base Excision Repair
Through Complex Formation 33
Karen H. Almeida and Robert W. Sobol
1. Introduction . 33
2. DNA Lesion Recognition and Removal . 36
3. Strand Incision . 42
4. Gap Filling and Religation . 46
5. XRCC1 Coordination . 49
6. Long Patch Repair . 52
7. Emerging Subpathways . 54
8. Conclusions . 54
References . 55
PART II. UV DAMAGE AND OTHER BULKY DNA ADDUCTS 65
4. Structure and Properties of DNA Photoproducts 67
John Stephen Taylor
1. Introduction . 67
2. Cyclobutane Pyrimidine Dimers . 69
3. Other Dimer Related Products . 79
4. (6 4) Products . 81
5. Dewar Photoproduct . 86
6. Spore Photoproduct . 88
7. TA* Product . 89
8. Conclusions . 90
References . 90
5. Damage Recognition by DNA Photolyases 95
Gwendolyn B. Sancar
1. Overview of Photolyases . 95
2. The Nature of the Substrates . 96
3. Characterization of Substrate Binding and Discrimination
by Photolyases . 97
4. Interactions at the Photolyase Photoproduct Interface: The
Molecular Basis for Substrate Binding and
Discrimination . 98
5. Substrate Binding In Vivo . 105
6. Summary and Future Directions . 107
References . 107
6. Damage Recognition by the Bacterial Nucleotide Excision
Repair Machinery HI
Deborah L. Croteau, Matthew J. DellaVecchia, Milan Skorvaga,
and Bennett Van Houten
1. Introduction . Ill
2. Diversity of DNA Lesions Recognized . 113
3. The Proteins and Their Structural Domains . 114
Contents vii
4. Reaction Pathway for Damage Detection and Processing . 123
5. DNA Damage Recognition within the Biological
Context of the Cell . 130
6. Similarities in Damage Recognition and Verification
Between Bacterial and Eukaryotic Nucleotide
Excision Repair Systems . 133
References . 133
7. Recognition of DNA Damage During Eukaryotic
Nucleotide Excision Repair 139
Hanspeter Naegeli
1. Introduction . 139
2. Nucleotide Excision Repair Substrates . 139
3. Eukaryotic NER Reaction . 140
4. Subunits of the Eukaryotic NER Machinery . 142
5. Stepwise Assembly of the Mammalian NER Recognition
Complex . 143
6. A Preassembled Repairosome in Yeast? . 144
7. Role of Damaged DNA Binding in Damage Recognition . 146
8. Recognition of Bulky Lesions During Transcription Coupled
DNA Repair . 147
9. 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
8. Interactions of the Transcription Machinery with DNA
Damage in Prokaryotes 165
Isabel Mellon
1. General Overview . 165
2. The Behavior of RNA Polymerase Complexes with Different
Types of DNA Damage . 168
3. The Behavior of RNA Polymerase Complexes
at Lesions and NER . 170
4. The Behavior of RNA Polymerase Complexes
at Lesions and BER . 173
5. Summary and Future Directions . 175
References . 175
viii Contents
9. DNA Repair in Actively Transcribed Genes
in Eukaryotic Cells 181
Moon shong Tang
1. Introduction . 181
2. Heterogeneity of DNA Repair . 182
3. Methods for Detecting TCR and GGR . 185
4. DNA Repair in Transcriptionally Active Genes in Different
Organisms . 188
5. Models of TCR in Eukaryotic Cells. . 193
6. 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
1. Introduction . 201
2. Nucleosomes: Heterogeneity in a Conserved Structure . 202
3. Dynamic Properties of Nucleosomes Regulate
DNA Accessibility . 203
4. Damage Tolerance of Nucleosomes . 208
5. Repair of Nucleosomes by Photolyase . 209
6. Repair of Nucleosomes by NER . 211
7. Site Specific Repair in Nucleosome and Damage
Recognition . 214
8. Chromatin Remodeling and DNA Repair . 214
9. 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
1. Introduction . 223
2. Discovery and Initial Characterization of S. pombe
UVDE . 224
3. Recognition and Processing of UV Photoproducts . 226
4. Recognition and Processing of Platinum
G G Diadducts . 227
5. Recognition and Processing of Abasic Sites . 227
6. Modified Bases not Recognized by UVDE . 229
7. Recognition and Processing of Base Base Mismatches . 230
8. Recognition and Processing of Insertion Deletion Loops . 231
9. 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
1. Background . 239
2. Introduction . 239
3. Structural Consequences of Platinum Binding to Double Stranded
DNA . 240
4. Recognition of cis DDP 1,2 Intrastrand Cross Link by Cellular
Proteins . 245
5. 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
1. Introduction . 263
2. Metabolism of PAH to Diol Epoxides and Formation
of Stereoisomeric DNA Adducts . 265
3. Methods . 267
4. PAH DNA Adducts: Conformational Motifs . 269
5. Insights into the Structural Motifs at the Nucleoside Adduct
Level Derived from Computational Approaches . 273
6. PAH DNA Adduct Conformational Motifs and NER . 274
7. Structural Differences Between Bay and Fjord Stereoisomeric
PAH iV^ Adenine Adducts and Correlations with NER
Susceptibilities . 276
8. Computational Analysis . 279
9. 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
1. The Base Excision Repair Pathway . 299
2. DNA Glycosylase Structural Families . 300
3. Specific Mechanisms for Recognition of Damage . 303
4. AP Endonucleases . 313
5. Emerging Questions . 315
References . 315
15. Repair of Oxidized Bases 323
Yoke Wah Kow
1. Biological Consequences of Oxidative Damage . 323
x Contents
2. Major Repair Enzymes that Recognize Oxidative Base
Damage . 326
3. Repair Pathways for Oxidative DNA Damage . 333
4. Conclusions . 335
References . 335
16. Recognition of Alkylating Agent Damage in DNA 339
Timothy R. O'Connor
1. Modification of DNA by Small Alkylating Agents . 339
2. DNA Repair Systems for Removal of Alkylating Agent
Damage . 341
3. O6 Alkylguanine DNA Methyltransferases—AGTs . 342
4. AlkB—2 oxoglutarate Dependent Fe(II) Dependent
Oxygenases . 355
5. DNA Glycosylases—Base Excision Repair . 362
6. Nucleotide Excision Repair . 377
References . 382
17. Deaminated Bases in DNA 389
Bernard Weiss
1. Introduction . 389
2. Lesions and Their Consequences . 389
3. Deaminating Agents . 390
4. Endonuclease V, An Enzyme Specific for Deaminated
Purines . 393
5. Hypoxanthine/Alkylpurine DNA Glycosylases . 396
6. Endonuclease VIII of E. coli . 399
7. Conclusions . 399
References . 399
18. New Paradigms for DNA Base Excision Repair
in Mammals . . 403
Sankar Mitra, Lee R. Wiederhold, Hong Don, Tadahide Izumi,
and Tapas K. Hazra
1. Introduction . 403
2. Oxidized Base Specific Glycosylases in E. coli
and Mammals . 404
3. Conclusions . 416
References . 417
19. Recognition and Repair of Abasic Sites 421
David M. Wilson III and David F. Lowry
1. AP Site Formation and Biological Impact . 421
2. AP DNA Dynamics and Structure . 423
Contents xi
3. AP Endonucleases . 425
4. AP Site Recognition and Processing . 426
5. AP Site Repair in General . 432
References . 436
20. Oxidative Mitochondrial DNA Damage Resistance and Repair . . . 445
GeraldS. Shadel
1. Introduction . 445
2. General Features of Human mtDNA . 446
3. Oxidative mtDNA Damage Resistance and Repair . 449
4. New Lessons About Oxidative mtDNA Damage from the Budding
Yeast, S. cerevisiae, Genetic Model System . 452
5. Conclusions and New Horizons . 455
References . 456
PART IV. MISMATCH REPAIR 461
21. Mechanism of DNA Mismatch Repair from
Bacteria to Human 463
Samir Acharya and Richard Fishel
1. Introduction . 463
2. Biochemistry of Mismatch Repair Proteins . 466
3. Mechanism of Mismatch Repair . 469
4. Implications . 474
References . 475
22. Interaction of the Escherichia coli Vsr with DNA and Mismatch
Repair Proteins 483
Ashok S. Bhagwat and Bernard Connolly
1. Introduction . 483
2. Structure of Vsr . 485
3. Summary and Concluding Remarks . 490
References . 490
PART V. REPLICATION AND BYPASS OF DNA LESIONS 493
23. Mechanism of Translesion DNA Synthesis in Escherichia coli . 495
Zvi Livneh, Ayelet Maor Shoshani, Moshe Goldsmith, Gali Arad,
Ayal Hendel, and Lior Izhar
1. Introduction . 495
2. Translesion DNA Synthesis and the SOS Response . 496
3. Overview on Pol V . 497
4. Fidelity of Pol V . 497
5. Lesion Bypass By Pol V . 498
6. Accessory Proteins Are Required for Lesion Bypass
By Pol V . 499
xii Contents
7. Other DNA Polymerases Involved in TLS in E. coli . 501
8. In Vivo Role of TLS . 502
References . 503
24. Mechanism of Bypass Polymerases in Eukaryotes 507
Zhigang Wang
1. Introduction . 507
2. Concepts of Translesion Synthesis . 509
3. Translesion Polymerases . 510
4. Mechanistic Models of Translesion Synthesis . 513
5. Translesion Synthesis of Various DNA Damage
in Eukaryotes . 515
6. Importance of Translesion Synthesis in Eukaryotic
Biology . 520
References . 521
25. Structural Features of Bypass Polymerases 529
Caroline Kisker
1. Introduction . 529
2. DNA Synthesis by the DINB Family Members from
the Sulfolobus Genus . 535
3. DNA Binding and Lesion Bypass in Polr) . 541
4. Recruitment of Y Family DNA Polymerases . 543
5. Lesion Specificity of the Y Family DNA Polymerases . 545
References . 546
26. Regulation of Damage Tolerance by the RAD6 Pathway 549
Helle D. Ulrich
1. Introduction . 549
2. Mechanisms of Damage Bypass . 550
3. The RAD6 Pathway . 554
4. Proliferating Cell Nuclear Antigen Modification
by the Ubiquitin Like Protein Sumo . 566
5. Mechanistic Considerations . 567
6. Interactions of the RAD6 Pathway with Other Factors . 570
7. Summary and Outlook . 573
References . 574
PART VI. DNA STRAND BREAKS 579
27. Biochemical and Cellular Aspects of Homologous
Recombination 581
Lieneke van Veelen, Joanna Wesoly, and Roland Kanaar
1. Introduction . 581
2. DNA Double Strand Break Repair Through Homologous
Recombination . 582
Contents xiii
3. Biochemical Properties of Homologous Recombination
Proteins . 582
4. Cellular Properties of Homologous Recombination
Proteins . 586
References . 602
28. The Mechanism of Vertebrate Nonhomologous DNA End Joining and Its
Role in Immune System Gene Rearrangements 609
Michael R. Lieber, Yunmei Ma, Kefei Yu, Ulrich Pannicke,
and Klaus Schwarz
1. Introduction . 609
2. Essential Aspects of Vertebrate Nonhomologous DNA
End Joining (NHEJ) . 609
3. Overview of V(D)J Recombination and its Utilization of NHEJ
in the Rejoining Process . 613
4. Overview of Immunoglobulin Class Switch Recombination and its
Utilization of NHEJ in the Rejoining Process . 615
5. Points of Biochemical Detail in the NHEJ Pathway . 619
6. Special Aspects of NHEJ as it Relates to V(D)J
Recombination . 622
7. Are There Multiple NHEJ Pathways? . 622
8. NHEJ and Human Disease . 624
9. Future Avenues of Study of the NHEJ Pathway . 624
References . 624
29. Structural Aspects of Ku and the DNA Dependent Protein
Kinase Complex 629
Eric A. Hendrickson, Joy L. Huffman, and John A. Tainer
1. Introduction . 629
2. The Ku Autoantigen . 634
3. DNA PKcs . 648
4. DNA PK, Telomeres and Genomic Stability . 655
5. Summary . 662
References . 663
30. Cellular Functions of Mammalian DNA Ligases 685
John B. Leppard, Julie Delia Maria Goetz, Teresa A. Motycka,
Zhiwan Dong, Wei Song, Hui Min Tseng, Sangeetha Vijayakumar,
and Alan E. Tomkinson
1. Introduction . 685
2. Reaction Mechanism . 686
3. DNA Ligase Structure . 686
4. Mammalian DNA Ligases . 687
5. Cellular Functions of DNA Ligase . 693
References . 697
xiv Contents
31. The Mrell/Rad50/Nbsl Complex 705
Karl Peter Hopfner
1. Introduction . 705
2. The Mrell Complex . 706
3. Cellular Biochemistry of the Mrell Complex . 710
4. Structural Biochemistry of the Mrell Complex . 714
5. Unified Model, Conclusions, and Outlook . 717
References . 718
32. Histone y H2AX Involvement in DNA Double Strand Break
Repair Pathways 723
Nikolaos A. A. Balatsos and Emmy P. Rogakou
1. Introduction . 723
2. Formation and Detection of y Phosphorylation . 724
3. y Phosphorylation of H2A(X) Spans Megabase Long
Domains in Chromatin . 726
4. Kinases Involved in y Phosphorylation of H2A(X)
Histone Family . 727
5. Recruitment of Repair Factors to y Phosphorylated
Chromatin . 728
6. Models and Speculations About the Biological Role of
Y H2AX Foci . 729
References . 732
33. DNA Strand Break Recognition, Signaling, and Resolution: The Role of
Poly(ADP Ribose) Polymerases 1 and 2 737
Emmanuelle Pion, Catherine Spenlehauer, Laurence Tartier,
Jean Christophe Ame, Francoise Dantzer, Valerie Schreiber,
Gerard Gradwohl, Josiane Menissier de Murcia, and Gilbert de Murcia
1. Background . 737
2. Introduction . 737
3. Nick Sensor Function of PARP 1 . 739
4. Dual Role of DNA Damage Induced PAR Synthesis: Break Signaling
and Recruitment of XRCC1 . 743
5. No Cross Talk Between PAR Synthesis and y H2AX Formation in
Response to DNA Strand Break Injury . 747
6. Conclusions and Future Prospects . 749
References . 750
PART VII. PERCEPTION OF DNA DAMAGE FOR INITIATING
REGULATORY RESPONSES 755
34. Cellular and Molecular Responses to Alkylation Damage
in DNA 757
James M. Bugni and Leona D. Samson
1. Introduction . 757
Contents xv
2. The E. coli Adaptive Response: Translating Methyl DNA Adducts
into a Transcriptional Signal . 760
3. Cellular Responses to 06MeG . 766
4. Cellular Responses to 3MeA . 771
5. Genome Wide Analysis of Responses to Alkylating
Agents . 775
6. Conclusions . 776
References . 776
35. Damage Signals Triggering the Escherichia coli SOS Response . . . 781
Mark D. Sutton
1. Introduction . 781
2. The E. coli SOS Response . 781
3. Structure Function of the LexA Protein Family . 784
4. RecA Protein DNA Interactions and LexA
Self Cleavage . 786
5. Role of DNA Damage in Inducing the E. coli SOS
Response . 789
6. Upregulation of DNA Repair and DNA Damage Tolerance Under
the SOS Response . 791
7. After the Damage is Repaired: Turning off the SOS Response and the
Return to Normalcy . 795
8. Concluding Remarks and Future Perspectives . 797
References . 798
36. Recognition of DNA Damage as the Initial Step of Eukaryotic
Checkpoint Arrest 803
Wolfram Siede
1. Introduction . 803
2. Early Studies Characterizing Checkpoint Triggering Damage
and Sensor Proteins . 804
3. The ATM Protein is a Kinase and a Putative Damage
Sensor . 805
4. The ATR Protein and its Targeting Subunit . 807
5. PCNA and RFC like Clamp and Clamp Loader Complexes
Function as Damage Sensors . 808
6. Crosstalk Between Sensors . 810
7. The MRN Complex Plays a Role in Checkpoint Arrests . 811
8. Synopsis: Independent But Communicating Sensors Are Linked By
Common Requirements . 812
9. The Generation of a Transducible Signal . 812
10. Other Sensor Candidates . 814
11. Sensing UV Damage . 815
12. Adaptation and Cell Cycle Restart . 816
References . 818
xvi Contents
37. Responses to Replication of DNA Damage 827
Maria Pia Longhese and Marco Foiani
1. Introduction . 827
2. How do Cells Deal with a Damaged Template During
DNA Replication? . 828
3. The S Phase Checkpoint . 830
4. Replication Related Genome Instability . 837
References . 837
Index . 841 |
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| illustrated | Illustrated |
| index_date | 2024-07-02T14:32:06Z |
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| isbn | 0824759613 9780824759612 |
| language | English |
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| spelling | DNA damage recognition ed. by Wolfram Siede ... New York, NY [u.a.] Taylor & Francis 2006 XXII, 845 S. Ill., graph. Darst. 26 cm txt rdacontent n rdamedia nc rdacarrier DNA repair DNA Damage physiology DNA Damage genetics DNA Repair genetics DNA Repair physiology DNS-Reparatur (DE-588)4150347-8 gnd rswk-swf DNS-Schädigung (DE-588)4150350-8 gnd rswk-swf DNS-Schädigung (DE-588)4150350-8 s DE-604 DNS-Reparatur (DE-588)4150347-8 s Siede, Wolfram Sonstige oth HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=014768372&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | DNA damage recognition DNA repair DNA Damage physiology DNA Damage genetics DNA Repair genetics DNA Repair physiology DNS-Reparatur (DE-588)4150347-8 gnd DNS-Schädigung (DE-588)4150350-8 gnd |
| subject_GND | (DE-588)4150347-8 (DE-588)4150350-8 |
| title | DNA damage recognition |
| title_auth | DNA damage recognition |
| title_exact_search | DNA damage recognition |
| title_exact_search_txtP | DNA damage recognition |
| title_full | DNA damage recognition ed. by Wolfram Siede ... |
| title_fullStr | DNA damage recognition ed. by Wolfram Siede ... |
| title_full_unstemmed | DNA damage recognition ed. by Wolfram Siede ... |
| title_short | DNA damage recognition |
| title_sort | dna damage recognition |
| topic | DNA repair DNA Damage physiology DNA Damage genetics DNA Repair genetics DNA Repair physiology DNS-Reparatur (DE-588)4150347-8 gnd DNS-Schädigung (DE-588)4150350-8 gnd |
| topic_facet | DNA repair DNA Damage physiology DNA Damage genetics DNA Repair genetics DNA Repair physiology DNS-Reparatur DNS-Schädigung |
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