DNA Damage Recognition

869 Pages·2006·14.472 MB·English

by  W. Siede, Y. Kow, P. Doetsch

DK3110_title 8/10/05 10:26 AM Page 1
DNA
Damage
Recognition
edited by
Wolfram Siede
University of North Texas Health Science Center
Fort Worth, Texas, U.S.A.
Yoke Wah Kow
Emory University School of Medicine
Atlanta, Georgia, U.S.A.
Paul W(cid:2) Doetsch
Emory University School of Medicine
Atlanta, Georgia, U.S.A.
New York London
DK3110_Discl.fm Page 1 Monday, August 15, 2005 1:41 PM
Published in 2006 by
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Preface
The topics of this book are the various molecular mechanisms that are involved in
the process of DNA damage recognition as the initial step of DNA damage repair
and of other related responses, such as damage tolerance and cell cycle checkpoint
regulation. The authors were asked to provide review-type articles designed with
the researcher in the field in mind. But sufficient introductory comments were
requested so that a non-expert or an interested advanced student with some back-
groundknowledgecanfollow.Whilewedidnothaveanarrowdefinitionofdamage
recognitioninmind,acompletedescriptionofcellularDNArepairmechanismswas
certainlynotourgoal.However,lookingatthescopeofthisimpressivecollectionof
in-depth reviews, it almost happened...
Inthebeginningofthebook,certaintheoreticalaspectsofdamagerecognition
that are common themes throughout the book have been addressed. How can one
imagine that recognition proteins find their rare targets? How can we envisage pro-
teinmovement—byrandomdiffusionor‘‘patrolling’’alongDNA?Anotherequally
important topic addresses proteincooperation that enhances recognition specificity.
ThereisclearlyanemphasisonstructuralaspectsofDNAdamagerecognition
throughoutthebook.Whereversuchinformationisavailable,itisexplainedindetail
how protein/DNA damage contacts are being accomplished and which types of
structuralfeaturesorconsequencesofDNAdamagearebeingprobedbytherecog-
nition apparatus in order to permit a distinction from undamaged DNA. In this
fashion,damagerecognitionisaddressedwithinthemajorpathwaysofDNArepair,
i.e., simple damage reversal, nucleotide excision repair, base excision repair,
mismatch repair, recombinational repair, and DNA endjoining. We interpret the
pathways of damage tolerance as a consequence of a combined recognition/accom-
modation process and thus we have also included chapters on translesion synthesis.
DNA recognition steps occur at several levels within a single repair pathway
and this complexity has been considered. How are repair intermediates being
recognized? How is a repair intermediate handed over to the next player? If there
is a competition between different mechanisms: how is a pathway choice accom-
plished?Whilewedonotemphasizedownstreamreactions,thestrategyoforiginat-
ing a transmissible downstream signal will be addressed wherever appropriate,
especially in the context of regulatory responses.
WewereequallyinterestedinputtingspecificaspectsofDNAdamagerecogni-
tion in the cellular context. Certain chapters provide the necessary backdrop by
givingup-to-datereviewsofcertainpathways.However,alsochromosomestructure,
iii
iv Preface
DNA structure, and sequence context, which may affect DNA damage recognition
positivelyornegatively,arebeingaddressed.Theinterferencewithcellularprocesses
such as replication and transcription is discussed for several examples since such
interference as a consequence of DNA damage may influence, aide, or even initiate
a recognition process.
Allthatisleftistothankourauthorsfortheirhardworkandsuperbcontribu-
tions. We would like to acknowledge the help of Stacy Harman Holloway. We are
also indebted to Anita Lekhwani, Moraima Suarez, Joseph Stubenrauch, and their
colleagues at Taylor & Francis Books for pursuing the idea and providing such
excellent editorial support. We also thank the National Institute of Environmental
Health Sciences for supporting a research collaboration amongst the three editors
as well as two other authors of individual chapters that made this book possible
(‘‘Cellular Responses to Genotoxic Stress’’ Program Project ES11163).
Wolfram Siede
Yoke Wah Kow
Paul W. Doetsch
Contents
Preface . . . . iii
Contributors . . . . xvii
PART I. MECHANISMS OF DAMAGERECOGNITION: 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(cid:1)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
v
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. UVDAMAGEAND OTHERBULKY 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(cid:2) 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 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
Deborah L. Croteau, Matthew J. DellaVecchia, Milan Skorvaga,
and Bennett Van Houten
1. Introduction . . . . 111
2. Diversity of DNA Lesions Recognized . . . . 113
3. The Proteins and Their Structural Domains . . . . 114
Contents vii
4. Reaction PathwayforDamageDetection 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. RoleofDamagedDNABindinginDamageRecognition . . . . 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-N6–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