DNA Polymerases: Discovery, Characterization and Functions in Cellular DNA Transactions

Preface......Page 6
Contents......Page 10
1.1 Discovering DNA: A First Step Towards Understanding the Basis of Life......Page 18
1.1.1 Nuclein......Page 20
1.1.2 Nucleic Acid......Page 22
1.1.3 Nucleic Acids Are Composed of Nucleotides......Page 23
1.1.4 DNA Is the Genetic Material......Page 24
1.1.5 Structure of DNA: TheWatson–Crick DNA Double Helix and Mechanism of DNA Replication......Page 27
1.2 Imaging an Enzyme that Assembles the Nucleotides into DNA......Page 29
1.2.1 DNA Polymerase Activity in Extracts of Escherichia coli......Page 32
1.2.2 Escherichia coli DNA Polymerase Can Synthesize DNA with Genetic Activity: Creating Life in theTestTube......Page 35
1.2.3 Bacteria Contain Many DNA Polymerases......Page 36
1.2.4 How Is a New DNA Chain Started? Discontinuous DNA Synthesis and the Need for an RNA Primer......Page 38
1.2.5 RNA Priming as a Mechanism for Initiation: DNA Primase......Page 39
1.3.1 DNA Structure Is Much More Complex, Rich of Conformational Flexibility and thus Full of Functional Potentialities than the One Proposed by Watson and Crick......Page 40
1.3.2 DNA Binding Proteins, DNA Helicases, DNA Topoisomerases......Page 41
1.4 Concluding Remarks, Parts 1.1–1.3......Page 42
1.5 Multiple DNA Polymerases in Eukaryotic Cells: DNA Polymerases α, β and γ as the First Ones......Page 43
1.5.1 DNA Polymerase α......Page 44
1.5.3 Lack of Relationship Between High and Low-Molecular Weight DNA Polymerases......Page 46
1.5.4 1975: First Nomenclature System for Eukaryotic DNA Polymerases......Page 47
1.5.5 DNA Polymerase γ......Page 48
1.6 Early Attempts to Ascribe an in vivo Function
to DNA Polymerases α, β and γ......Page 49
1.6.1 Positive Correlation of DNA Polymerase α with Cellular DNA Replication and Development......Page 50
1.6.2 DNA Polymerase γ Is the Mitochondrial DNA Polymerase and Replicates Mitochondrial DNA......Page 52
1.6.3 Further Evidence for a Major Involvement of DNA Polymerase α in DNA Replication and of DNA Polymerase β in DNA Repair......Page 55
1.7 DNA Polymerases δ and ε......Page 57
1.8 1985: Polymerase Chain Reaction (PCR), a Concept with Tremendous Practical Applications......Page 58
1.9 Yeast DNA Polymerases......Page 61
1.9.1 Revised Nomenclature for Eukaryotic DNA Polymerases......Page 62
1.10 Plant Cell DNA Polymerases......Page 63
1.11.1 Herpes Virus DNA Polymerase......Page 65
1.11.3 DNA Polymerase Activity in Hepatitis B Particle......Page 66
1.12.1 DNA Polymerase ζ, the Lesion Extender......Page 67
1.12.3 The ComplexY Family of DNA Polymerases......Page 68
1.13 Concluding Remarks, Parts 1.5–1.12......Page 69
References......Page 72
2.1 Synthesis and Maintenance of DNA in Nature Need DNA Polymerases......Page 76
2.2 The DNA Polymerase Reaction......Page 78
2.3 The Universal Structure of a DNA Polymerase Resembles a Human Right Hand......Page 80
2.4 The Seven DNA Polymerase Families and Their Functions: An Overview......Page 81
2.5 DNA Polymerase Holoenzymes......Page 87
2.6 DNA Polymerases, Ring-Like Clamps and Clamp Loaders......Page 90
2.7 DNA Polymerases, Alternative Clamps and Clamp Loaders......Page 92
2.8 Replicative DNA Polymerases Interacting with Other Proteins......Page 95
2.9 DNA Polymerases and the Single-Stranded DNA Binding Protein Replication Protein A......Page 96
2.10 Chapter Summary......Page 97
References......Page 99
3.1.1 Family A: DNA Polymerase I......Page 102
3.1.2 Family B: DNA Polymerase II......Page 105
3.1.3 Family C: DNA Polymerase III Holoenzyme......Page 106
3.1.4 FamilyY: DNA Polymerases IV and V......Page 110
3.2.1 Family A: DNA Polymerase I......Page 113
3.2.2 Family C: DNA Polymerase C and DnaE......Page 114
3.2.4 FamilyY: DNA Polymerases Y1 and Y2......Page 115
3.3.1 Mycobacteria......Page 116
3.3.2 Deinococcus radiodurans......Page 117
3.4.1 Family B: DNA Polymerase B......Page 118
3.4.2 Family D: DNA Polymerase D......Page 119
3.4.3 FamilyY: DNA Polymerases Dbh and Dpo4......Page 120
3.5 Chapter Summary......Page 122
References......Page 123
4.1 The High Number of Specialized Pathways in Eukaryotic Cells Requires a Plethora of Specialized DNA Synthesizing Enzymes......Page 128
4.2.1 Common Features......Page 130
4.2.2 Specific Features of the Different Families......Page 132
4.3 Eukaryotic DNA Polymerases Accessory Subunits......Page 137
4.4 Eukaryotic DNA Polymerase Fidelity: Structural and Functional Aspects......Page 140
4.5.1 Family A DNA Polymerases......Page 144
4.5.2 Family B DNA Polymerases......Page 148
4.5.3 Family X DNA Polymerases......Page 154
4.5.4 FamilyY DNA Polymerases......Page 159
4.6 Interaction with Auxiliary Factors......Page 163
4.7 Eukaryotic DNA Polymerases Are Tightly Regulated in the Cell Cycle......Page 165
References......Page 169
5.1 Fifteen DNA Polymerases: Share ofWorkload and Redundancies......Page 178
5.2 DNA Replication in Living Organisms Requires Three DNA Polymerase Molecules at the Replication Fork......Page 182
5.2.1.1 Bacteriophage T7: The simplest but best known replisome......Page 183
5.2.1.2 The Escherichia coli replisome......Page 185
5.2.2 Eukaryotes......Page 188
5.2.3 Proofreader versus Non-proofreader DNA Polymerases......Page 189
5.3 Different DNA Repair Pathways Have Their Own DNA Polymerases, But Can also Borrow Them from the Replication Machinery......Page 190
5.4 Translesion DNA Synthesis in Eukaryotes Generally Requires Two DNA Polymerases: An Inserter and an Extender......Page 194
5.5 Expression of DNA Polymerases......Page 199
5.6.1 Prokaryotes......Page 200
5.6.2 Eukaryotes......Page 202
5.6.2.1 Posttranslational modifications of PCNA......Page 203
5.6.2.2 DNA pol switches due to PCNA ubiquitination......Page 204
5.6.2.3 Other ways to regulate DNA polymerases......Page 207
5.7 Functions of DNA Polymerases in Checkpoint Control......Page 209
5.8 Chapter Summary......Page 210
References......Page 211
6.1 Bacteriophage T4 DNA Polymerase......Page 216
6.2 Bacteriophage T7 DNA Polymerase......Page 220
6.3 HSV-1 DNA Polymerase......Page 224
6.4.1 Adenovirus DNA Polymerase......Page 228
6.4.2 Bacteriophage φ29 DNA Polymerase......Page 231
6.5 African Swine Virus DNA Polymerase......Page 234
6.6 RNA-Dependent DNA Synthesis: Reverse Transcriptases......Page 236
6.6.1.1 The retro-transcription reaction......Page 237
6.6.1.2 Structural features of HIV-1 reverse transcriptase......Page 241
6.6.1.3 Enzymatic features of HIV-1 reverse transcriptase......Page 242
6.6.1.4 The RNase H activity of HIV-1 reverse transcriptase......Page 244
6.6.2.2 Murine Leukemia Virus (MLV) reverse transcriptase......Page 245
6.6.2.5 Mouse Mammary Tumor Virus (MMTV) reverse transcriptase......Page 246
6.6.3.2 Schizosaccharomyces pombe Tf1 reverse transcriptase......Page 247
6.6.4 Hepadnavirus Reverse Transcriptase......Page 248
References......Page 251
7.1 Why Design Enzymes with Novel Properties?......Page 258
7.2 DNA Polymerases Have a Tight Active Site to Which the Substrates Fit......Page 259
7.3.1 Detection and Characterization of DNA Polymerases and Mutants Thereof by Functional Complementation in Escherichia coli......Page 262
7.3.2 DNA Polymerase Evolution by Random Point Mutagenesis......Page 263
7.3.3 DNA Polymerase Evolution by Compartmentalized Self-Replication (CSR)......Page 264
7.3.5 DNA Polymerase Evolution by Oligonucleotide Addressed Enzyme Assay (OAEA)......Page 265
7.4 Applications of DNA Polymerases with Novel Properties......Page 267
7.5.1 Increased Fidelity......Page 270
7.5.3 Amplification of Damaged and Ancient DNA......Page 272
7.5.5 Evolving the dNTP Substrates and Expansion of the Genetic Code......Page 273
7.6 Chapter Summary......Page 275
References......Page 276
8.2 DNA Polymerases and Genetic Stability......Page 278
8.3 DNA Polymerases and Resistance to Chemotherapy......Page 288
8.4 DNA Polymerase γ and Human Diseases......Page 290
8.5 Chapter Summary......Page 292
References......Page 293
9.1 DNA Polymerases Are Important Chemotherapeutic Targets......Page 298
9.2.1 Substrate Analogs......Page 299
9.2.3 Novel in silico Technologies for Designing Inhibitors of DNA Polymerases......Page 301
9.3.1 Anti-Herpetic Nucleoside Analogs Require Activation by the Viral Thymidine Kinase (TK)......Page 304
9.3.2 Nucleoside Analogs Modified in the Base Ring......Page 306
9.3.3.1 Arabinonucleosides......Page 308
9.3.3.2 Acyclic nucleoside analogs......Page 310
9.3.3.3 Carbocyclic nucleoside analogs......Page 312
9.3.3.4 Phosphonate nucleoside analogs......Page 313
9.4 The Lack of Enantioselectivity of Viral and Human Enzymes and the L-Enantiomers of Nucleosides: The Dawn of a New Generation of Antiviral Drugs......Page 314
9.4.1 Herpesvirus Thymidine Kinase Has Low Enantioselectivity......Page 315
9.4.2 The Discovery of a Relaxed Enantioselectivity of Human and Viral DNA Polymerases......Page 316
9.4.3 Lack of Enantiospecificity of Human 2 -Deoxycytidine Kinase: Relevance for the Activation of L-Deoxycytidine Analogs......Page 317
9.5.1 Nucleoside Reverse Transcriptase Inhibitors......Page 318
9.5.1.1 Intracellular anabolism of nucleoside reverse transcriptase inhibitors......Page 320
9.5.1.2 Catabolism of nucleoside reverse transcriptase inhibitors......Page 323
9.5.2 Non-nucleoside Reverse Transcriptase Inhibitors......Page 324
9.5.2.1 Metabolism of non-nucleoside reverse transcriptase inhibitors......Page 325
9.5.3 Combined Toxicities of Reverse Transcriptase Inhibitors......Page 327
9.5.4 Molecular Interactions of HIV-1 Reverse Transcriptase with Nucleoside- and Non-nucleoside Inhibitors: The Problem of Drug Resistance......Page 329
9.5.4.1 NRTIs drug resistance......Page 330
9.5.4.2 NNRTIs drug resistance......Page 332
9.6 Inhibitors of Hepatitis B DNA Polymerase......Page 333
9.7 Chapter Summary......Page 335
References......Page 336