DNA Polymerases Discovery Characterization and Functions in Cellular DNA Transactions 1st Edition by Ulrich Hübscher, Silvio Spadari, Giuseppe Villani, Giovanni Maga 9814299162 9789814299169

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ISBN 10: 9814299162

ISBN 13: 9789814299169

Author: Ulrich Hübscher, Silvio Spadari, Giuseppe Villani, Giovanni Maga

Maintenance of the information embedded in the genomic DNA sequence is essential for life. DNA polymerases play pivotal roles in the complex processes that maintain genetic integrity. Besides their tasks in vivo, DNA polymerases are the workhorses in numerous biotechnology applications such as the polymerase chain reaction (PCR), cDNA cloning, genome sequencing, nucleic acids-based diagnostics and in techniques to analyze ancient and otherwise damaged DNA. Moreover, some diseases are related to DNA polymerase defects, and chemotherapy through inhibition of DNA polymerases is used to fight HIV, Herpes and Hepatitis B and C infections. We have recently witnessed the discovery of an abundance of novel DNA polymerases in viruses, bacteria, archaea and eukaryotes with specialized properties whose physiological functions are only beginning to be understood. This book summarizes the current knowledge of these fascinating enzymes. It is intended for a wide audience from basic scientists, to diagnostic laboratories and to clinicians who seek a better understanding of these fascinating enzymes.

DNA Polymerases Discovery Characterization and Functions in Cellular DNA Transactions 1st Table of contents:

1. History and Discovery of DNA Polymerases

1.1 Discovering DNA: A First Step Towards Understanding the Basis of Life

1.1.1 Nuclein

1.1.2 Nucleic Acid

1.1.3 Nucleic Acids Are Composed of Nucleotides

1.1.4 DNA Is the Genetic Material

1.1.5 Structure of DNA: TheWatson–Crick DNA Double Helix and Mechanism of DNA Replication

1.2 Imaging an Enzyme that Assembles the Nucleotides into DNA

1.2.1 DNA Polymerase Activity in Extracts of Escherichia coli

1.2.2 Escherichia coli DNA Polymerase Can Synthesize DNA with Genetic Activity: Creating Life in the

1.2.3 Bacteria Contain Many DNA Polymerases

1.2.4 How Is a New DNA Chain Started? Discontinuous DNA Synthesis and the Need for an RNA Primer

1.2.5 RNA Priming as a Mechanism for Initiation: DNA Primase

1.3 Late 1960s to Early 1970s: DNA Replication Shows Its Complexity

1.3.1 DNA Structure Is Much More Complex, Rich of Conformational Flexibility and thus Full of Functi

1.3.2 DNA Binding Proteins, DNA Helicases, DNA Topoisomerases

1.4 Concluding Remarks, Parts 1.1–1.3

1.5 Multiple DNA Polymerases in Eukaryotic Cells: DNA Polymerases α, β and γ as the First Ones

1.5.1 DNA Polymerase α

1.5.2 DNA Polymerase β

1.5.3 Lack of Relationship Between Highand Low-MolecularWeight DNA Polymerases

1.5.4 1975: First Nomenclature System for Eukaryotic DNA Polymerases

1.5.5 DNA Polymerase γ

1.6 Early Attempts to Ascribe an in vivo Function to DNA Polymerases α, β and γ

1.6.1 Positive Correlation of DNA Polymerase α with Cellular DNA Replication and Development

1.6.2 DNA Polymerase γ Is the Mitochondrial DNA Polymerase and Replicates Mitochondrial DNA

1.6.3 Further Evidence for a Major Involvement of DNA Polymerase α in DNA Replication and of DNA Po

1.7 DNA Polymerases δ and ε

1.8 1985: Polymerase Chain Reaction (PCR), a Concept with Tremendous Practical Applications

1.9 Yeast DNA Polymerases

1.9.1 Revised Nomenclature for Eukaryotic DNA Polymerases

1.10 Plant Cell DNA Polymerases

1.11 Virus-Induced DNA Polymerases

1.11.1 Herpes Virus DNA Polymerase

1.11.2 Vaccinia Virus DNA Polymerase

1.11.3 DNA Polymerase Activity in Hepatitis B Particle

1.11.4 Retroviruses Reverse Transcriptase

1.12 1999–2000: Nucleotide Sequence Analysis of Eukaryotic Organisms Allowed the Identification of

1.12.1 DNA Polymerase ζ, the Lesion Extender

1.12.2 DNA Polymerases λ and µ, Two Family X DNA Polymerases

1.12.3 The ComplexY Family of DNA Polymerases

1.12.4 Present Nomenclature for Eukaryotic DNA Polymerases

1.13 Concluding Remarks, Parts 1.5–1.12

References

2. DNA Polymerases in the Three Kingdoms of Life: Bacteria, Archaea and Eukaryotes

2.1 Synthesis and Maintenance of DNA in Nature Need DNA Polymerases

2.2 The DNA Polymerase Reaction

2.3 The Universal Structure of a DNA Polymerase Resembles a Human Right Hand

2.4 The Seven DNA Polymerase Families and Their Functions: An Overview

2.5 DNA Polymerase Holoenzymes

2.6 DNA Polymerases, Ring-Like Clamps and Clamp Loaders

2.7 DNA Polymerases, Alternative Clamps and Clamp Loaders

2.8 Replicative DNA Polymerases Interacting with Other Proteins

2.9 DNA Polymerases and the Single-Stranded DNA Binding Protein Replication Protein A

2.10 Chapter Summary

References

3. Structural and Functional Aspects of the Prokaryotic and Archaea DNA Polymerase Families

3.1 Escherichia coli

3.1.1 Family A: DNA Polymerase I

3.1.2 Family B: DNA Polymerase II

3.1.3 Family C: DNA Polymerase III Holoenzyme

3.1.4 FamilyY: DNA Polymerases IV and V

3.2 Bacillus subtilis

3.2.1 Family A: DNA Polymerase I

3.2.2 Family C: DNA Polymerase C and DnaE

3.2.3 Family X: DNA Polymerase X

3.2.4 FamilyY: DNA Polymerases Y1 and Y2

3.3 Other Bacteria

3.3.1 Mycobacteria

3.3.2 Deinococcus radiodurans

3.4 Archaea

3.4.1 Family B: DNA Polymerase B

3.4.2 Family D: DNA Polymerase D

3.4.3 FamilyY: DNA Polymerases Dbh and Dpo4

3.5 Chapter Summary

References

4. Structural and Functional Aspects of the Eukaryotic DNA Polymerase Families

4.1 The High Number of Specialized Pathways in Eukaryotic Cells Requires a Plethora of Specialized D

4.2 Eukaryotic DNA Polymerase Structure: The “Right Hand” of the Cell

4.2.1 Common Features

4.2.2 Specific Features of the Different Families

4.3 Eukaryotic DNA Polymerases Accessory Subunits

4.4 Eukaryotic DNA Polymerase Fidelity: Structural and Functional Aspects

4.5 Biochemical and Functional Properties of the Different Eukaryotic DNA Polymerases

4.5.1 Family A DNA Polymerases

4.5.2 Family B DNA Polymerases

4.5.3 Family X DNA Polymerases

4.5.4 FamilyY DNA Polymerases

4.6 Interaction with Auxiliary Factors

4.7 Eukaryotic DNA Polymerases Are Tightly Regulated in the Cell Cycle

4.8 Chapter Summary

References

5. Global Functions of DNA Polymerases

5.1 Fifteen DNA Polymerases: Share ofWorkload and Redundancies

5.2 DNA Replication in Living Organisms Requires Three DNA Polymerase Molecules at the Replication F

5.2.1 Prokaryotes

5.2.1.1 Bacteriophage T7: The simplest but best known replisome

5.2.1.2 The Escherichia coli replisome

5.2.2 Eukaryotes

5.2.3 Proofreader versus Non-proofreader DNA Polymerases

5.3 Different DNA Repair Pathways Have Their Own DNA Polymerases, But Can also Borrow Them from the

5.4 Translesion DNA Synthesis in Eukaryotes Generally Requires Two DNA Polymerases: An Inserter and

5.5 Expression of DNA Polymerases

5.6 DNA Polymerases Switch between Different DNA Transactions

5.6.1 Prokaryotes

5.6.2 Eukaryotes

5.6.2.1 Posttranslational modifications of PCNA

5.6.2.2 DNA pol switches due to PCNA ubiquitination

5.6.2.3 Other ways to regulate DNA polymerases

5.7 Functions of DNA Polymerases in Checkpoint Control

5.8 Chapter Summary

References

6. Viral DNA Polymerases

6.1 Bacteriophage T4 DNA Polymerase

6.2 Bacteriophage T7 DNA Polymerase

6.3 HSV-1 DNA Polymerase

6.4 Protein Primed DNA Replication: Adenoviruses and Bacteriophage φ29

6.4.1 Adenovirus DNA Polymerase

6.4.2 Bacteriophage φ29 DNA Polymerase

6.5 African Swine Virus DNA Polymerase

6.6 RNA-Dependent DNA Synthesis: Reverse Transcriptases

6.6.1 HIV-1 Reverse Transcriptase

6.6.1.1 The retro-transcription reaction

6.6.1.2 Structural features of HIV-1 reverse transcriptase

6.6.1.3 Enzymatic features of HIV-1 reverse transcriptase

6.6.1.4 The RNase H activity of HIV-1 reverse transcriptase

6.6.2 Other Retroviral Reverse Transcriptases

6.6.2.1 HIV-2 reverse transcriptase

6.6.2.2 Murine Leukemia Virus (MLV) reverse transcriptase

6.6.2.3 Equine Infectious Anemia Virus (EIAV) reverse transcriptase

6.6.2.4 Feline Immunodeficiency Virus (FIV) reverse transcriptase

6.6.2.5 Mouse Mammary Tumor Virus (MMTV) reverse transcriptase

6.6.3 Reverse Transcriptase Activity of Mobile Genetic Elements: The Retrotransposons

6.6.3.1 Saccharomyces cerevisiae Ty reverse transcriptase

6.6.3.2 Schizosaccharomyces pombe Tf1 reverse transcriptase

6.6.3.3 Bombyx mori R2 reverse transcriptase

6.6.4 Hepadnavirus Reverse Transcriptase

6.7 Chapter Summary

References

7. Synthetic Evolution of DNA Polymerases with Novel Properties

7.1 Why Design Enzymes with Novel Properties?

7.2 DNA Polymerases Have a Tight Active Site to Which the Substrates Fit

7.3 Methods to Evolve DNA Polymerases with Novel Properties

7.3.1 Detection and Characterization of DNA Polymerases and Mutants Thereof by Functional Complement

7.3.2 DNA Polymerase Evolution by Random Point Mutagenesis

7.3.3 DNA Polymerase Evolution by Compartmentalized Self-Replication (CSR)

7.3.4 DNA Polymerase Evolution by Phage Display

7.3.5 DNA Polymerase Evolution by Oligonucleotide Addressed Enzyme Assay (OAEA)

7.4 Applications of DNA Polymerases with Novel Properties

7.5 DNA Polymerases with Novel Properties

7.5.1 Increased Fidelity

7.5.2 Decreased Fidelity

7.5.3 Amplification of Damaged and Ancient DNA

7.5.4 A DNA Polymerase Becomes an RNA Polymerase

7.5.5 Evolving the dNTP Substrates and Expansion of the Genetic Code

7.6 Chapter Summary

References

8. DNA Polymerases and Diseases

8.1 Introduction

8.2 DNA Polymerases and Genetic Stability

8.3 DNA Polymerases and Resistance to Chemotherapy

8.4 DNA Polymerase γ and Human Diseases

8.5 Chapter Summary

References

9. DNA Polymerases and Chemotherapy

9.1 DNA Polymerases Are Important Chemotherapeutic Targets

9.2 Strategies and Problems for the Design of Inhibitors of DNA Polymerases

9.2.1 Substrate Analogs

9.2.2 Non-substrate Analogs

9.2.3 Novel in silico Technologies for Designing Inhibitors of DNA Polymerases

9.3 Inhibitors of Herpesvirus DNA Replication

9.3.1 Anti-Herpetic Nucleoside Analogs Require Activation by the Viral Thymidine Kinase (TK)

9.3.2 Nucleoside Analogs Modified in the Base Ring

9.3.3 Nucleoside Analogs Modified in the Sugar Moiety

9.3.3.1 Arabinonucleosides

9.3.3.2 Acyclic nucleoside analogs

9.3.3.3 Carbocyclic nucleoside analogs

9.3.3.4 Phosphonate nucleoside analogs

9.3.4 Active-Site Directed Non-nucleoside Inhibitors of Herpesvirus DNA Polymerases

9.4 The Lack of Enantioselectivity of Viral and Human Enzymes and the L-Enantiomers of Nucleosides:

9.4.1 Herpesvirus Thymidine Kinase Has Low Enantioselectivity

9.4.2 The Discovery of a Relaxed Enantioselectivity of Human and Viral DNA Polymerases

9.4.3 Lack of Enantiospecificity of Human 2 -Deoxycytidine Kinase: Relevance for the Activation of L

9.5 Inhibitors of HIV-1 Reverse Transcriptase

9.5.1 Nucleoside Reverse Transcriptase Inhibitors

9.5.1.1 Intracellular anabolism of nucleoside reverse transcriptase inhibitors

9.5.1.2 Catabolism of nucleoside reverse transcriptase inhibitors

9.5.2 Non-nucleoside Reverse Transcriptase Inhibitors

9.5.2.1 Metabolism of non-nucleoside reverse transcriptase inhibitors

9.5.3 Combined Toxicities of Reverse Transcriptase Inhibitors

9.5.4 Molecular Interactions of HIV-1 Reverse Transcriptase with Nucleoside- and Non-nucleoside Inhi

9.5.4.1 NRTIs drug resistance

9.5.4.2 NNRTIs drug resistance

9.6 Inhibitors of Hepatitis B DNA Polymerase

9.7 Chapter Summary

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Ulrich Hübscher,Silvio Spadari,Giuseppe Villani,Giovanni Maga,Polymerases