Jane Flint - Principles of Virology, Volume 1

References 6 Synthesis of RNA from RNA Templates Introduction The Nature of the RNA Template The RNA Synthesis Machinery Mechanisms of RNA Synthesis Paradigms for Viral RNA Synthesis Origins of Diversity in RNA Virus Genomes Perspectives References 7 Synthesis of RNA from DNA Templates Introduction Transcription by RNA Polymerase II Transcription of Viral DNA Templates by the Cellular Machinery Alone Viral Proteins That Govern Transcription of DNA Templates Transcription of Viral Genes by RNA Polymerase III Inhibition of the Cellular Transcriptional Machinery Unusual Functions of Cellular Transcription Components in Virus-Infected Cells Viral DNA-Dependent RNA Polymerases Perspectives References 8 Processing Introduction Covalent Modification during Viral Pre-mRNA Processing Export of RNAs from the Nucleus Posttranscriptional Regulation of Viral or Cellular Gene Expression by Viral Proteins Regulation of Turnover of Viral and Cellular mRNAs in the Cytoplasm Noncoding RNAs Perspectives References 9 Replication of DNA Genomes Introduction DNA Synthesis by the Cellular Replication Machinery Mechanisms of Viral DNA Synthesis Exponential Accumulation of Viral Genomes Limited Replication of Viral DNA Genomes Origins of Genetic Diversity in DNA Viruses Perspectives References 10 Reverse Transcription and Integration Retroviral Reverse Transcription Retroviral DNA Integration Hepadnaviral Reverse Transcription Perspectives References 11 Protein Synthesis Introduction Mechanisms of Eukaryotic Protein Synthesis The Diversity of Viral Translation Strategies Regulation of Translation during Viral Infection Perspectives References 12 Intracellular Trafficking Introduction Assembly within the Nucleus Assembly at the Plasma Membrane Interactions with Internal Cellular Membranes Transport of Viral Genomes to Assembly Sites Perspectives References 13 Assembly, Release, and Maturation Introduction Methods of Studying Virus Assembly and Egress Assembly of Protein Shells Selective Packaging of the Viral Genome and Other Components of Virus Particles Acquisition of an Envelope Release of Virus Particles Maturation of Progeny Virus Particles Cell-to-Cell Spread Perspectives References 14 The Infected Cell Introduction Signal Transduction Gene Expression Metabolism Remodeling of Cellular Organelles Perspectives References

8 APPENDIX: Structure, Genome Organization, and Infectious Cycles of Viruses Featured in This BookAdenoviruses Arenaviruses Coronaviruses Filoviruses Flaviviruses Hepadnaviruses Herpesviruses Orthomyxoviruses Paramyxoviruses Parvoviruses Picornaviruses Polyomaviruses Poxviruses Reoviruses Retroviruses Rhabdoviruses Togaviruses

9 Glossary

10 Index

11 End User License Agreement

1 Chapter 2 Table 2.1 Particle-to-PFU ratios of some animal viruses

2 Chapter 3 Table 3.1 Some viral vectors

3 Chapter 4 Table 4.1 Functions of virion proteins Table 4.2 Nomenclature used in description of virus structureTable 4.3 Some virion enzymes

4 Chapter 7Table 7.1 Strategies of transcription of viral DNA templatesTable 7.2 Eukaryotic RNA polymerases synthesize different classes of cellular an...Table 7.3 Properties and functions of some viral transcriptional regulatorsTable 7.4 Viral RNA polymerase III transcription units

5 Chapter 9Table 9.1 Viral origin recognition proteinsTable 9.2 Replication systems of large DNA virusesTable 9.3 Viral enzymes of nucleic acid metabolism

6 Chapter 10Table 10.1 Comparison of retroviral integration site preferences in human cellsTable 10.2 Comparison of retroviral and hepadnaviral reverse transcription

7 Chapter 12Table 12.1 Some viral envelope glycoprotein precursors processed by secretory pa...

8 Chapter 13Table 13.1 Common sequence motifs required for budding of enveloped virus partic...

1 Chapter 1 Figure 1.1 The human virome. Our knowledge of the diversity of viruses that ca... Figure 1.2 Tracking ancient human migrations by the viruses they carried. The ... Figure 1.3 References to viral diseases from the ancient literature. (A)An im... Figure 1.4 Three Broken Tulips . A painting by Nicolas Robert (1624–1685), now ... Figure 1.5 Characteristic smallpox lesions in a young victim. Illustrations li... Figure 1.6 Pasteur’s famous swan-neck flasks provided passive exclusion of micro... Figure 1.7 The pace of discovery of new infectious agents in the dawn of virolog... Figure 1.8 Filter systems used to characterize/purify virus particles. (A)The... Figure 1.9 Electron micrographs of virus particles following negative staining. ... Figure 1.10 Size matters. (A)Sizes of animal and plant cells, bacteria, virus... Figure 1.11 Lesions induced by tobacco mosaic virus on an infected tobacco leaf.... Figure 1.12 The Baltimore classification. The Baltimore classification assigns... Figure 1.13 Viral families sorted according to the nature of the viral genomes. ... Figure 1.14 Landmarks in the study of viruses. Key discoveries and technical a...

2 Chapter 2 Figure 2.1 The viral infectious cycle. The infectious cycle of poliovirus is s... Figure 2.2 Different types of cell culture used in virology. Confluent cell mo... Figure 2.3 Production of organoids from stem cells. The different germ layers ... Figure 2.4 Production of airway-liquid interface cultures of bronchial epithel... Figure 2.5 Development of cytopathic effect. (A)Cell rounding and lysis durin... Figure 2.6 Growth of viruses in embryonated eggs. The cutaway view of an embry... Figure 2.7 Plaques formed by different animal viruses. (A)Photomicrograph of ... Figure 2.8 The dose-response curve of the plaque assay. The number of plaques ... Figure 2.9 Transformation assay. Chicken cells transformed by two different st... Figure 2.10 Hemagglutination assay. ( Top) Samples of different influenza virus... Figure 2.11 Polysome analysis. To study the association of mRNAs with ribosome... Figure 2.12 Direct and indirect methods for antigen detection. (A)The sample ... Figure 2.13 Detection of viral antigen or antibodies against viruses by enzyme... Figure 2.14 Lateral flow immunochromatographic assay. A slide or “dipstick” co... Figure 2.15 Using fluorescent proteins to study virus particles and virus-infe... Figure 2.16 Polymerase chain reaction. The DNA to be amplified is mixed with n... Figure 2.17 Workflow for VS-Virome. Shown is the computational pipeline design... Figure 2.18 Comparison of bacterial and viral reproduction. (A)Growth curve f... Figure 2.19 One-step growth curves of animal viruses. (A)Growth of a nonenvel... Figure 2.20 Chromatin immunoprecipitation and DNA sequencing, ChiP-seq. This t... Figure 2.21 Interactions between human proteins and Nipah virus proteins. Netw... Figure 2.22 Single-cell virology. (A)A microfluidic device with 6,400 wells i...

3 Chapter 3 Figure 3.1 The Baltimore classification. All viruses must produce mRNA that ca... Figure 3.2 Structure and expression of viral double-stranded DNA genomes. (A)... Figure 3.3 Structure and expression of viral gapped, circular, double-stranded D... Figure 3.4 Structure and expression of viral single-stranded DNA genomes. (A)... Figure 3.5 Structure and expression of viral double-stranded RNA genomes. (A)... Figure 3.6 Structure and expression of viral single-stranded (+) RNA genomes. Figure 3.7 Structure and expression of viral single-stranded (+) RNA genomes wit... Figure 3.8 Structure and expression of viral single-stranded (–) RNA genomes. Figure 3.9 Genome structures in cartoons and in real life. (A)Linear represen... Figure 3.10 Information retrieval from viral genomes. Different strategies for... Figure 3.11 Reassortment of influenza virus RNA segments. (A)Progeny viruses ... Figure 3.12 Recovery of infectivity from cloned DNA of RNA viruses. (A)The in... Figure 3.13 Use of RNAi, haploid cells, and CRISPR-Cas9 to study virus-host inte... Figure 3.14 Adenovirus vectors. High-capacity adenovirus “gutless” vectors con... Figure 3.15 Adeno-associated virus vectors. (A)Map of the genome of wild-type... Figure 3.16 Retroviral vectors. The minimal viral sequences required for retro...

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