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Comparative Plant Virology, 2nd Edition

Roger Hull 
Academic Press  January 2009  



Hardcover  400 pp  ISBN 9780123741547      £48.00
A comprehensive testbook covering all aspects of plant viruses.

Of interest to Advanced undergraduate and graduate students in basic and applied plant virology, plant pathology, microbiology, genetics and molecular biology, biological control, ecology, evolution, and related aspects of plant science

Contents

Section I: Introduction to Plant Viruses

Chapter 1. What is a virus?
I Introduction II History III Definition of a virus A How viruses differ from other plant pathogens B Are viruses alive? IV Classification and nomenclature of viruses A Virus classification B Families, genera and species C Naming of virus species D. Acronyms and abbreviations E Plant virus classification F Virus strains G Use of virus names V Viruses of other kingdoms VI Summary

Chapter 2. Overview of plant viruses
I. Introduction II Economic losses due to plant viruses III Virus profiles IV Macroscopic symptoms A. Local symptoms B. Systemic symptoms 1. Effects on plant size 2. Mosaic patterns and related symptoms 3. Yellows diseases 4. Leaf rolling 5 Ring spot diseases 6 Necrotic diseases 7. Developmental abnormalities 8 Wilting 9. Recovery from disease 10. Genetic effects C. The cryptoviruses D. Diseases caused by viral complexes E. Agents inducing virus-like symptoms V Histological changes A. Necrosis B. Hypoplasia C. Hyperplasia 1. Cells are larger than normal 2. Cell division in differentiated cells 3. Abnormal division in cambial cells VI Cytopathological effects A. Effects on cell structures 1. Nuclei 2. Mitochondria 3. Chloroplasts 4. Cell walls 5. Cell death B. Virus induced structures in the cytoplasm 1. Accumulations of virus particles 2. Aggregates of virus-encoded proteins 3. Caulimovirus inclusions C. Why inclusion bodies? D. Cytoplasmic structures resembling those induced by viruses. VII The host range of viruses A. Limitations in host range studies B. Patterns of host range C. The determinants of host range 1. Initial events 2. Expression and replication 3. Cell-to-cell movement 4. Stimulation of host-cell defences VIII Viruses of other kingdoms IX Summary

Chapter 3. Agents that resemble or alter plant virus diseases
I Viroids A Classification of viroids B. Pathology of viroids 1. Macroscopic disease symptoms 2. Cytopathic effects 3. Location of viroids in plants 4. Movement in the plant 5. Transmission 6. Epidemiology C Properties of viroid RNAs 1. Sequence and structure 2. Replication 3. Recombination between viroids D. Molecular basis for biological activity E. Diagnostic procedures for viroids II Phytoplasma III Satellite viruses and satellite RNAs A Satellite plant viruses (A-type) B. Satellite RNAs (satRNAs) 1. Large satellite RNAs (B-type) 2. Small linear satellite RNAs (C-type) 3. Small circular satellite RNAs (D-type) 4. Satellite-like RNAs a. A satellite RNA of Groundnut rosette virus (GRV). b Ancillary RNAs of Beet necrotic yellow vein virus (BNYVV) 5. Molecular basis for symptom modulation C. Satellite DNAs D. Discussion IV Defective and defective-interfering nucleic acids 1. Group 1: Single deletion D-RNAs 2. Group 2: Multiple deletion D- and DI-RNAs 3. Defective DNAs associated with DNA viruses V. Other kingdoms VI Summary

Chapter 4. Plant virus origins and evolution
I. Introduction II Virus evolution A Origins of viruses B Virus variation C Types of evolution 1. Microevolution and macroevolution 2. Sequence divergence or convergence 3. Modular evolution 4. Sources of viral genes a. Replicases i. RNA replicases ii. Reverse transcriptase iii DNA replicases b. Proteases c. Coat proteins d. Cell-to-cell movement proteins e. Suppressors of gene silencing D Selection pressures for evolution 1. Adaptation to niches 2. Maximizing the variation 3. Controlling the variation a. Muller?s ratchet b. Does Muller?s ratchet operate with plant viruses? 4. Role of selection pressure 5. Selection pressure by host plants E. Timeline for evolution 1. Non-constant rates of evolution 2. Estimated rates of evolution III Evidence for virus evolution A. Geminiviruses B. Closteroviruses C. Luteoviruses IV Co-evolution of viruses with their hosts and vectors V Other kingdoms VI Summary

Section II: What is a Virus Made of?

Chapter 5. Architecture and assembly of virus particles
I. Introduction II. Methods A Chemical and biochemical studies B. Methods for studying size and fine structure of viruses 1. Hydrodynamic measurements 2. Electron microscopy 3. X-ray crystallography 4. Neutron small-angle scattering 5. Atomic force microscopy 6. Mass spectrometry 7. Serological methods 8. Stabilizing bonds III VII Enveloped viruses VIII Assembly of icosahedral viruses A Bromoviruses B. RNA selection during assembly of plant reoviruses IX General considerations X Viruses of other kingdoms XI Summary

Chapter 6. Plant viral genomes
I. Introduction II. General properties of plant viral genomes A. Information content B Economy of use of genomic nucleic acids C. The functions of viral gene products 1. Functional proteins a. Proteins initiating infection b. Proteins that replicate the viral genome c. Proteins that process viral gene products d. Proteins that facilitate viral movement through the host e. Overcoming host defence systems f. Proteins that facilitate host to host movement D. Nucleic acids 1. Multipartite genomes 2. Nucleic acid structures 3. Non-coding regions a. Eng-group structures b. 5' and 3' non-coding regions c. Intergenic regions III. Plant viral genome organization A. The structure of the genome B. Recognizing activities of viral genes 1. Location of spontaneous or artificially-induced mutations 2. Recombinant viruses 3. Expression of the gene in a transgenic plant 4. Hybrid arrest and hybrid select procedures 5. Sequence comparison with genes of known function 6. Functional regions within a gene IV Other kingdoms V. Summary

Chapter 7. Expression of viral genomes
I Stages in virus infection cycle II Virus entry and uncoating A. Virus entry B. Uncoating 1. Uncoating of TMV 2. Uncoating of Brome mosaic virus and Southern bean mosaic virus 3. Uncoating of Turnip yellow mosaic virus 4. Uncoating other plant viruses III Initial translation of the viral genome IV Synthesis of mRNAs A. Negative-sense single-stranded RNA viruses B. Double-stranded RNA viruses C. DNA viruses 1. Caulimoviridae 2. Geminiviridae V Plant viral genome strategies A. The eukaryotic translation system constraint B. Virus strategies to overcome Eukaryotic translation constraints 1. Strategy 1: Polyproteins 2. Strategy 2: Sub-genomic RNAs 3. Strategy 3: Multipartite genomes 4. Strategy 4. Splicing 5. Strategy 5: Translation of both viral and complementary strands (ambisense) 6. Strategy 6: Internal initiation 7. Strategy 7: Leaky scanning a. Two initiation sites on one ORF (two start) b. Overlapping ORFs c. Two or more consecutive ORFs 8. Strategy 8: Non-AUG start codons 9. Strategy 9: Transactivation 10. Strategy 10: Translational (ribosome) shunt 11. Strategy 11: Read-through proteins 12. Strategy 12: Frameshift proteins C. Control of translation 1. Cap but no Poly(A) tail 2. Poly(A) tail but no cap 3. Neither cap or Poly (A) tail 4. Cap snatching 5. 5' UTR D. Discussion VI Other kingdoms VII Summary

Chapter 8 Virus replication
I. Host functions used by plant viruses II. Methods for studying viral replication III. Replication of plus-sense single-stranded RNA viruses A. Viral templates B. Replicase 1. RNA-dependent RNA polymerase 2. Helicases 3. Methyl transferase activity 4. Organization of functional domains in viral ORFs C. Sites of replication D. Mechanism of replication E. Discussion IV. Replication of negative-sense single-stranded RNA viruses V. Replication of double-stranded RNA viruses VI. Replication of reverse transcribing viruses A. Introduction B. Reverse transcriptase C. Replication of 'caulimoviruses' 1. Replication pathway 2. Inclusion bodies VII. Replication of single-stranded DNA viruses A. Geminivirus replication B. Geminivirus Rep proteins VIII Faults in replication A. Mutation B. Recombination 1. DNA virus recombination 2. RNA virus recombination 3. Recombination and integrated

Chapter 9 Virus-host interactions: 1. Plant level
I Movement and final distribution A. Intracellular movement B. Intercellular movement 1. Plasmodesmata 2. Movement proteins (MPs) 3. What actually moves 4. Cell-to-cell movement of viroids 5. Complementation 6. Rate of cell-to-cell movement C Systemic movement 1. Steps in systemic movement 2. Form in which virus is transported 3. Rate of systemic movement 4. Movement in the xylem D. Final distribution in the plant E. Outstanding questions on plant virus movement II Effects on plant metabolism A. Nucleic acids and proteins B. Lipids C. Carbohydrates D. Photosynthesis E. Respiration F. Transpiration G. Low molecular weight compounds III Processes involved in symptom production A. Sequestration of raw materials B. Effects on growth C. Effects on chloroplasts D. Mosaic symptoms E. Role of membranes IV Other kingdoms V Summary

Chapter 10. Virus-plant interactions: 2. Molecular level
I. Introduction II. Host response to inoculation A. Immunity B. Subliminal infection C. Non-permissive infection 1. Local infection a. Host protein changes in hypersensitive response b. Local acquired resistance 2. Systemic infection 3. Systemic acquired resistance 4. Programmed cell death D. Permissive infection 1. Systemic host response 2. Virus genes involved III Interactions between viruses A. Interactions between related viruses B. Interactions between unrelated viruses 1. Complete dependence for disease 2. Incomplete dependence for disease 3. Synergistic effects on viral replication 4. Effects on virus movement C. Interactions between viruses and other plant pathogens IV Other kingdoms V. Summary

Chapter 11. Virus-plant interactions 2. RNA silencing
I. Introduction II. Mechanism of silencing A. The basic pathway B. Components of the system 1. dsRNA 2. Dicer 3. Products of Dicer 4. RISC C. Results of the system III. Systemic silencing IV. Overcoming silencing A. Suppression of silencing 1. Protein suppressors of silencing 2. Nucleic acid suppressors of silencing B. Avoidance of silencing V. Silencing and symptoms A. Recovery B. Dark-green islands and mosaics C. miRNA D. siRNA effects E. Synergistic effects F. Other activities of silencing suppressors VI. Transcriptional and translational silencing VII. Evolutionary aspects VIII. RNA silencing in animal and other viruses IX. Summary

IV: Plant Viruses in Agriculture and Industry

Chapter 12. Plant to plant movement
I. Introduction II. Transmission via plant material A. Mechanical transmission B. Seed transmission C. Pollen transmission D. Vegetative transmission E. Grafting III. Transmission by invertebrates A. Relationship between plant viruses and insects B. Non-persisten transmission by insects 1. Features of non-persistent transmission 2. Virus-vector relationships a. Direct capsid interaction b. Indirect interaction involving helper components C. Persistent transmission by insects 1. Circulative viruses a. Features of circulative virus-vector interaction b. Dependent transmission 2. Propagative viruses 3. Thrip transmission of Tospoviruses D. Transmission by beetles E. Nematode transmission of viruses 1. Features of nematode transmission 2. Virus-nematode relationships IV. Fungal transmission of viruses V. Other Kingdoms VI. Summary

Chapter 13. Plant viruses in the field: Diagnosis, epidemiology and ecology
I. Diagnosis A. Introduction B. Methods involving biology of the virus 1. Indicator hosts 2. Host range 3. Methods of transmission 4. Cytological effects 5. Mixed infections. C. Methods depending on physical properties of the virus particle 1. Physical properties 2. Electron microscopy D. Methods depending on properties of viral proteins 1. Serology 2. Types of antisera 3. Methods for detecting antibody-virus combination a. ELISA procedures b. Serologically specific electron microscopy c. Electrophoretic procedures d. Dot blots E. Methods involving properties of the viral nucleic acid 1. Type and size of nucleic acid 2. Cleavage patterns of DNA 3. Hybridization procedures 4. Dot blots 5. Polymerase chain reaction 6. DNA microarray F. Decision making on diagnosis II Epidemiology and ecology A. Epidemiology of viruses in agriculture 1. Primary infections 2. Secondary spread B. Plant viruses in the natural environment C. Emergence of new viruses III Other kingdoms IV Summary

Chapter 14. Conventional control
I Introduction II Avoiding infection A. Removal of sources of infection B. Virus-free seed C. Virus-free vegetative stocks D Modified agronomic practices E. Quarantine regulations III. Stopping the vector A. Airborne vectors 1. Insecticides 2. Insect deterrents 3. Agronomic techniques B. Soilborne vectors 1. Nematodes 2. Fungi IV. Protecting the plant A. Protection by a plant pathogen B. Antiviral chemicals. V. Conventional resistance to plant viruses A. Introduction B. Genetics of resistance to viruses C. Tolerance D. Use of conventional resistance for control 1. Immunity 2. Field resistance 3. Tolerance VI. Strategies for control VII. Other Kingdoms VII. Summary

Chapter 15. Transgenic plants and viruses
I. Transgenic protection against plant viruses A. Introduction B. Natural resistance genes II Pathogen-derived resistance A. Protein-based protection 1. Transgenic plants expressing viral coat protein 2. Other viral proteins B. Nucleic acid ?based protection 1. RNA-mediated protection 2. Molecular basis of RNA-mediated protection 3. Sequences for RNA-mediated protection 4. Ribozymes 5. Relationship between natural cross protection and protection in transgenic plants. 6. Transgenic protection by satellite and DI nucleic acid C. Other forms of transgenic protection D. Field release of transgenic plants 1. Potential risks 2. Field performance III. Possible uses of plant viruses in gene technology A. DNA viruses as gene vectors 1. Caulimoviruses 2. Geminiviruses B. RNA viruses as gene vectors C. Viruses as sources of control elements for transgenic plants 1. DNA promoters 2. RNA promoters 3. Translation enhancers D. Viruses for producing vaccines 1. Vaccines using plant virus vectors 2. Viruses for presenting heterologous peptides a. Cowpea mosaic virus b. Tobacco mosaic virus E. Viruses in plant functional genomics F. Plant viruses in nanotechnology IV. Other kingdoms V. Summary

Appendix
Profiles
Subject Index

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