Section I: Introduction to Plant VirusesChapter 1. What is a virus?I IntroductionII HistoryIII 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 namesV Viruses of other kingdomsVI SummaryChapter 2. Overview of plant virusesI. IntroductionII Economic losses due to plant virusesIII Virus profilesIV 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 symptomsV 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 cellsVI 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 defencesVIII Viruses of other kingdomsIX SummaryChapter 3. Agents that resemble or alter plant virus diseasesI 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 viroidsII PhytoplasmaIII 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. DiscussionIV 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 virusesV. Other kingdomsVI SummaryChapter 4. Plant virus origins and evolutionI. IntroductionII 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 evolutionIII Evidence for virus evolution A. Geminiviruses B. Closteroviruses C. LuteovirusesIV Co-evolution of viruses with their hosts and vectorsV Other kingdomsVI SummarySection II: What is a Virus Made of?Chapter 5. Architecture and assembly of virus particlesI. IntroductionII. 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 bondsIII Architecture of rod-shaped virusesA. IntroductionB. Structure of TMV1. General features2. Virus structureC. Assembly of TMV1. Properties of the coat protein2. Assembly of TMV coat protein3. Assembly of the TMV roda. Assembly in vitrob. Assembly in vivoIV Architecture of isometric virusesA. IntroductionB. Possible icosahedraC. Clustering of subunitsD. QuasiequivalenceV Small icosahedral viruses A. Subunit structure B Virion structure 1. T = 1 particles 2. Other particles based on T = 1 symmetry a. Bacilliform particles based on T = 1 symmetry b. Geminiviruses 3. T = 3 particles a. Bacilliform particles based on T = 3 symmetry b. Pseudo T = 3 symmetry 4. T = 7 particles C The arrangement of nucleic acid within icosahedral viruses 1. RNA structure 2. Interactions between RNA and protein in small isometric viruses D. Stabilization of small isometric particles 1. Protein-RNA stabilization 2. Protein-protein stabilization 3. Protein-protein + protein-RNA stabilizationVI. More complex isometric virusesVII Enveloped virusesVIII Assembly of icosahedral viruses A Bromoviruses B. RNA selection during assembly of plant reovirusesIX General considerationsX Viruses of other kingdomsXI SummaryChapter 6. Plant viral genomesI. IntroductionII. 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 regionsIII. 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 kingdomsV. SummaryChapter 7. Expression of viral genomesI Stages in virus infection cycleII Virus entry and uncoating A. Virus entryB. Uncoating1. Uncoating of TMV2. Uncoating of Brome mosaic virus and Southern bean mosaic virus3. Uncoating of Turnip yellow mosaic virus4. Uncoating other plant virusesIII Initial translation of the viral genomeIV Synthesis of mRNAs A. Negative-sense single-stranded RNA viruses B. Double-stranded RNA viruses C. DNA viruses 1. Caulimoviridae 2. GeminiviridaeV 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. DiscussionVI Other kingdomsVII Summary Chapter 8 Virus replicationI. Host functions used by plant virusesII. Methods for studying viral replicationIII. Replication of plus-sense single-stranded RNA virusesA. Viral templatesB. Replicase1. RNA-dependent RNA polymerase2. Helicases3. Methyl transferase activity4. Organization of functional domains in viral ORFsC. Sites of replicationD. Mechanism of replicationE. DiscussionIV. Replication of negative-sense single-stranded RNA virusesV. Replication of double-stranded RNA virusesVI. Replication of reverse transcribing virusesA. IntroductionB. Reverse transcriptaseC. Replication of “caulimoviruses¿1. Replication pathway2. Inclusion bodiesVII. Replication of single-stranded DNA virusesA. Geminivirus replicationB. Geminivirus Rep proteinsVIII Faults in replication A. Mutation B. Recombination 1. DNA virus recombination 2. RNA virus recombination 3. Recombination and integrated viral sequencesIX Other kingdomsX SummarySection III: How do Plant Viruses Work?Chapter 9 Virus-host interactions: 1. Plant levelI 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 movementII Effects on plant metabolismA. Nucleic acids and proteinsB. LipidsC. CarbohydratesD. PhotosynthesisE. RespirationF. TranspirationG. Low molecular weight compoundsIII Processes involved in symptom productionA. Sequestration of raw materialsB. Effects on growthC. Effects on chloroplastsD. Mosaic symptomsE. Role of membranesIV Other kingdomsV SummaryChapter 10. Virus-plant interactions: 2. Molecular levelI. IntroductionII. Host response to inoculationA. ImmunityB. Subliminal infectionC. Non-permissive infection1. Local infectiona. Host protein changes in hypersensitive responseb. Local acquired resistance2. Systemic infection3. Systemic acquired resistance4. Programmed cell deathD. Permissive infection1. Systemic host response2. Virus genes involved III Interactions between virusesA. Interactions between related virusesB. Interactions between unrelated viruses1. Complete dependence for disease2. Incomplete dependence for disease3. Synergistic effects on viral replication4. Effects on virus movementC. Interactions between viruses and other plant pathogens IV Other kingdoms V. SummaryChapter 11. Virus-plant interactions – 2. RNA silencingI. IntroductionII. Mechanism of silencingA. The basic pathwayB. Components of the system1. dsRNA2. Dicer3. Products of Dicer4. RISCC. Results of the systemIII. Systemic silencingIV. Overcoming silencingA. Suppression of silencing1. Protein suppressors of silencing2. Nucleic acid suppressors of silencingB. Avoidance of silencingV. Silencing and symptoms A. Recovery B. Dark-green islands and mosaics C. miRNA D. siRNA effects E. Synergistic effects F. Other activities of silencing suppressorsVI. Transcriptional and translational silencingVII. Evolutionary aspectsVIII. RNA silencing in animal and other virusesIX. SummarySection IV: Plant Viruses in Agriculture and Industry Chapter 12. Plant to plant movementI. IntroductionII. Transmission via plant materialA. Mechanical transmissionB. Seed transmissionC. Pollen transmissionD. Vegetative transmissionE. GraftingIII. Transmission by invertebratesA. Relationship between plant viruses and insectsB. Non-persistent transmission by insects1. Features of non-persistent transmission2. Virus-vector relationshipsa. Direct capsid interactionb. Indirect interaction involving helper componentsC. Persistent transmission by insects1. Circulative virusesa. Features of circulative virus-vector interactionb. Dependent transmission2. Propagative viruses3. Thrip transmission of TospovirusesD. Transmission by beetlesE. Nematode transmission of viruses1. Features of nematode transmission2. Virus-nematode relationshipsIV. Fungal transmission of virusesV. Other KingdomsVI. SummaryChapter 13. Plant viruses in the field: Diagnosis, epidemiology and ecologyI. 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 diagnosisII Epidemiology and ecologyA. Epidemiology of viruses in agriculture1. Primary infections2. Secondary spreadB. Plant viruses in the natural environmentC. Emergence of new virusesIII Other kingdomsIV SummaryChapter 14. Conventional controlI IntroductionII Avoiding infection A. Removal of sources of infection B. Virus-free seed C. Virus-free vegetative stocks D Modified agronomic practices E. Quarantine regulationsIII. Stopping the vector A. Airborne vectors 1. Insecticides 2. Insect deterrents 3. Agronomic techniques B. Soilborne vectors 1. Nematodes 2. FungiIV. Protecting the plant A. Protection by a plant pathogenB. 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. ToleranceVI. Strategies for controlVII. Other KingdomsVII. SummaryChapter 15. Transgenic plants and virusesI. Transgenic protection against plant viruses A. Introduction B. Natural resistance genesII Pathogen-derived resistanceA. Protein-based protection1. Transgenic plants expressing viral coat protein2. Other viral proteinsB. Nucleic acid –based protection1. RNA-mediated protection2. Molecular basis of RNA-mediated protection3. Sequences for RNA-mediated protection4. Ribozymes5. Relationship between natural cross protection and protection in transgenic plants.6. Transgenic protection by satellite and DI nucleic acidC. Other forms of transgenic protectionD. Field release of transgenic plants1. Potential risks2. Field performanceIII. Possible uses of plant viruses in gene technologyA. DNA viruses as gene vectors1. Caulimoviruses2. GeminivirusesB. RNA viruses as gene vectorsC. Viruses as sources of control elements for transgenic plants1. DNA promoters2. RNA promoters3. Translation enhancersD. Viruses for producing vaccines1. Vaccines using plant virus vectors2. Viruses for presenting heterologous peptidesa. Cowpea mosaic virusb. Tobacco mosaic virusE. Viruses in plant functional genomicsF. Plant viruses in nanotechnologyIV. Other kingdomsV. SummaryAppendix – ProfilesSubject Index