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By Roger Hull, John Innes Center, Norwich, UK
Audience
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 Architecture of rod-shaped viruses
A. Introduction
B. Structure of TMV
1. General features
2. Virus
structure
C. Assembly of TMV
1. Properties of the coat protein
2. Assembly of TMV coat protein
3. Assembly of the TMV rod
a. Assembly
in vitro
b. Assembly in vivo
IV Architecture of isometric viruses
A. Introduction
B. Possible icosahedra
C. Clustering of subunits
D.
Quasiequivalence
V 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 stabilization
VI. More complex isometric
viruses
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 viral sequences
IX Other kingdoms
X Summary
Section III: How do Plant Viruses Work?
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
Section 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-persistent 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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