Plant Virology

About the Author

Preface

Chapter 1 Introduction

I. Historical Background

II. Definition of a Virus

III. About this Edition

Chapter 2 Nomenclature and Classification of Plant Viruses

I. Nomenclature

A. Historical Aspects

B. Systems for Classification

C. Families, Genera, Species and Groups

D. Plant Virus Families, Genera and Orders

E. Use of Virus Names

II. Criteria Used for Classifying Viruses

A. Structure of the virus particle

B. Physicochemical Properties of Virus Particles

C. Properties of Viral Nucleic Acids

D. Viral Proteins

E. Serological Relationships

F. Activities in the Plant

G. Methods of Transmission

III. Families and Genera of Plant Viruses

A. Family Caulimoviridae

B. Family Geminiviridae

C. Family Circoviridae

D. Family Reoviridae

E. Family Partitiviridae

F. No Family

G. Family Rhabdoviridae

H. Family Bunyaviridae

I. No Family

J. Family Bromoviridae

K. Family Comoviridae

L. Family Potyviridae

M. Family Tombusviridae

N. Family Sequiviridae

O. Family Closteroviridae

P. Family Luteoviridae

Q. Floating Genera

IV. Retroelements

A. Family Pseudoviridae

B. Family Metaviridae

VI. Viruses of Lower Plants

A. Viruses of Algae

B. Viruses of Fungi

C. Viruses of Ferns

D. Viruses of Gymnosperms

E. Summary

VI. Discussion

Chapter 3 Disease Symptoms and Host Range

I. Economic Losses due to Plant Viruses

II. Macroscopic Symptoms

A. Local Symptoms

B. Systemic Symptoms

C. Agents Inducing Virus-Like Symptoms

D. The Cryptoviruses

III. Histological Changes

A. Necrosis

B. Hypoplasia

C. Hyperplasia

IV. Cytological Effects

A. Methods

B. Effects on Cell Structures

C. Virus-induced Structures in the Cytoplasm

D. Cytological Structures Resembling those Induced by Viruses

E. Discussion

V. The Host Range of Viruses

A. Limitations in Host Range Studies

B. Patterns of Host Range

C. The Determinants of Host Range

VI. Discussion and Summary

Chapter 4 Purification and Composition of Plant Viruses

I. Introduction

II. Isolation

A. Choice of Plant Material

III. Components

A. Nucleic Acids

B. Proteins

C. Other Components in Viruses

D. Discussion and Summary

Chapter 5 Architecture and Assembly of Virus Particles

I. Introduction

II. Methods

A. Chemical and Biochemical Studies

B. Methods for Studying Size of Viruses

C. Fine Structure Determination: Electron Microscopy

D. X-ray Crystallograpic Analysis

E. Neutron Small-Angle Scattering

F. Mass Spectrometry

G. Serological Methods

H. Methods for Studying Stabilizing Bonds

III. Architecture of Rod-Shaped Viruses

A. Introduction

B. Tobamovirus Genus

C. Tobravirus Genus

D. Other Helical Viruses

IV. Assembly of Rod-Shaped Viruses

A. TMV

B. Other Rod-shaped Viruses

V. Architecture of Isometric Viruses

A. Introduction

B. Quasi-Equivalence

C. Possible Icosahedra

D. Clustering of Subunits

E. 'True' and 'Quasi' Symmetries

F. Bacilliform Particles

VI. Small Icosahedral Viruses

A. Subunit Structure

B. Virion Structure

C. The Arrangement of Nucleic Acid within Icosahedral Viruses

VII. More Complex Isometric Viruses

VIII. Enveloped Viruses

A. Rhabdoviridae

B. Tospoviruses

IX. Assembly of Icosahedral Viruses

A. Bromoviruses

B. Alfalfa Mosaic Virus

C. Other Viruses

D. RNA Selection During Assembly of Plant Reoviruses

X. Discussion and Summary

Chapter 6 Genome Organization

I. Introduction

II. General Properties of Plant Viral Genomes

A. Information Content

B. Economy in the Use of Genomic Nucleic Acids

C. The Functions of Viral Gene Products

D. Non-coding Regions

III. Plant Viral Genome Organization

IV. Double-Stranded DNA Viruses

A. Family Caulimoviridae

V. Single-Stranded DNA Viruses

A. Family Geminiviridae

B. Family Circoviridae

VI. Double-Stranded RNA Viruses

A. Family Reoviridae

B. Family Partitiviridae

C. Genus Varicosavirus

VII. Negative-Sense Single-Stranded RNA Genomes

A. Family Rhabdoviridae

B. Family Bunyaviridae

VIII. Positive-Sense Single-Stranded RNA Genomes

A. Family Bromoviridae

B. Family Comoviridae

C. Family Potyviridae

D. Family Tombusviridae

E. Family Sequiviridae

F. Family Closteroviridae

G. Family Luteoviridae

H. Floating Genera

IX. Summary and Discussion

Chapter 7 Expression of Viral Genomes

I. Introduction

II. Virus Entry and Uncoating

A. Virus Entry

B. Uncoating of TMV

C. Uncoating of Bromoviruses

D. Uncoating of SBMV

E. Uncoating of TYMV

F. Discussion

III. Viral Genome Expression

A. Structure of the Genome

B. Defining Functional ORFs

C. Recognizing Activities of Viral Genes

D. Matching Gene Activities with Functional ORFs

IV. Synthesis of mRNAs

A. Negative-Sense Single-Stranded RNA Viruses

B. Double-Stranded RNAviruses

C. DNA Viruses

V. Plant Viral Genome Strategies

A. The Eukaryotic Protein-Synthesizing System

B. Virus Strategies to Overcome Eukaryotic Translation Constraints

C. Control of Translation

D. Discussion

E. Positive-Sense ssRNA Viruses that Have More than One Strategy

F. Negative-Sense Single-Stranded RNA Viruses

G. Double-stranded RNAviruses

H. DNA Viruses

VI. Discussion

Chapter 8 Virus Replication

I. Introduction

II. Host Functions Used by Plant Viruses

A. Components for Virus Synthesis

B. Energy

C. Protein Synthesis

D. Nucleic Acid Synthesis

E. Structural Components of the Cell

III. Methods for Studying Viral Replication

A. In Vivo Systems

B. In Vitro Systems

IV. Replication of Positive-Sense Single-Stranded RNA Viruses

A. Viral Templates

B. Replicase

C. Sites of Replication

D. Mechanism of Replication

E. Replication of Brome Mosaic Virus

F. Replication of Cucumber Mosaic Virus

G. Replication of Alfalfa Mosaic Virus

H. Replication of Tobacco Mosaic Virus

I. Replication of Potyviruses

J. Replication of Comoviridae

K. Replication of Turnip Yellow Mosaic Virus

L. Replication of Other (+)-Strand RNA Viruses

M. Discussion

V. Replication of Negative-Sense Single-Stranded RNA Viruses

A. Plant Rhabdoviridae

B. Tospoviruses

VI. Replication of Double-Stranded RNA Viruses

A. Plant Reoviridae

VII. Replication of Reverse Transcribing Viruses

A. Reverse Transcriptase

B. Replication of 'Caulimoviruses'

C. Replication of 'badnaviruses'

VIII. Replication of Single-Stranded DNA Viruses

A. Methods for Studying Geminivirus Teplication

B. In Vivo Observations on Geminiviruses

C. Rolling-Circle Replication

D. Geminivirus Replication

E. Nanovirus Replication

IX. Mutation and Recombination

A. Mutation

B. Recombination

C. Defective and Defective Interfering Nucleic Acids and Particles

X. Mixed Virus Assembly

XI. Discussion

Chapter 9 Induction of Disease 1" Virus Movement through the Plant and Effects on Plant Metabolism

I. Introduction

II. Movement and Final Distribution

A. Routes by Which Viruses Move Through Plants

B. Methods for Studying Virus Movement

C. Transport Across Nuclear Membranes

D. Cell-to-Cell Movement

E. Time of Movement from First Infected Cells

F. Rate of Cell-to-Cell Movement

G. Long-Distance Movement

H. Rate of Systemic Movement

I. Movement in the Xylem

J. Final Distribution in the Plant

K. Host Factors

L. Discussion

III. Effects on Plant Metabolism

A. Experimental Variables

B. Nucleic Acids and Proteins

C. Lipids

D. Carbohydrates

E. Cell Wall Compounds

F. Respiration

G. Photosynthesis

H. Transpiration

I. Activities of Specific Enzymes

J. Hormones

K. Low-Molecular-Weight Compounds

L. Summary

IV. Processes Involved in Symptom Induction

A. Sequestration of Raw Materials

B. Effects on Growth

C. Effects on Chloroplasts

D. Mosaic Symptoms

E. The Role of Membranes

V. Discussion

Chapter 10 Induction of Disease 2: Virus-Plant Interactions

I. Introduction

II. Definitions and Terminology of Host Responses to Inoculation

A. R Genes

III. Steps in the Induction of Disease

A. Ability of Virus to Replicate in Initial Cell

B. Ability of Virus to Move out of First Cell

C. Hypersensitive Local Response

D. HR Induced by TMV in N-Gene Tobacco

E. Other Viral-Host Hypersensitive Responses

F. Host Protein Changes in the Hypersensitive Response

G. Other Biochemical Changes During the Hypersensitive Response

H. Systemic Necrosis

I. Programmed Cell Death and Plant Viruses

J. Local Acquired Resistance

K. Systemic Acquired Resistance

L. Wound Healing Responses

M. Antiviral Factors

N. Ability of Virus to Spread Through Various Barriers

O. Systemic Host Response

P. Development of Mosaic Disease

Q. Symptom Severity

R. Recovery

IV. Inherent Host Response

A. Gene Silencing

B. Transcriptional and Post-Transcriptional Gene Silencing

C. Genes Involved in Post-Transcriptional Gene Silencing

D. Mechanism of Post-Transcriptional Gene Silencing

E. PTGS Systemic Signaling

F. Induction and Maintenance

G. PTGS in Virus-Infected Plants

H. Suppression of Gene Silencing

I. Other Mechanisms of Avoiding PTGS

J. Discussion

V. Influence of Other Agents

A. Viroids and Satellite RNAs

B. Defective Interfering Nucleic Acids

C. Other Associated Nucleic Acids

D. Cross-Protection

E. Concurrent Protection

F. Interactions between Unrelated Viruses

G. Interactions between Viruses and Fungi

VI. Discussion and Summary

Chapter 11 Transmission 1: By Invertebrates, Nematodes and Fungi

I. Introduction

II. Transmission by Invertebrates

A. Arthropoda

B. Nematoda

C. Relationships between Plant Viruses and Invertebrates

III. Aphids (Aphididae)

A. Aphid Life Cycle and Feeding Habits

B. The Vector Groups of Aphids

C. Aphid Transmission by Cell Injury

D. Types of Aphid-Virus Relationship

E. Non-Persistent Transmission

F. Semi-Persistent Transmission

G. Bimodal Transmission

H. Persistent Transmission

IV. Leafhoppers and Planthoppers (Auchenorrhyncha)

A. Structure and Life Cycle

B. Kinds of Virus-Vector Relationship

C. Semi-Persistent Transmission

D. Persistent Transmission

V. Whiteflies (Aleyrodidae)

A. Whiteflies

B. Begomoviruses

C. Closteroviruses and Criniviruses

VI. Thrips (Thysanoptera)

A. Thrip Anatomy

B. Tospovirus Transmission

C. Virus-Vector Relationship

D. Route Through the Thrips

VIII Other Sucking and Piercing Vector Groups

A. Mealybugs (Coccoidea and Pseudococcoidea)

B. Bugs (Miridae and Piesmatidae)

VIII. Insects with Biting Mouthparts

A. Vector Groups and Feeding Habits

B. Viruses Transmitted by Beetles

C. Beetle-Virus Relationships

IX. Mites (Arachnida)

A. Eriophyidae

B. Tetranychidae

X. Pollinating Insects

XI. Nematodes (Nematoda)

A. Criteria for Demonstrating Nematode Transmission

B. Nematode Feeding

C. Virus-Nematode Relationships

D. Virus-Vector Molecular Interactions

XII. Fungi

A. In Vitro Fungal Transmission

B. In Vivo Fungal Transmission

XIII. Discussion and Summary

Chapter 12 Transmission 2: Mechanical, Seed, Pollen and Epidemiology

I. Mechanical Transmission

A. Source and Preparation of Inoculum

B. Applying the Inoculum

II. Factors Influencing the Course of Infection and Disease

A. The Plant Being Inoculated

B. Development of Disease

C. Viral Nucleic Acid as Inoculum

D. Nature and Number of Infectible Sites

E. Number of Particles Required to Give an Infection

F. Mechanical Transmission in the Field

G. Abiotic Transmission in Soil

H. Summary and Discussion

III. Direct Passage in Living Higher Plant Material

A. Through the Seed

B. By Vegetative Propagation

C. By Grafting

D. By Dodder

E. Summary and Discussion

IV. Ecology and Epidemiology

A. Biological Factors

B. Physical Factors

C. Survival Through the Seasonal Cycle

D. Disease Forecasting

E. Conclusions

Chapter 13 New Understanding of the Functions of Plant Viruses

I. Introduction

II. Early Events

III. Mid-stage Events

A. Host and Virus Translation

B. Host and Virus Replication

C. Spatial Factors in Virus Expression and Replication

D. Plant Viruses and Cytoskeletal Elements

IV. Late Events

V. Systemic Interactions with Plants

VI. Discussion

Chapter 14 Viroids, Satellite Viruses and Satellite RNAs

I. Viroids

A. Classification of Viroids

B. Pathology of Viroids

C. Structure of Viroids

D. Replication of Viroids

E. Molecular Basis for Biological Activity

F. Diagnostic Procedures for Viroids

II. Satellite Viruses and Satellite RNAs

A. Satellite Plant Viruses

B. Satellite RNAs (satRNAs)

C. Satellite DNAs

D. Complex-Dependent Viruses

E. Discussion

Chapter 15 Methods for Assay, Detection and Diagnosis

I. Introduction

II. Methods Involving Biological Activities of the Virus

A. Infectivity Assays

B. Indicator Hosts for Diagnosis

C. Host Range in Diagnosis

D. Symptom-Related Methods

E. Methods of Transmission in Diagnosis

F. Cytological Effects for Diagnosis

G. Mixed Infections

H. Preservation of Virus Inoculum

III. Methods Depending on Physical Properties of the Virus Particle

A. Stability and Physicochemical Properties

B. Ultracentrifugation

C. Electron Microscopy

D. Chemical Assays for Purified Viruses

E. Assay Using Radioisotopes

IV. Methods Depending on Properties of Viral Proteins

A. Serological Procedures

B. Methods for Detecting Antibody-Virus Combination

C. Collection, Preparation and Storage of Samples

D. Monoclonal Antibodies

E. Phage-Displayed Single-Chain Antibodies

F. Serologically Specific Electron Microscopy

G. Fluorescent Antibody

H. Neutralization of Infectivity

I. Electrophoretic Procedures

V. Methods Involving Properties of the Viral Nucleic Acid

A. Type and Size of Nucleic Acid

B. Cleavage Patterns of DNA

C. Hybridization Procedures

D. Polymerase Chain Reaction

VI. Discussion and Summary

Chapter 16 Control and Uses of Plant Viruses

I. Introduction

II. Removal or Avoidance of Sources of Infection

A. Removal of Sources of Infection in or Near the Crop

B. Virus-Free Seed

C. Virus-Free Vegetative Stocks

D. Propagation and Maintenance of Virus-Free Stocks

E. Modified Planting and Harvesting Procedures

III. Control or Avoidance of Vectors

A. Air-Borne Vectors

B. Soil-Borne Vectors

IV. Protecting the Plant from Systemic Disease

A. Mild Strain Protection (Cross-Protection)

B. Satellite-Mediated Protection

C. Antiviral Chemicals

V. Conventional Resistance to Plant Viruses

A. Kinds of Host Response

B. Genetics of Resistance to Viruses

C. Tolerance

D. Use of Conventional Resistance for Control

VI. Transgenic Protection Against Plant Viruses

A. Introduction

B. Natural Resistance Genes

VII. Pathogen-Derived Resistance

A. Protein-Based Protection

B. Nucleic Acid-Based Protection

C. Other Forms of Transgenic Protection

D. Field Releases of Transgenic Plants

E. Potential Risks Associated with Field Release of Virus Transgenic Plants

VIII. Discussion and Conclusions

IX. Possible Uses of Viruses for Gene Technology

A. Viruses as Gene Vectors

B. Viruses as Sources of Control Elements for Transgenic Plants

C. Viruses for Presenting Heterologous Peptides

D. Viruses in Functional Genomics of Plants

E. Summary and Discussion

Chapter 17 Variation, Evolution and Origins of Plant Viruses

I. Strains of Viruses

A. Quasi-Species

B. Virus Strains

II. Criteria for the Recognition of Strains

A. Structural Criteria

B. Serological Criteria

C. Biological Criteria

D. Discussion

III. Isolation of Strains

A. Strains Occurring Naturally in Particular Hosts

B. Isolation from Systemically Infected Plants

C. Selection by Particular Hosts or Conditions of Growth

D. Isolation by Means of Vector

E. Isolation of Artificially Induced Mutants

F. Isolation of Strains by Molecular Cloning

IV. The Molecular Basis of Variation

A. Mutation (Nucleotide Changes)

B. Recombination

C. Deletions and Additions

D. Nucleotide Sequence Re-Arrangement

E. Re-Assortment of Multi-Particle Genomes

F. The Origin of Strains in Nature

V. Constraints on Variation

A. Muller's Ratchet

B. Does Muller's Ratchet Pperate with Plant Viruses?

VI. Virus Strains in the Plant

A. Cross-Protection

B. Selective Survival in Specific Hosts

C. Loss of Infectivity for one Host Following Passage Through Another

D. Double Infections In Vivo

E. Selective Multiplication Under Different Environmental Conditions

VII. Correlations between Criteria for Characterizing Viruses and Virus Strains

A. Criteria for Identity

B. Strains and Viruses

C. Correlations for Various Criteria

VIII. Discussion and Summary

IX. Speculations on Origins and Evolution

X. Types of Evolution

A. Microevolution and Macroevolution

B. Sequence Divergence or Convergence

C. Modular Evolution

D. Evidence for Virus Evolution

XI. Sources of Viral Genes

A. Replicases

B. Proteinases

C. Coat Proteins

D. Cell-to-Cell Movement Proteins

E. Suppressors of Gene Silencing

XII. Origins of Viruses, Viroids and Satellites

A. Origins of Viruses

B. Origin of Viroids

C. Origin of Satellite Viruses and Nucleic Acids

XIII. Selection Pressures for Evolution

A. Maximizing the Variation

B. Controlling the Variation

C. Adaptation to Niches

D. Rates of Evolution

XIV. Co-evolution of Viruses with Their Hosts and Vectors

A. Co-evolution of Viruses, Host Plants and Invertebrate Vectors

B. Evolution of Angiosperms and Insects

C. Horizontal Transmission through Plants of Viruses Infecting Only Insects

D. Affinities of Viruses that Replicate in Both Insects and Plants

E. Adaptation of Plant Viruses to Their Present Invertebrate Vectors

XV. Discussion and Summary

Appendix 1A

Appendix 1B

Appendix 2A

Appendix 2B

Appendix 3

References

Index