COMPARATIVEPLANT VIROLOGY

SECOND EDITION

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Comparative Plant Virology, Second Edition,by Roger HullRevision to Fundamentals of Plant Virology written by R. Matthews

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COMPARATIVEPLANT

VIROLOGYSECOND EDITION

ROGER HULLEmeritus Fellow

Department of Disease and Stress Biology

John Innes Centre

Norwich, UK

AMSTERDAM • BOSTON • HEIDELBERG • LONDONNEW YORK • OXFORD • PARIS • SAN DIEGO

SAN FRANCISCO • SINGAPORE • SYDNEY • TOKYO

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Cover Credits:

BSMV leaf — Mild stripe mosaic; Symptom of BSMV in barley. Image courtesy ofA.O. Jackson.

BSMV genome: The infectious genome (BSMV) is divided between 3 species of positivesense ssRNA that are designated a, b, and g. Image courtesy of Roger Hull.

BSMV particles. Image courtesy of Roger Hull.

Diagram showing systemic spread of silencing signal: The signal is generated in the initiallyinfected cell (bottom, left hand) and spreads to about 10–15 adjacent cellswhere it is amplified.It moves out of the initially infected leaf via the phloem sieve tubes and then spreadsthroughout systemic leaves being amplified at various times. Image courtesy of Roger Hull.

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Library of Congress Cataloging-in-Publication Data

Hull, Roger, 1937-Comparative plant virology / Roger Hull. –

2nd ed.p. cm.

ISBN 978-0-12-374154-7 (hardcover : alk. paper) 1. Plant viruses. I. Title.QR351.H85 2009579.208–dc22

2008040333British Library Cataloguing in Publication DataA catalogue record for this book is available from the British Library

ISBN 13: 978-0-12-374154-7

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Contents

Preface xiiiList of Abbreviations xv

Section IINTRODUCTION TO PLANT

VIRUSES

Chapter 1. What Is a Virus?

I. Introduction 3II. History 3III. Definition of a Virus 9

A. How Viruses Differ from Other PlantPathogens 9

B. Are Viruses Alive? 13IV. Classification and Nomenclature of Viruses 13

A. Virus Classification 13B. Families, Genera, and Species 14C. Naming Viruses (Species) 15D. Acronyms or Abbreviations 16E. Plant Virus Classification 17F. Virus Strains 17G. Use of Virus Names 19

V. Viruses of Other Kingdoms 20VI. Summary 21

Chapter 2. Overview of Plant Viruses

I. Introduction 23II. Economic Losses Due to Plant Viruses 24III. Virus Profiles 24IV. Macroscopic Symptoms 25

A. Local Symptoms 25B. Systemic Symptoms 26

1. Effects on Plant Size 262. Mosaic Patterns and Related Symptoms 263. Yellow Diseases 284. Leaf Rolling 285. Ring Spot Diseases 286. Necrotic Diseases 287. Developmental Abnormalities 288. Wilting 299. Recovery from Disease 2910. Genetic Effects 29

C. The Cryptoviruses 29D. Diseases Caused by Viral Complexes 29E. Agents Inducing Virus-Like Symptoms 30

V. Histological Changes 30A. Necrosis 30B. Hypoplasia 30C. Hyperplasia 32

1. Cell Size 322. Cell Division in Differentiated Cells 323. Abnormal Division in Cambial Cells 32

VI. Cytological Effects 32A. Effects on Cell Structures 32

1. Nuclei 322. Mitochondria 333. Chloroplasts 334. Cell Walls 335. Cell Death 34

B. Virus-Induced Structures in theCytoplasm 341. Accumulations of Virus Particles 342. Aggregates of Virus-Encoded Proteins 353. Caulimovirus Inclusions 35

C. Why Inclusion Bodies? 37D. Cytological Structures 37

VII. The Host Range of Viruses 38A. Limitations in Host Range Studies 38B. Patterns of Host Range 39

v

C. The Determinants of Host Range 391. Initial Events 392. Expression and Replication 393. Cell-to-Cell Movement 404. Stimulation of Host-Cell Defences 40

VIII. Viruses in Other Kingdoms 40IX. Summary 40

Chapter 3. Agents That Resemble or AlterPlant Virus Diseases

I. Viroids 43A. Classification of Viroids 44B. Pathology of Viroids 44

1. Macroscopic Disease Symptoms 442. Cytopathic Effects 443. Location of Viroids in Plants 454. Movement in the Plant 455. Transmission 456. Epidemiology 45

C. Properties of Viroid RNAs 451. Sequence and Structure 452. Replication 473. Recombination Between Viroids 494. Interference Between Viroids 49

D. Molecular Basis for Biological Activity 50E. Diagnostic Procedures for Viroids 50

II. Phytoplasma 50III. Satellite Viruses and Satellite RNAs 51

A. Satellite Plant Viruses (A-type) 52B. Satellite RNAs (satRNAs) 53

1. Large Satellite RNAs (B-type) 532. Small Linear Satellite RNAs (C-type) 533. Small Circular Satellite RNAs (D-type) 544. Satellite-Like RNAs 55

a. A Satellite RNA of Groundnut Rosette

Virus (GRV) 55b. Ancillary RNAs of Beet Necrotic Yellow

Vein Virus (BNYVV) 565. The Molecular Basis for Symptom

Modulation 56C. Satellite DNAs 57D. Discussion 58

IV. Defective and Defective Interfering NucleicAcids 58

A. Group 1: Single Deletion D RNAs 60

B. Group 2: Multiple Deletion D and DI RNAs 60

C. Defective DNAs Associated with DNAViruses 60

V. Viruses of Other Kingdoms 60VI. Summary 61

Chapter 4. Plant Virus Origins andEvolution

I. Introduction 63II. Virus Evolution 64

A. Origins of Viruses 64B. Virus Variation 65C. Types of Evolution 65

1. Microevolution and Macroevolution 652. Sequence Divergence or

Convergence 673. Modular Evolution 674. Sources of Viral Genes 67

a. Replicases 67b. Proteinases 68c. Coat Proteins 70d. Cell-to-Cell Movement Proteins 71e. Suppressors of Gene Silencing 71

D. Selection Pressures for Evolution 711. Adaptation to Niches 712. Maximising the Variation 713. Controlling the Variation 72

a. Muller’s Ratchet 73b. Muller’s Ratchet and Plant

Viruses 734. Role of Selection Pressure 735. Selection Pressure by Host

Plants 74E. Timeline for Evolution 74

1. Nonconstant Rates of Evolution 742. Estimated Rates of Evolution 74

III. Evidence for Virus Evolution 75A. Geminiviruses 75B. Closteroviruses 75C. Luteoviruses 75

IV. Coevolution of Viruses with Their Hosts andVectors 80

V. Viruses of Other Kingdoms 80VI. Summary 80

Section IIWHAT IS A VIRUS MADE OF?

Chapter 5. Architecture and Assembly ofVirus Particles

I. Introduction 85II. Methods 86

vi CONTENTS

A. Chemical and Biochemical Studies 86B. Methods for Studying Size and Fine Structure

of Viruses 861. Hydrodynamic Measurements 862. Electron Microscopy 873. X-Ray Crystallography 874. Neutron Small-Angle Scattering 875. Atomic Force Microscopy 876. Mass Spectrometry 887. Serological Methods 888. Stabilising Bonds 88

III. Architecture of Rod-Shaped Viruses 88A. Introduction 88B. Structure of TMV 89

1. General Features 892. Virus Structure 90

C. Assembly of TMV 921. Properties of the Coat Protein 922. Assembly of TMV Coat Protein 923. Assembly of the TMV Rod 92

a. Assembly in vitro 92b. Assembly in vivo 94

IV. Architecture of Isometric Viruses 94A. Introduction 94B. Possible Icosahedra 94C. Clustering of Subunits 97D. Quasiequivalence 97

V. Small Icosahedral Viruses 97A. Subunit Structure 97B. Virion Structure 98

1. T ¼ 1 Particles 982. Other Particles Based on T ¼ 1

Symmetry 98a. Bacilliform Particles Based on T ¼ 1

Symmetry 98b. Geminiviruses 99

3. T ¼ 3 Particles 99a. Bacilliform Particles Based on T ¼ 3

Symmetry 100b. Pseudo T ¼ 3 Symmetry 100

4. T ¼ 7 Particles 100C. The Arrangement of Nucleic Acid Within

Icosahedral Viruses 1001. RNA Structure 1002. Interactions Between RNA and Protein in

Small Isometric Viruses 100D. Stabilisation of Small Isometric Particles 101

1. Protein-RNA Stabilisation 1012. Protein-Protein Stabilisation 1013. Protein-Protein þ Protein-RNA

Stabilisation 101

VI. More Complex Isometric Viruses 101VII. Enveloped Viruses 101VIII. Assembly of Icosahedral Viruses 102

A. Bromoviruses 102B. RNA Selection During Assembly of Plant

Reoviruses 102IX. General Considerations 103X. Viruses of Other Kingdoms 104XI. Summary 104

Chapter 6. Plant Viral Genomes

I. Introduction 105II. General Properties of Plant Viral

Genomes 105A. Information Content 106B. Economy in the Use of Genomic Nucleic

Acids 106C. The Functions of Viral Gene Products 107

1. Functional Proteins 107a. Proteins That Initiate Infection 107b. Proteins That Replicate the Viral

Genome 108c. Proteins That Process Viral Gene

Products 108d. Proteins That Facilitate Viral Movement

Through the Host 109e. Overcoming Host Defence Systems 109f. Proteins That Facilitate the Host to Host

Movement of Viruses 109D. Nucleic Acids 109

1. Multipartite Genomes 1092. Nucleic Acid Structures 1093. Noncoding Regions 109

a. End-Group Structures 109b. 50 and 30 Noncoding Regions 112c. Intergenic Regions 112

III. Plant Viral Genome Organisation 112A. Structure of the Genome 112B. Recognising Activities of Viral

Genes 1141. Location of Spontaneous or Artificially

Induced Mutations 1142. Recombinant Viruses 1153. Expression of the Gene in a Transgenic

Plant 1154. Hybrid Arrest and Hybrid Selection

Procedures 1155. Sequence Comparison with Genes of Known

Function 1166. Functional Regions Within a Gene 116

viiCONTENTS

IV. Viruses of Other Kingdoms 116V. Summary 116

Chapter 7. Expression of Viral Genomes

I. Stages in Virus Infection Cycle 117II. Virus Entry and Uncoating 119

A. Virus Entry 119B. Uncoating 119

1. Uncoating of TMV 1192. Uncoating of Brome Mosaic Virus and

Southern Bean Mosaic Virus 1193. Uncoating of Turnip Yellow Mosaic

Virus 1214. Uncoating Other Plant Viruses 122

III. Initial Translation of Viral Genome 122IV. Synthesis of mRNAs 123

A. Negative-Sense Single-Stranded RNAViruses 123

B. Double-Stranded RNA Viruses 123C. DNA Viruses 124

1. Caulimoviridae 1242. Geminiviridae 125

V. Plant Viral Genome Strategies 125A. The Eukaryotic Translation System

Constraints 125B. Virus Strategies to Overcome Eukaryotic

Translation Constraints 1261. Strategy 1. Polyproteins 1262. Strategy 2. Subgenomic RNAs 1293. Strategy 3. Multipartite Genomes 1314. Strategy 4. Splicing 1315. Strategy 5. Translation of Both Viral and

Complementary Strands (Ambisense) 1316. Strategy 6. Internal Initiation 1317. Strategy 7. Leaky Scanning 133

a. Two Initiation Sites on One ORF(Two Start) 133

b. Overlapping ORFs 133c. Two or More Consecutive ORFs 133

8. Strategy 8. Non-AUG Start Codon 1339. Strategy 9. Transactivation 13310. Strategy 10. Translational (Ribosome)

Shunt 13411. Strategy 11. Read-Through Proteins 13412. Strategy 12. Frameshift Proteins 135

C. Control of Translation 1361. Cap but No Poly(A) Tail 136

2. Poly(A) Tail but No Cap 1363. Neither Cap nor Poly(A) Tail 1364. Cap Snatching 1365. 50 UTR 137

D. Discussion 137VI. Viruses of Other Kingdoms 137VII. Summary 137

Chapter 8. Virus Replication

I. Host Functions Used by Plant Viruses 139II. Methods for Studying Viral Replication 140III. Replication of Plus-Sense Single-Stranded RNA

Viruses 140A. Viral Templates 140B. Replicase 143

1. RNA-Dependent RNA Polymerase 1432. Helicases 1433. Methyl Transferase Activity 1444. Organisation of Functional Domains in Viral

ORFs 144C. Sites of Replication 146D. Mechanism of Replication 147E. Discussion 147

IV. Replication of Negative-Sense Single-StrandedRNA Viruses 152

V. Replication of Double-Stranded RNAViruses 152

VI. Replication of Reverse TranscribingViruses 153A. Introduction 153B. Reverse Transcriptase 154C. Replication of “Caulimoviruses” 154

1. Replication Pathway 1542. Inclusion Bodies 155

VII. Replication of Single-Stranded DNAViruses 156A. Geminivirus Replication 156B. Geminivirus Rep Proteins 156

VIII. Faults in Replication 158A. Mutation 158B. Recombination 159

1. DNA Virus Recombination 1592. RNA Virus Recombination 1593. Recombination and Integrated Viral

Sequences 161IX. Viruses of Other Kingdoms 161X. Summary 163

viii CONTENTS

Section IIIHOW DO PLANT VIRUSES

WORK?

Chapter 9. Virus-Host Interactions — PlantLevel

I. Movement and Final Distribution 167A. Intracellular Movement 168B. Intercellular Movement 168

1. Plasmodesmata 1682. Movement Proteins (MPs) 1693. What Actually Moves 1754. Cell-to-Cell Movement of Viroids 1755. Complementation 1766. Rate of Cell-to-Cell Movement 176

C. Systemic Movement 1761. Steps in Systemic Movement 1762. Form in Which Virus Is Transported 1793. Rate of Systemic Movement 1794. Movement in the Xylem 180

D. Final Distribution in the Plant 180E. Outstanding Questions on Plant Virus

Movement 181II. Effects on Plant Metabolism 181

A. Nucleic Acids and Proteins 181B. Lipids 182C. Carbohydrates 182D. Photosynthesis 184E. Respiration 184F. Transpiration 184G. Low-Molecular-Weight Compounds 184

III. Processes Involved in Symptom Production 185A. Sequestration of Raw Materials 185B. Effects on Growth 186C. Effects on Chloroplasts 186D. Mosaic Symptoms 186E. Role of Membranes 187

IV. Other Kingdoms 188V. Summary 188

Chapter 10. Virus-Plant Interactions:1. Molecular Level

I. Introduction 191II. Host Responses to Inoculation 192

A. Immunity 192

B. Subliminal Infection 195C. Nonpermissive Infection 195

1. Local Infection 195a. Host Protein Changes in the Hypersensi-

tive Response 197b. Local Acquired Resistance 198

2. Systemic Infection 1983. Systemic Acquired Resistance 1984. Programmed Cell Death 200

D. Permissive Infection 2001. Systemic Host Response 2002. Virus Genes Involved 200

III. Interactions Between Viruses 202A. Interactions Between Related Viruses 202B. Interactions Between Unrelated Viruses 203

1. Complete Dependence for Disease 2032. Incomplete Dependence for Disease 2033. Synergistic Effects on Virus

Replication 2034. Effects on Virus Movement 203

C. Interactions Between Viruses and Other PlantPathogens 203

IV. Viruses of Other Kingdoms 204V. Summary 204

Chapter 11. Virus-Plant Interactions:2. RNA Silencing

I. Introduction 207II. Mechanism of Silencing 208

A. The Basic Pathway 208B. Components of the System 208

1. dsRNA 2082. Dicer 2093. Products of Dicer 2094. RISC 211

C. Results of the System 211III. Systemic Silencing 211IV. Overcoming Silencing 211

A. Suppression of Silencing 2111. Protein Suppressors of Silencing 2112. Nucleic Acid Suppressors of

Silencing 214B. Avoidance of Silencing 214

V. Silencing and Symptoms 214A. Recovery 215B. Dark Green Islands and Mosaics 216C. miRNA 216D. siRNA Effects 216

ixCONTENTS

E. Synergistic Effects 216F. Other Activities of Silencing

Suppressors 217VI. Transcriptional and Translational Repression 218VII. Evolutionary Aspects 218VIII. RNA Silencing in Animal and Other

Viruses 218IX. Summary 218

Section IVPLANT VIRUSES IN

AGRICULTURE AND INDUSTRY

Chapter 12. Plant-to-Plant Movement

I. Introduction 223II. Transmission via Plant Material 223

A. Mechanical Transmission 223B. Seed Transmission 224C. Pollen Transmission 225D. Vegetative Transmission 225E. Grafting 225

III. Transmission by Invertebrates 225A. Relationships Between Plant Viruses and

Insects 228B. Nonpersistent Transmission by Insects 231

1. Features of NonpersistentTransmission 231

2. Virus-Vector Relationships 231a. Direct Capsid Interaction 232b. Indirect Interaction Involving Helper

Components 232C. Persistent Transmission by Insects 235

1. Circulative Viruses 235a. Features of Circulative Virus: Vector

Interaction 235b. Dependent Transmission 237

2. Propagative Viruses 2373. Thrip Transmission of Tospoviruses 238

D. Virus Transmission by Beetles 238E. Nematode Transmission of Viruses 239

1. Features of Nematode Transmission 2392. Virus-Nematode Relationships 239

IV. Fungal Transmission of Viruses 240V. Viruses of Other Kingdoms 242VI. Summary 242

Chapter 13. Plant Viruses in the Field: Diagnosis,Epidemiology, and Ecology

I. Diagnosis 245A. Introduction 245B. Methods Involving Biology of the Virus 246

1. Indicator Hosts 2462. Host Range 2463. Methods of Transmission 2474. Cytological Effects 2475. Mixed Infections 247

C. Methods That Depend on Physical Propertiesof the Virus Particle 2471. Stability and Physicochemical

Properties 2472. Electron Microscopy 247

D. Methods That Depend on Properties of ViralProteins 2491. Serology 2492. Types of Antisera 2493. Methods for Detecting Antibody-Virus

Combination 249a. ELISA Procedures 249b. Serologically Specific Electron

Microscopy 255c. Electrophoretic Procedures 256d. Dot Blots 256

E. Methods That Involve Properties of the ViralNucleic Acid 2561. Type and Size of Nucleic Acid 2562. Cleavage Patterns of DNA 2573. Hybridization Procedures 2574. Dot Blots 2575. Polymerase Chain Reaction 2576. DNA Microarray 259

F. Decision Making on Diagnosis 260II. Epidemiology and Ecology 260

A. Epidemiology of Viruses in Agriculture 2611. Primary Infections 2612. Secondary Spread 264

B. Plant Viruses in the Natural Environment 267C. Emergence of New Viruses 267

III. Viruses of Other Kingdoms 268IV. Summary 268

Chapter 14. Conventional Control

I. Introduction 269II. Avoiding Infection 271

x CONTENTS

A. Removal of Sources of Infection 271B. Virus-Free Seed 271C. Virus-Free Vegetative Stocks 271D. Modified Agronomic Practices 272E. Quarantine Regulations 273

III. Stopping the Vector 274A. Air-Borne Vectors 274

1. Insecticides 2752. Insect Deterrents 2753. Agronomic Techniques 275

B. Soil-Borne Vectors 2771. Nematodes 2772. Fungi 277

IV. Protecting the Plant 277A. Protection by a Plant Pathogen 277B. Antiviral Chemicals 278

V. Conventional Resistance to Plant Viruses 280A. Introduction 280B. Genetics of Resistance to Viruses 281C. Tolerance 281D. Use of Conventional Resistance for

Control 2821. Immunity 2822. Field Resistance 2823. Tolerance 282

VI. Strategies for Control 283VII. Viruses of Other Kingdoms 283VIII. Summary 283

Chapter 15. Transgenic Plants and Viruses

I. Transgenic Protection Against Plant Viruses 285A. Introduction 285B. Natural Resistance Genes 285

II. Pathogen-Derived Resistance 286A. Protein-Based Protection 286

1. Transgenic Plants Expressing a Viral CoatProtein 286

2. Other Viral Proteins 286B. Nucleic Acid–Based Protection 287

1. RNA-Mediated Protection 288

2. Molecular Basis of RNA-MediatedProtection 288

3. Sequences for RNA-MediatedProtection 289

4. Ribozymes 2895. Relationship Between Natural

Cross-Protection and Protection inTransgenic Plants 289

6. Transgenic Protection by Satellite and DINucleic Acids 290

C. Other Forms of Transgenic Protection 290D. Field Releases of Transgenic Plants 290

1. Potential Risks 2902. Field Performance 293

III. Possible Uses of Plant Viruses for GeneTechnology 293A. DNA Viruses as Gene Vectors 293

1. Caulimoviruses 2942. Geminiviruses 294

B. RNA Viruses as Gene Vectors 294C. Viruses as Sources of Control Elements for

Transgenic Plants 2951. DNA Promoters 2952. RNA Promoters 2953. Translation Enhancers 295

D. Viruses for Producing Vaccines 2951. Vaccines Using Plant Virus Vectors 2962. Viruses for Presenting Heterologous

Peptides 296a. Cowpea Mosaic Virus (CPMV) 296b. Tobacco Mosaic Virus (TMV) 298

E. Viruses in Functional Genomics ofPlants 298

F. Plant Viruses in Nanotechnology 298IV. Viruses of Other Kingdoms 300V. Summary 301

Appendix: Profiles 303Index 363

xiCONTENTS

Preface

This book has been developed from and isa revision to Fundamentals of Plant Virology writ-ten by R. E. F. Matthews in 1992. Since thenmajor advances have been made in the under-standing of the molecular biology of viruses,how they function and how they interact withtheir hosts. This has revealed similarities anddifferences between viruses infecting membersof the different kingdoms of living organisms,plants, animals, fungi, and bacteria. In thischanging environment of teaching virology,this book does not just deal with plant virusesalone but places them in context in relation toviruses of members of other kingdoms.

This book has been written for students ofplant virology, plant pathology, virology, andmicrobiology who have no previous know-ledge of plant viruses or of virology in general.An elementary knowledge of molecular biologyis assumed, especially of the basic structures ofDNAs, RNAs, and proteins, of the genetic code,and of the processes involved in protein syn-thesis. As some of these students may not havea grounding in the structure and function inplants including the main subcellular struc-tures found in typical plant cells, these features

which are important to the understanding ofhow viruses interact with plants are illustrated.In each chapter there is a list of further readingto enable the student to explore specific topicsin depth.

The fifteen chapters in this book can bedivided into four major sections that form alogical progression in gaining an understand-ing of the subject. The first four chapters intro-duce plant viruses describing: what is a virus,giving an overview of plant viruses, discussingother agents that cause diseases that resembleplant virus diseases, and considering factorsthat are involved in virus evolution. The pointsraised in this latter chapter are equally relevantto viruses of other kingdoms. The next fourchapters deal with what viruses are made of.The chapter on virus architecture and assemblyis also very relevant to viruses of other king-doms as are the major points raised in chapterson plant virus genome organization, genomeexpression, and genome replication. The nextsection on how do plant viruses work is morespecific to plant viruses and highlights differ-ences and similarities between virus interac-tions with plant, animal, and bacterial hosts.

xiii

These interactions are described at the plantlevel (movement of the virus within the plantand effects on plant metabolism) and at themolecular level including a chapter devoted tothe newly understood host defence system ofRNA silencing. The last four chapters deal withplant viruses and agriculture and industry. Thedescription of how plant viruses move be-tween hosts which often involves specificmolecular interactions leads into discussion ofthe epidemiology of viruses in the field andhow they are controlled. The last chapter is onthe use of recombinant DNA technology incontrolling viruses and also in using them com-mercially in, for instance, the pharmaceuticaland nanotechnology industries.

A unique feature of this book is a series of“profiles” on 32 plant viruses that feature in thetext. These profiles describe briefly the major

properties of the viruses including their taxo-nomic position, their biology, their particles,and their genomes. References are given toenable students to acquire even more informa-tion on these targeted viruses.

I am very grateful to a large number of col-leagues for their helpful discussion on varioustopics and in providingmaterial prior to publica-tion. I am especially indebted to John Carr, AndyJackson, Mark Stevens, and Peter Waterhouse fortheir helpful comments on various sections of thebook and on providing illustrative material. Myeternal gratitude goes to my wife who hastolerated “piles of paper” around the house andwho has given me continuous encouragement.

Roger HullNorwich, UK

July, 2008

xiv PREFACE

List of Abbreviations

3’OH 3’ hydroxyl groupA Angstrom (10�10 meter)AAB Association of Applied BiologistsDPV Descriptions of Plant VirusesADP Adenosine diphosphateAR Aberrante ratioATP Adenosine triphosphatecDNA Complentary (or copy) DNACI Cylindrical inclusionDdDp DNA-dependent DNA

polymeraseD RNA/DNA

Defective RNA or DNA

DI RNA/DNA

Defective interfering RNA orDNA

dsDNA Double-stranded DNAdsRNA Double-stranded RNAEDTA Ethylene diamino tetra-acetic acidELISA Enzyme-linked inmuno-sorbent

assayEM Electron MicroscopeER Endoplasmic reticulumGTP Guanosine triphosphateGM Genetically modifiedHC-Pro Helper component proteaseHEL Helicase

HR Hypersensitive responseHSP Heat-shock proteinICR Inter-cistronic regionICTV International Committee on the

Taxonomy of VirusesIRES Internal ribosome entry siteISEM Immunoabsorbent electron

microscopykb KilobasekDa KilodaltonLRR Leucine-rich repeatMab Monoclonal antibodyMP Movement proteinmRNA Messenger RNAMiRNA MicroRNAMTR Methyl transferaseMW Molecular weightNBS Nucleotide binding siteNI Nuclear inclusionnm NanometerORF Open reading framePCD Programmed cell deathPCR Polymerase chain reaction (IC-

PCR, immune-capture PCR; RT-PCR, reverse transcription PCR)

PDR Pathogen-derived resistance

xv

Pol PolymerasePR(protein)

Pathogenesis-related (protein)

PRO ProteasePTGS Post-transcriptional gene

silencingRb(protein)

Retinoblastoma (protein)

RdRp RNA-directed RNA PolymeraseRF Replicative formRFLP Restriction fragment length

polymorphismRI Replicative intermediateRISC RNA-induced silencing complexRNAi RNA interferingRT Reverse transcriptaseSA Salicylic acidSAR Systemic acquired resistance

SDS-PAGE

Sodium dodecyl sulphatepolyacrylamide gelelectrophoresis

SEL Size exclusion limitSg RNA Subgenomic RNASi RNA Small interfering RNAssDNA Single-stranded DNASSEM Serologically-specific electron

microscopyssRNA Single-stranded RNATAV TransactivatorTGB Triple gene blockTGS Transcriptional gene silencingtRNA Transfer RNAUTR Untranslated regionVIGS Virus-induced gene silencingVPg Virus protein genome-linked

xvi LIST OF ABBREVIATIONS