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COMPARATIVE PLANT VIROLOGY SECOND EDITION ELSEVIER science & technology books Companion Web Site: http://www.elsevierdirect.com/companions/9780123741547 Comparative Plant Virology, Second Edition, by Roger Hull Revision to Fundamentals of Plant Virology written by R. Matthews Resources for Professors: (cid:129) Image bank (cid:129) Virus profiles TOOLS ALL YOUR TEACHING NEEDS FOR textbooks.elsevier.com ACADEMIC PRESS To adopt this book for course use, visit http://textbooks.elsevier.com COMPARATIVE PLANT VIROLOGY SECOND EDITION R H OGER ULL EmeritusFellow DepartmentofDiseaseandStressBiology JohnInnesCentre Norwich, UK AMSTERDAM (cid:129) BOSTON (cid:129) HEIDELBERG (cid:129) LONDON NEW YORK (cid:129) OXFORD (cid:129) PARIS (cid:129) SAN DIEGO SAN FRANCISCO (cid:129) SINGAPORE (cid:129) SYDNEY (cid:129) TOKYO Academic Press is an imprint of Elsevier CoverCredits: BSMV leaf—Mildstripemosaic;SymptomofBSMVinbarley.Imagecourtesy of A.O.Jackson. BSMV genome:Theinfectious genome(BSMV) isdividedbetween3species ofpositive sensessRNAthataredesignateda,b,andg.Image courtesyofRogerHull. BSMV particles.ImagecourtesyofRogerHull. Diagramshowingsystemicspreadofsilencingsignal:Thesignalisgeneratedintheinitially infectedcell(bottom,lefthand)andspreadstoabout10–15adjacentcellswhereitisamplified. Itmovesoutoftheinitiallyinfectedleafviathephloemsievetubesandthenspreads throughoutsystemicleavesbeingamplifiedatvarioustimes.ImagecourtesyofRogerHull. Elsevier AcademicPress 30CorporateDrive,Suite400,Burlington,MA01803,USA 525BStreet,Suite1900,SanDiego, California92101-4495,USA 84Theobald’sRoad,London WC1X8RR,UK This bookisprintedonacid-freepaper. Copyright#2009,ElsevierInc.Allrightsreserved. Nopartofthispublication maybe reproducedor transmitted inanyformor byany means,electronicormechanical,includingphotocopy,recording,or anyinformation storageandretrievalsystem,without permissioninwritingfromthe publisher. Permissionsmaybesoughtdirectly fromElsevier’sScience&TechnologyRights Department inOxford,UK:phone: (þ44)1865843830,fax:(þ44)1865853333,E-mail: [email protected]. Youmayalsocompleteyourrequest on-linevia theElsevier homepage(http://elsevier.com), byselecting“CustomerSupport” andthen“Obtaining Permissions.” Library ofCongress Cataloging-in-Publication Data Hull, Roger,1937- Comparativeplant virology/RogerHull.– 2nded. p.cm. ISBN 978-0-12-374154-7(hardcover:alk.paper) 1. Plantviruses. I.Title. QR351.H852009 579.208–dc22 2008040333 British Library CataloguinginPublicationData Acatalogue recordfor thisbookisavailablefrom theBritishLibrary ISBN 13:978-0-12-374154-7 ForallinformationonallElsevierAcademic Presspublications visitourWebsiteat www.elsevierdirect.com Printed inChina 09 10 9 8 7 6 5 4 3 2 1 Contents Preface xiii 1. EffectsonPlantSize 26 2. MosaicPatternsandRelatedSymptoms 26 List of Abbreviations xv 3. YellowDiseases 28 4. LeafRolling 28 Section I 5. RingSpotDiseases 28 6. NecroticDiseases 28 INTRODUCTION TO PLANT 7. DevelopmentalAbnormalities 28 8. Wilting 29 VIRUSES 9. RecoveryfromDisease 29 10. GeneticEffects 29 C. TheCryptoviruses 29 Chapter 1. What Is a Virus? D. DiseasesCausedbyViral Complexes 29 E. AgentsInducingVirus-Like Symptoms 30 I. Introduction 3 V. Histological Changes 30 II. History 3 A. Necrosis 30 III. DefinitionofaVirus 9 B. Hypoplasia 30 A. HowVirusesDifferfromOther Plant C. Hyperplasia 32 Pathogens 9 1. CellSize 32 B. AreViruses Alive? 13 2. CellDivision inDifferentiatedCells 32 IV. ClassificationandNomenclature ofViruses 13 3. AbnormalDivision inCambialCells 32 A. VirusClassification 13 VI. Cytological Effects 32 B. Families,Genera,andSpecies 14 A. Effects onCellStructures 32 C. NamingViruses (Species) 15 1. Nuclei 32 D. AcronymsorAbbreviations 16 2. Mitochondria 33 E. PlantVirusClassification 17 3. Chloroplasts 33 F. VirusStrains 17 4. CellWalls 33 G. UseofVirusNames 19 5. CellDeath 34 V. VirusesofOtherKingdoms 20 B. Virus-Induced Structures in the VI. Summary 21 Cytoplasm 34 1. AccumulationsofVirusParticles 34 Chapter 2. Overview of Plant Viruses 2. AggregatesofVirus-EncodedProteins 35 3. CaulimovirusInclusions 35 I. Introduction 23 C. WhyInclusionBodies? 37 II. EconomicLosses DuetoPlantViruses 24 D. CytologicalStructures 37 III. VirusProfiles 24 VII. TheHostRange ofViruses 38 IV. MacroscopicSymptoms 25 A. LimitationsinHostRangeStudies 38 A. LocalSymptoms 25 B. PatternsofHostRange 39 B. SystemicSymptoms 26 v vi CONTENTS C. TheDeterminantsofHostRange 39 Chapter 4. Plant Virus Origins and 1. InitialEvents 39 Evolution 2. ExpressionandReplication 39 3. Cell-to-CellMovement 40 I. Introduction 63 4. StimulationofHost-Cell Defences 40 II. VirusEvolution 64 VIII. Viruses inOtherKingdoms 40 A. Origins ofViruses 64 IX. Summary 40 B. VirusVariation 65 C. TypesofEvolution 65 Chapter 3. Agents That Resemble or Alter 1. Microevolutionand Macroevolution 65 Plant Virus Diseases 2. SequenceDivergence or Convergence 67 I. Viroids 43 3. Modular Evolution 67 A. ClassificationofViroids 44 4. SourcesofViralGenes 67 B. Pathology ofViroids 44 a. Replicases 67 1. MacroscopicDiseaseSymptoms 44 b. Proteinases 68 2. CytopathicEffects 44 c. Coat Proteins 70 3. LocationofViroidsinPlants 45 d. Cell-to-Cell MovementProteins 71 4. MovementinthePlant 45 e. SuppressorsofGeneSilencing 71 5. Transmission 45 D. SelectionPressuresforEvolution 71 6. Epidemiology 45 1. AdaptationtoNiches 71 C. Properties ofViroidRNAs 45 2. MaximisingtheVariation 71 1. SequenceandStructure 45 3. ControllingtheVariation 72 2. Replication 47 a. Muller’sRatchet 73 3. RecombinationBetweenViroids 49 b. Muller’sRatchet and Plant 4. InterferenceBetweenViroids 49 Viruses 73 D. MolecularBasisforBiologicalActivity 50 4. RoleofSelectionPressure 73 E. DiagnosticProceduresforViroids 50 5. SelectionPressurebyHost II. Phytoplasma 50 Plants 74 III. Satellite Virusesand Satellite RNAs 51 E. Timeline forEvolution 74 A. Satellite PlantViruses (A-type) 52 1. Nonconstant RatesofEvolution 74 B. Satellite RNAs (satRNAs) 53 2. EstimatedRates ofEvolution 74 1. LargeSatellite RNAs(B-type) 53 III. EvidenceforVirusEvolution 75 2. SmallLinearSatellite RNAs(C-type) 53 A. Geminiviruses 75 3. SmallCircularSatelliteRNAs(D-type) 54 B. Closteroviruses 75 4. Satellite-LikeRNAs 55 C. Luteoviruses 75 a. ASatellite RNAofGroundnutRosette IV. CoevolutionofViruses withTheirHostsand Virus(GRV) 55 Vectors 80 b. Ancillary RNAsofBeetNecrotic Yellow V. VirusesofOtherKingdoms 80 VeinVirus(BNYVV) 56 VI. Summary 80 5. TheMolecular BasisforSymptom Modulation 56 C. Satellite DNAs 57 Section II D. Discussion 58 IV. Defective and DefectiveInterferingNucleic WHAT IS A VIRUS MADE OF? Acids 58 A. Group1:SingleDeletion DRNAs 60 B. Group2:MultipleDeletionDandDIRNAs 60 Chapter 5. Architecture and Assembly of C. DefectiveDNAsAssociatedwithDNA Virus Particles Viruses 60 V. Viruses ofOther Kingdoms 60 I. Introduction 85 VI. Summary 61 II. Methods 86 vii CONTENTS A. Chemicaland BiochemicalStudies 86 VI. MoreComplexIsometricViruses 101 B. MethodsforStudyingSizeand FineStructure VII. EnvelopedViruses 101 ofViruses 86 VIII. AssemblyofIcosahedralViruses 102 1. HydrodynamicMeasurements 86 A. Bromoviruses 102 2. ElectronMicroscopy 87 B. RNASelectionDuringAssemblyofPlant 3. X-RayCrystallography 87 Reoviruses 102 4. NeutronSmall-Angle Scattering 87 IX. General Considerations 103 5. AtomicForceMicroscopy 87 X. Viruses ofOther Kingdoms 104 6. Mass Spectrometry 88 XI. Summary 104 7. SerologicalMethods 88 8. StabilisingBonds 88 Chapter 6. Plant Viral Genomes III. ArchitectureofRod-ShapedViruses 88 A. Introduction 88 I. Introduction 105 B. StructureofTMV 89 II. General Properties ofPlantViral 1. General Features 89 Genomes 105 2. VirusStructure 90 A. InformationContent 106 C. AssemblyofTMV 92 B. Economy inthe UseofGenomicNucleic 1. Properties oftheCoat Protein 92 Acids 106 2. AssemblyofTMVCoatProtein 92 C. TheFunctionsofViralGeneProducts 107 3. AssemblyoftheTMVRod 92 1. FunctionalProteins 107 a. Assemblyinvitro 92 a. ProteinsThatInitiate Infection 107 b. Assemblyinvivo 94 b. ProteinsThat ReplicatetheViral IV. ArchitectureofIsometricViruses 94 Genome 108 A. Introduction 94 c. ProteinsThatProcess ViralGene B. PossibleIcosahedra 94 Products 108 C. ClusteringofSubunits 97 d. ProteinsThat FacilitateViralMovement D. Quasiequivalence 97 ThroughtheHost 109 V. SmallIcosahedralViruses 97 e. OvercomingHostDefenceSystems 109 A. SubunitStructure 97 f. Proteins ThatFacilitatetheHost toHost B. VirionStructure 98 Movement ofViruses 109 1. T¼1Particles 98 D. NucleicAcids 109 2. OtherParticlesBasedonT¼1 1. MultipartiteGenomes 109 Symmetry 98 2. NucleicAcidStructures 109 a. Bacilliform ParticlesBasedonT ¼1 3. NoncodingRegions 109 Symmetry 98 a. End-GroupStructures 109 b. Geminiviruses 99 b. 50 and30 NoncodingRegions 112 3. T¼3Particles 99 c. IntergenicRegions 112 a. Bacilliform ParticlesBasedonT ¼3 III. PlantViralGenome Organisation 112 Symmetry 100 A. StructureoftheGenome 112 b. Pseudo T¼3 Symmetry 100 B. Recognising ActivitiesofViral 4. T¼7Particles 100 Genes 114 C. TheArrangementofNucleicAcidWithin 1. LocationofSpontaneousorArtificially Icosahedral Viruses 100 InducedMutations 114 1. RNAStructure 100 2. RecombinantViruses 115 2. InteractionsBetween RNAand Proteinin 3. ExpressionoftheGeneinaTransgenic SmallIsometricViruses 100 Plant 115 D. Stabilisation ofSmallIsometricParticles 101 4. HybridArrest andHybridSelection 1. Protein-RNAStabilisation 101 Procedures 115 2. Protein-Protein Stabilisation 101 5. SequenceComparisonwithGenesofKnown 3. Protein-Protein þProtein-RNA Function 116 Stabilisation 101 6. FunctionalRegionsWithinaGene 116 viii CONTENTS IV. Viruses ofOther Kingdoms 116 2. Poly(A)Tail butNoCap 136 V. Summary 116 3. Neither Capnor Poly(A)Tail 136 4. CapSnatching 136 Chapter 7. Expression of Viral Genomes 5. 50 UTR 137 D. Discussion 137 I. Stages inVirusInfectionCycle 117 VI. VirusesofOtherKingdoms 137 II. VirusEntryand Uncoating 119 VII. Summary 137 A. VirusEntry 119 B. Uncoating 119 Chapter 8. Virus Replication 1. UncoatingofTMV 119 2. UncoatingofBrome MosaicVirusand I. HostFunctionsUsedbyPlantViruses 139 SouthernBeanMosaicVirus 119 II. MethodsforStudyingViralReplication 140 3. UncoatingofTurnipYellowMosaic III. ReplicationofPlus-Sense Single-StrandedRNA Virus 121 Viruses 140 4. UncoatingOtherPlantViruses 122 A. Viral Templates 140 III. InitialTranslationofViral Genome 122 B. Replicase 143 IV. Synthesis ofmRNAs 123 1. RNA-DependentRNAPolymerase 143 A. Negative-Sense Single-Stranded RNA 2. Helicases 143 Viruses 123 3. MethylTransferase Activity 144 B. Double-StrandedRNAViruses 123 4. OrganisationofFunctionalDomainsinViral C. DNAViruses 124 ORFs 144 1. Caulimoviridae 124 C. Sites ofReplication 146 2. Geminiviridae 125 D. MechanismofReplication 147 V. PlantViralGenome Strategies 125 E. Discussion 147 A. TheEukaryoticTranslationSystem IV. ReplicationofNegative-Sense Single-Stranded Constraints 125 RNAViruses 152 B. VirusStrategiestoOvercome Eukaryotic V. ReplicationofDouble-StrandedRNA TranslationConstraints 126 Viruses 152 1. Strategy1.Polyproteins 126 VI. ReplicationofReverse Transcribing 2. Strategy2.Subgenomic RNAs 129 Viruses 153 3. Strategy3.Multipartite Genomes 131 A. Introduction 153 4. Strategy4.Splicing 131 B. Reverse Transcriptase 154 5. Strategy5.TranslationofBothViraland C. Replication of“Caulimoviruses” 154 ComplementaryStrands(Ambisense) 131 1. Replication Pathway 154 6. Strategy6.InternalInitiation 131 2. InclusionBodies 155 7. Strategy7.LeakyScanning 133 VII. ReplicationofSingle-Stranded DNA a. TwoInitiationSitesonOneORF Viruses 156 (TwoStart) 133 A. Geminivirus Replication 156 b. OverlappingORFs 133 B. GeminivirusRepProteins 156 c. TwoorMoreConsecutiveORFs 133 VIII. FaultsinReplication 158 8. Strategy8.Non-AUGStartCodon 133 A. Mutation 158 9. Strategy9.Transactivation 133 B. Recombination 159 10. Strategy10.Translational (Ribosome) 1. DNAVirusRecombination 159 Shunt 134 2. RNAVirusRecombination 159 11. Strategy11.Read-Through Proteins 134 3. Recombinationand IntegratedViral 12. Strategy12.FrameshiftProteins 135 Sequences 161 C. ControlofTranslation 136 IX. VirusesofOtherKingdoms 161 1. CapbutNoPoly(A) Tail 136 X. Summary 163 ix CONTENTS Section III B. Subliminal Infection 195 C. NonpermissiveInfection 195 HOW DO PLANT VIRUSES 1. LocalInfection 195 a. HostProteinChanges intheHypersensi- WORK? tiveResponse 197 b. LocalAcquiredResistance 198 Chapter 9. Virus-Host Interactions — Plant 2. SystemicInfection 198 Level 3. SystemicAcquiredResistance 198 4. ProgrammedCellDeath 200 I. Movementand FinalDistribution 167 D. PermissiveInfection 200 A. IntracellularMovement 168 1. SystemicHostResponse 200 B. IntercellularMovement 168 2. VirusGenes Involved 200 1. Plasmodesmata 168 III. Interactions BetweenViruses 202 2. Movement Proteins(MPs) 169 A. InteractionsBetweenRelated Viruses 202 3. WhatActuallyMoves 175 B. Interactions BetweenUnrelated Viruses 203 4. Cell-to-CellMovement ofViroids 175 1. CompleteDependence forDisease 203 5. Complementation 176 2. IncompleteDependence forDisease 203 6. RateofCell-to-CellMovement 176 3. SynergisticEffectsonVirus C. Systemic Movement 176 Replication 203 1. StepsinSystemicMovement 176 4. EffectsonVirusMovement 203 2. ForminWhichVirusIsTransported 179 C. InteractionsBetween VirusesandOther Plant 3. RateofSystemicMovement 179 Pathogens 203 4. Movement intheXylem 180 IV. Viruses ofOther Kingdoms 204 D. Final DistributioninthePlant 180 V. Summary 204 E. OutstandingQuestionsonPlantVirus Movement 181 Chapter 11. Virus-Plant Interactions: II. EffectsonPlantMetabolism 181 2. RNA Silencing A. Nucleic Acidsand Proteins 181 B. Lipids 182 I. Introduction 207 C. Carbohydrates 182 II. MechanismofSilencing 208 D. Photosynthesis 184 A. TheBasicPathway 208 E. Respiration 184 B. Components oftheSystem 208 F. Transpiration 184 1. dsRNA 208 G. Low-Molecular-Weight Compounds 184 2. Dicer 209 III. ProcessesInvolvedinSymptom Production 185 3. ProductsofDicer 209 A. Sequestration ofRawMaterials 185 4. RISC 211 B. EffectsonGrowth 186 C. ResultsoftheSystem 211 C. Effects onChloroplasts 186 III. Systemic Silencing 211 D. MosaicSymptoms 186 IV. Overcoming Silencing 211 E. RoleofMembranes 187 A. SuppressionofSilencing 211 IV. OtherKingdoms 188 1. ProteinSuppressorsofSilencing 211 V. Summary 188 2. NucleicAcidSuppressorsof Silencing 214 Chapter 10. Virus-Plant Interactions: B. Avoidance ofSilencing 214 1. Molecular Level V. Silencingand Symptoms 214 A. Recovery 215 I. Introduction 191 B. Dark GreenIslandsand Mosaics 216 II. HostResponsestoInoculation 192 C. miRNA 216 A. Immunity 192 D. siRNAEffects 216