Molecular Biology of Plant Viruses PDF
Preview Molecular Biology of Plant Viruses
MOLECULAR BIOLOGY OF PLANT VIRUSES MOLECULAR BIOLOGY OF PLANT VIRUSES edited by c. L. Mandahar Botany Department Panjab University, India ...... " SPRINGER SCIENCE+BUSINESS MEDIA, LLC Library of Congress Cataloging-in-Publication Data Molecular biology of plant viruses I edited by C.L. Mandahar. p. cm. Includes bibliographical references and index. ISBN 978-1-4613-7302-5 ISBN 978-1-4615-5063-1 (eBook) DOI 10.1007/978-1-4615-5063-1 1. Plant molecular virology. I. Mandahar, C.L. QR351.M63 1999 572.8'2928--DC21 99-28569 CIP Copyright © 1999 by Springer Science+Business Media New York Originally published by Kluwer Academic Publishers in 1999 Softcover reprint of the hardcover 1s t edition 1999 All rights reserved. No part of this publication rnay be reproduced, stored in a retrieval system or transmitted in any form or by any means, mechanical, photo copying, recording, or otherwise, without the prior written permission of the publisher, Springer Science+Business Media, LLC. Printed on acid-free paper. CONTENTS List of Figures xiii List of Tables xv List of Contributors xvii Preface xxi Acknowledgements xxxi 1. Genome of RNA Viruses 1-28 Franc;ois Hericourt, Isabelle Jupin, and Anne-Liss Haenni. Introduction Specific Gene Classes 1 Polymerase-Associated Functions 1 Coat Protein 9 CeU-to-Cell Movement 10 Systemic Movement 11 Proteinases 11 Vector Transmission 11 Symptoms 12 Non-Coding Functions of Viral RNAs 12 Cis-Acting Elements Required for Translation 12 Cis-Acting Elements Required for Replication 14 Interactions with Coat Protein 17 Conclusions 18 References 18 2. Genome of DNA Viruses 29-46 Thomas Frischmuth Introduction 29 Genome Organization 30 Family Geminiviridae 30 Genus Nanovirus 31 Family Caulimoviridae 32 Genus Caulimovirus 32 Genus Badnavirus 33 Gene Functions 34 Family Geminiviridae 34 Genus Nanovirus 36 Family Caulimoviridae 36 vi Genus Caulimovirus 36 Genus Badnavirus 37 Gene Expression 38 Family Geminiviridae and Genus Nanovirus 38 Family Caulimoviridae 39 References 41 3. Genome Organization in RNA Viruses 47-98 Sergey Morozov and Andrey Solovyev Introduction 47 Genome Maps of Positive-Stranded RNA Viruses 48 Picorna-like Supergroup 48 Family Potyviridae 49 Family Sequiviridae 51 Family Comoviridae 52 Sobemo-like Supergroup 53 Genus Sobemovirus 53 Genus Polerovirus 55 Genus Enamovirus 55 Carno-like Supergroup 56 Genus Umbravirus 57 Beet Western Yellows Virus ST9-associated RNA 58 Genus Luteovirus 58 Family Tombusviridae 58 Alpha-like Supergroup 61 Family Closteroviridae 62 Family Bromoviridae 63 Family "Tubiviridae" 66 Order "Tymovirales" 73 Genome Maps of Plant Negative-Stranded RNA Viruses 77 Family Rhabdoviridae 78 Family Bunyaviridae 78 Genus Tenuivirus 79 Genome Maps of Plant Double-Stranded RNA Viruses 80 Family Reoviridae 80 Family Partitiviridae 81 Conclusions 81 Acknowledgements 82 References 82 4. Gene Expression in Positive Strand RNA Viruses: 99-119 Conventional and Aberrant Strategies Alexy Agranovsky and Sergey Morozov vii Introduction 99 Viral Genomic RNA as a Single Translation Unit 100 Initiation Codon Choice and Translation in Plants 100 Conventional Scanning and Initiation 100 Non-AUG Initiation Codons in Plant Virus RNAs 101 Role of5'-and 3'-Noncoding Regions in Initiation of Translation 101 Access to Internal Genes 103 Divided versus Monopartite Genomes 104 Transcriptional Control: Subgenomic RNAs 104 Non-Orthodox Mechanisms of Initiation 107 Leaky Scanning 107 Internal Ribosome Entry Sites (IRES Elements) 107 Non-Orthodox Mechanisms of Elongation and Termination 108 Readthrough of Leaky Stop Codons 108 Ribosomal Frameshifiting 109 Proteolytic Processing 110 Chymotrypsin-like Serine or Cysteine Proteinases 112 Papain-like Cysteine Proteinases 112 Conclusions 113 References 114 5. Molecular Basis of Genetic Variability in RNA Viruses 121-141 Jozef J. Bujarski Introduction 121 Genetic Mechanisms of Variability 121 Mutation 121 Point Mutations 122 Insertions and Deletions 123 Frameshift Mutations 123 Mutant Stability 124 Effects of Mutations on Host-Virus Interactions 124 RNA Recombination 125 Natural Sequence Rearrangement 126 Recombination between Viral and Host RNAs 126 Role of RNA Structure 127 Role of Replicase Proteins 130 Pseudorecombination 131 Defective Interfering RNAs 132 Conclusions 134 Acknowledgements 136 References 136 viii 6. Genetic Variability and Evolution 143-159 F. Garcia-Arenal, A. Fraile, and J. M. Malpica Introduction 143 Variability under Experimental Conditions 143 Variability under Natural Conditions 145 Factors Determining Genetic Structure of Virus Populations 149 Founder Effects 149 Selection 150 Complementation 152 Conclusions 153 Acknowledgements 155 References 155 7. Molecular Basis of Virus Transport in Plants 161-182 Scott M. Leisner Introduction 161 Pathways of Virus Movement 161 Identification of Viral Movement Protein Genes 163 Characteristics of Plant Viral Movement Proteins 164 Tubules 169 Models of Cell-to-Cell Movement 169 Movement Protein-Host Interactions 174 Viral Genes Influencing Vascular Movement 174 Conclusions 176 Acknowledgements 177 References 177 8. Molecular Basis of Virus Transmission 183-200 Johannes F. J. M. van den Heuvel, Alexander W. E. Franz, and Frank van der Wilk Introduction 183 Transmission by Arthropod Vectors 183 Noncirculative Virus Transmission by Insects 184 Circulative Virus Transmission by Insects 185 Putative Receptors 186 Persistence in Hemolymph of Vectors 187 Transmission by Soil-Inhabiting Nematodes 188 Transmission by Zoosporic Fungi 190 Persistent Transmission 190 Non-persistent Transmission 191 Transmission by Seed and Pollen 192 ix V iral Genetic Determinants 193 Host Genetic Determinants 195 References 195 9. Molecular Basis of Symptomatology 201-210 A. L. N. Rao. Introduction 201 Genetic Basis of Symptom Expression 201 Molecular Biology of Symptom Expression 203 Role of Viral Coat Protein 203 Role of Movement Protein 206 Role of Viral Replicases 206 Other Factors 207 Conclusions 207 References 207 10. Gene-for-Gene Interactions 211-224 Christopher D. Dardick and James N. Culver Introduction 211 Host Factors 213 Characterization of R Genes 214 Similarities to Pathogen Resistance in Animals 215 Organization of Pathogen Recognition Loci 216 Virus Factors 216 Capsid Protein as a Virulence Factor 216 Tobamovirus Capsid Proteins as Elicitors of Hypersensitive Response 216 Potexvirus X Capsid Protein as Elicitor of Hypersensitive Response 217 Virulence Generated by Different Virus Functions 217 Tobacco Mosaic Tobamovirus Movement Protein 217 Tobacco Mosaic Tobamovirus Replicase 218 Cauliflower Mosaic Caulimovirus (CaMV) Gene VI 218 Multiple Virus Determinants in Tomato Bushy Stunt Virus 218 Plant Viruses Evolve to Evade Host Recognition 219 Other Virus-Host Interactions Leading to Resistance 219 Applications 220 R Genes can be transferred across Species Barriers 220 Rational Design of R Genes 221 Engineering Broad-Spectrum Resistance 221 References 221 x 11. Molecular Biology ofViroids 225-239 Ricardo Flores, Marcos de la Pefia, Jose Antonio Navarro, Silvia Ambr6s, and Beatriz Navarro Introduction 225 Viroids : The Simplest Genetic Systems 225 Nucleotide Sequence 225 Domains in Proposed Secondary Structure and Elements of Tertiary Structure 226 Role of Specific Domains 227 Genomic Diversity 228 Variability and Viroid Quasispecies 228 Selection Mechanisms 228 Recombination 229 Origin and Evolution 229 Viroids as Relics of RNA World 229 Phylogenetic Reconstructions 230 Classification 230 Replication 231 Rolling Circle Model 231 Transcription, Processing and Ligation, Hammerhead Ribozymes 232 Genetic Determinants of Pathogenesis and Symptomatology 234 Pathogenic Domains 234 Symptomatology 234 Host Range 235 Genetic Determinants of Other Viroid Functions 236 Transmission 236 Viroid Transport in Host Plants 236 References 237 12. Molecular Biology of Transgenic Plants 241-254 Chuni L. Mandahar Introduction 241 Genetic Variability of Challenge Virus 243 Recombination 243 Mutation 245 Heteroencapsidation 246 Transmission of Non-transmissible Virus Isolates 247 Complementation 247 Extension of Host Range 248 Inheritance 248 Synergism 249 Other Effects 249 Conclusions 250 Xl References 251 13. Gene Silencing 255-269 Chuni L. Mandahar Introduction 255 Types of Gene Silencing 257 Mechanisms of Gene Silencing 258 Transcriptional Gene Silencing 258 Post-transcriptional Gene Silencing 258 Threshold Model 259 Ectopic Pairing Model 260 Third Model 260 Transmission Signal 261 Effects of Gene Silencing 262 Resistance in Transgenic and Non-transgenic Plants 263 Recovery of Transgenic and Non-transgenic Plants from Disease 264 Green Islands 265 Conclusions 266 References 266 Subject Index 271-281
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