Jawaid A. Khan Jeanne Dijkstra Editors Plant Viruses As Molecular Pathogens Pre-publication REVIEWS, COMMENTARIES, EVALUATIONS . his book is both up-to-date and his book covers a wide range of “Tvery informative for traditional “Tsubjects, and it is refreshing to and new generations of plant virolo- have most of the chapters written by gists in both industrialized and devel- people who have not reviewed the spe- oping nations of the world. Moreover, cific topics before, which gives new per- some chapters present very interesting spectives to their coverage. As a concepts regarding the use of molecu- particular example, I refer to the chapter lar techniques to gain new insight into ‘Natural Resistance to Viruses’ by Jari long-standing pathological issues, such Valkonen; he covers the field well, and as virus evolution, host adaptation, and postulates how resistance is engendered. epidemiology. I was also pleased to see In addition, some subjects, such as the a good deal of information on plant vi- transmission of viruses by nematodes, by ruses of importance in the tropics, such fungi, or through the seed, have not been as potyviruses, begomoviruses, and reviewed for many years and have been in some emerging plant viruses transmit- need of updating. There are also some ted by fungal vectors. Altogether, a chapters dealing with molecular tech- very valuable collection of themes on niques that students and researchers will the new art and science of plant virol- find useful.” ogy.” Milton Zaitlin, PhD Francisco J. Morales, PhD Professor Emeritus, Head Virology Research Unit, Department of Plant Pathology, International Center for Tropical College of Agriculture and Life Sciences, Agriculture (CIAT), Cornell University, Miami, Florida Ithaca, New York NOTES FOR PROFESSIONAL LIBRARIANS AND LIBRARY USERS This is an original book title published by Food Products Press®,an imprint of The Haworth Press, Inc. Unless otherwise noted in specific chapters with attribution, materials in this book have not been previ- ously published elsewhere in any format or language. CONSERVATION AND PRESERVATION NOTES All books published by The Haworth Press, Inc. and its imprints are printed on certified pH neutral, acid free book grade paper. This paper meets the minimum requirements of American National Standard for Information Sciences-Permanence of Paper for Printed Material, ANSI Z39.48-1984. Plant Viruses As Molecular Pathogens FOOD PRODUCTS PRESS Crop Science Amarjit S. Basra, PhD Senior Editor New, Recent, and Forthcoming Titles of Related Interest: Dictionary of Plant Genetics and Molecular Biology by Gurbachan S. Miglani Advances in Hemp Research by Paolo Ranalli Wheat: Ecology and Physiology of Yield Determination by Emilio H. Satorre and Gustavo A. Slafer Mineral Nutrition of Crops: Fundamental Mechanisms and Implications by Zdenko Rengel Conservation Tillage in U.S. Agriculture: Environmental, Economic, and Policy Issues by Noel D. Uri Cotton Fibers: Developmental Biology, Quality Improvement, and Textile Processing edited by Amarjit S. Basra Heterosis and Hybrid Seed Production in Agronomic Crops edited by Amarjit S. Basra Intensive Cropping: Efficient Use of Water, Nutrients, and Tillage by S. S. Prihar, P. R. Gajri, D. K. Benbi, and V. K. Arora Physiological Bases for Maize Improvement edited by María E. Otegui and Gustavo A. Slafer Plant Growth Regulators in Agriculture and Horticulture: Their Role and Commercial Uses edited by Amarjit S. Basra Crop Responses and Adaptations to Temperature Stress edited by Amarjit S. Basra Plant Viruses As Molecular Pathogens by Jawaid A. Khan and Jeanne Dijkstra Barley Science: Recent Advances from Molecular Biology to Agronomy of Yield and Quality edited by Gustavo A. Slafer, José Luis Molina-Cano, Roxana Savin, José Luis Araus, and Ignacio Romagosa In Vitro Plant Breeding by Acram Taji, Prakash Kumar, and Prakash Lakshmanan Crop Improvement: Challenges in the Twenty-First Century edited by Manjit S. Kang Tillage for Sustainable Cropping by P. R. Gajri, V. K. Arora, and S. S. Prihar Plant Viruses As Molecular Pathogens Jawaid A. Khan Jeanne Dijkstra Editors Food Products Press® An Imprint of The Haworth Press, Inc. New York • London • Oxford Published by Food Products Press®, an imprint of The Haworth Press, Inc., 10 Alice Street, Binghamton, NY 13904-1580 © 2002 by The Haworth Press, Inc. All rights reserved. No part of this work may be reproduced or utilized in any form or by any means, electronic or mechanical, including photocopying, microfilm, and recording, or by any information storage and retrieval system, without permission in writing from the publisher. Printed in the United States of America. Cover illustrations: (figure on left) symptom induction in Nicotiana benthamiana leaves inoculated with cucumovirus recombinants, courtesy of Chikara Masuta; (figure on right) schematic diagram showing a geminivirus infection cycle, courtesy of Rafael F. Rivera-Bustamante. Cover design by Jennifer M. Gaska. Library of Congress Cataloging-in-Publication Data Khan, Jawaid A. Plant viruses as molecular pathogens / Jawaid A. Khan, Jeanne Dijkstra. p. cm. Includes bibliographical references (p. ). ISBN 1-56022-894-6 (hardcover : alk. paper)—ISBN 1-56022-895-4 (softcover : alk. paper) 1. Plant viruses. 2. Virus diseases of plants. I. Dijkstra, Jeanne, 1930-II. Title. QR351 .K476 2001 579.2'8—dc21 00-049452 CONTENTS About the Editors xii Contributors xiii Preface xvii SECTION I: TAXONOMY Chapter 1. The Principles and Current Practice of Plant Virus Taxonomy 3 Mike A. Mayo Introduction 3 The Underlying Principles 4 The Role of ICTV 7 The Current System of Plant Virus Classification 8 Future Prospects 21 Chapter 2. How to Write the Names of Virus Species 25 Marc H. V. Van Regenmortel SECTION II: VIRUS TRANSMISSION AND TRANSPORT Chapter 3. Genes Involved in Insect-Mediated Transmission of Plant Viruses 31 Juan José Lopez-Moya Introduction 31 Insect Vectors of Plant Viruses 32 Classification of Transmission Modes 32 Nonpersistent and Semipersistent Transmission 34 Circulative Nonpropagative Transmission 41 Circulative Propagative Transmission 47 Conclusions 49 Chapter 4. Characteristic Features of Virus Transmission by Nematodes 63 Jeanne Dijkstra Jawaid A. Khan Introduction 63 Vector Nematodes 63 Viruses Transmitted by Nematodes 64 Mechanism of Virus Transmission 67 Control of Nematode-Transmitted Viruses 70 Chapter 5. Virus Transmission by Fungal Vectors 77 Jeanne Dijkstra Jawaid A. Khan Introduction 77 Fungal Vectors 77 Fungus-Transmitted Viruses 80 Modes of Transmission 93 Mechanism of Virus-Vector Association 94 Epidemiology and Control of Fungus-Borne Viruses 97 Conclusions 98 Chapter 6. Seed Transmission of Viruses: Biological and Molecular Insights 105 Jawaid A. Khan Jeanne Dijkstra Introduction 105 Biological Characteristics 107 Genetic Determinants 111 Conclusions 122 Chapter 7. Molecular Biology of Plant Virus Movement 127 Ayala L. N. Rao Yoon Gi Choi Introduction 127 Movement of Plant Viruses 128 Current Status 138 SECTION III: MOLECULAR BIOLOGY OF RNA VIRUSES Chapter 8. Mechanism of RNA Synthesis by a Viral RNA-Dependent RNA Polymerase 147 Kailayapillai Sivakumaran Jin-Hua Sun C. Cheng Kao Introduction 147 Initiation of RNA Synthesis 148 Abortive Synthesis 151 Transition from Initiation to Elongation 159 Termination of RNA Synthesis 167 Comparison of RNA-Dependent and DNA-Dependent RNA Synthesis 167 Final Comments 170 Chapter 9. Gene Expression Strategies of RNA Viruses 175 Uli Commandeur Wolfgang Rohde Rainer Fischer Dirk Prüfer Introduction 175 Subgenomic RNAs and Genome Segmentation 176 Initiation of Translation 181 Elongation of Translation 188 Termination of Translation 189 Polyprotein Processing and Host Factors 190 Outlook 191 Chapter 10. Recombination in Plant RNA Viruses 203 Chikara Masuta Introduction 203 Overview of Research History on the Recombination of Plant RNA Viruses 203 Recombination in Cucumoviruses 209 Newly Evolved Recombinant Viruses Between CMV and TAV Under Selection Pressure 211 Summary and Conclusion 219 Chapter 11. Variability and Evolution of Potato Virus Y, the Type Species of the Potyvirus Genus 225 Laurent Glais Camille Kerlan Christophe Robaglia Introduction 225 The Family Potyviridae 225 Relationships Between Potyviruses Species 230 Biological Diversity of PVY 231 Genetic Variability of PVY 235 Mechanisms Leading to RNA Genome Polymorphisms 239 Conclusions 244 SECTION IV: MOLECULAR BIOLOGY OF DNA VIRUSES Chapter 12. Geminivirus Replication and Gene Expression 257 Zulma I. Monsalve-Fonnegra Gerardo R. Argüello-Astorga Rafael F. Rivera-Bustamante Introduction 257 Geminivirus Classification 258 Genome Structure 258 Geminivirus Infection Cycle: A Brief Overview 261 Geminivirus Replication 263 Control of Viral Gene Expression 267 Concluding Remarks 275 Chapter 13. The Molecular Epidemiology of Begomoviruses 279 Judith K. Brown Introduction 279 Begomoviruses: Distribution and Characteristics 280 Detection, Identification, and Classification of Begomoviruses 284 Begomovirus Suscepts and Hosts in Relation to Epidemiology 287 Whitefly Vector Biology That Influences Epidemiology 293 The Influence of Vector Biotypes, Races, and Variants on Virus Spread 295 New Diseases, Epidemics, and Pandemics 300 Conclusions 307 Chapter 14. Translational Strategies in Members of the Family Caulimoviridae 317 Mikhail M. Pooggin Lyubov A. Ryabova Thomas Hohn Introduction 317 Architecture of Viral RNA 320 General Enhancement of Expression 321 Shunting 322 Leaky Scanning (Bacilliform Caulimoviruses)