Berkeley, California. Charlottesville, Virginia. THE VIRUSES: Catalogue, Characterization, and Classification Heinz Fraenkel-Conrat

Transcription

1 The Viroids

2 THE VmUSES Series Editors HEINZ FRAENKEL-CONRAT, University of California Berkeley, California ROBERT R. WAGNER, University of Virginia School of Medicine Charlottesville, Virginia THE VIRUSES: Catalogue, Characterization, and Classification Heinz Fraenkel-Conrat THE ADENOVIRUSES Edited by Harold S. Ginsberg THE HERPESVIRUSES Volumes 1-3 Edited by Bernard Roizman Volume 4 Edited by Bernard Roizman and Carlos Lopez THE PAPOVAVIRIDAE Volume 1 Edited by Norman P. Salzman Volume 2 Edited by Norman P. Salzman and Peter M. Howley THE PARVOVIRUSES Edited by Kenneth I. Berns THE PLANT VIRUSES Volume 1 Edited by R. I. B. Francki Volume 2. Edited by M. H. V. Van Regenmortel and Heinz Fraenkel-Conrat Volume 3 Edited by Renate Koenig THE REOVIRIDAE Edited by Wolfgang K. Joklik THE RHABDOVIRUSES Edited by Robert R. Wagner THE TOGA VIRIDAE AND FLA VIVIRIDAE Edited by Sondra Schlesinger and Milton J. Schlesinger THE VIROIDS Edited by T. O. Diener

3 The Viroids Edited by T. o. DIENER Microbiology and Plant Pathology Laboratory Agricultural Research Service U.S. Department of Agriculture Beltsville, Maryland PLENUM PRESS NEW YORK AND LONDON

4 Library of Congress Cataloging in Publication Data The Viroids. (The Viruses) Includes bibliographies and index. 1. Viroids. I. Diener, T. O. (Theodor Otto), II. Series. QR500.V '.6483 ISBN-13: e-isbn-13: DOl: / Plenum Press, New York Softcover reprint of the hardcover 1st edition 1987 A Division of Plenum Publishing Corporation 233 Spring Street, New York, N.Y All rights reserved No part of this book may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording, or otherwise, without written permission from the Publisher

5 Contribu tors Patricia Broadbent, Biological and Chemical Research Institute, New South Wales Department of Agriculture, Rydalmere, 2116, Australia Paul R. Desjardins, Department of Plant Pathology, University of California, Riverside, California T. O. Diener, Microbiology and Plant Pathology Laboratory, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, Maryland Gail Dinter-Gottlieb, Department of Bioscience and Biotechnology, Drexel University, Philadelphia, Pennsylvania R. I. B. Francki, Department of Plant Pathology, Waite Agricultural Research Institute, University of Adelaide, Glen Osmond, 5064, South Australia Jorge Galindo A., Centro de Fitopatologia, Colegio de Postgraduados, Montecillos, Texcoco, Mexico S. M. Garnsey, Agricultural Research Service, U.S. Department of Agriculture, Orlando, Florida Rosemarie W. Hammond, Microbiology and Plant Pathology Laboratory, Plant Protection Institute, Beltsville Agricultural Research Center, U.S. Department of Agriculture, Beltsville, Maryland R. Kenneth Horst, Department of Plant Pathology, Cornell University, Ithaca, New York Paul Keese, Department of Biochemistry, University of Adelaide, Adelaide, 5000, South Australia; Present address: Research School of Biological Sciences, Australian National University, Canberra, A.C.T. 2600, Australia Roger H. Lawson, Florist and Nursery Crops Laboratory, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, Maryland v

6 vi CONTRIBUTORS Robert A. Owens, Microbiology and Plant Pathology Laboratory, Plant Protection Institute, Beltsville Agricultural Research Center, U.S. Department of Agriculture, Beltsville, Maryland Tien Po, Institute of Microbiology, Academia Sinica, Beijing, China John W. Randles, Department of Plant Pathology, Waite Agricultural Research Institute, University of Adelaide, Glen Osmond, 5064, South Australia Detlev Riesner, Institut fur Physikalische Biologie, Universitat Dusseldorf, D-4000 Dusseldorf, Federal Republic of Germany Heinz L. Sanger, Max-Planck-Institut fur Biochemie, Abteilung Viroidforschung, D-8033 Planegg-Martinsried, Federal Republic of Germany Eishiro Shikata, Department of Botany, Faculty of Agriculture, Hokkaido University, Sapporo, Japan Robert H. Symons, Department of Biochemistry, University of Adelaide, Adelaide, 5000, South Australia B. Walter, INRA, Station de Pathologie Vegetale, B.P. 507, Colmar, France Chen Wei, Institute of Microbiology, Academia Sinica, Beijing, China

7 Preface More than seven years have passed since the first monograph on viroids was published. At that time, the existence of viroids as a novel type of pathogen far smaller than viruses had been amply demonstrated and some of their unusual molecular properties had been elucidated, but the entry of molecular biology into viroid research was still in its infancy. Since that time, our knowledge of the molecular properties of viroids has increased exponentially and viroids have become even more fascinating than was the case seven years ago. Today, aside from transfer RNA, viroids are probably the best known type of RNA-at least from a structural standpoint. Much less is known of the mechanisms of viroid function, such as the exact pathway and enzymology of viroid replication and the biochemistry of viroid pathogenesis. Recently, however, emphasis in viroid research has shifted from structural to functional themes and important beginnings have been made in the elucidation of viroid structure-function relationships. With the discovery of viroidlike RNAs within the capsids of certain plant viruses and the finding of surprising structural similarities between viroids and plant satellite RNAs, the conceptual gap between viroids and conventional viruses has significantly narrowed. Even beyond virology, connecting links with cellular RNAs have come to light and the long isolation of viroids land "viroidologists"j has come to an end. It is hoped not only that the present volume brings the reader up to date on our present knowledge of viroids and viroid diseases, but that it also reflects some of the excitement and enthusiasm that motivates viroid investigators and permeates the field. It has been pointed out before that, in contrast to many other areas of virology or plant pathology, our knowledge of the molecular aspects of viroids is far greater than that of more traditional aspects, such as the mechanisms of viroid spread in the field, possible vector transmission of viroids, and all aspects of disease epidemiology. vii

8 viii PREFACE It is for this reason that this volume is divided into two parts: a general section that is mostly dedicated to the physical-chemical and biological properties that viroids have in common and a special section that treats each viroid in tum with emphasis on those properties that are peculiar to each and concentrating on the plant pathological aspects of the diseases that each viroid causes. I wish to thank all the authors who contributed to the volume for their excellent and up-to-date treatments, and I hope that the book will prove useful not only to viroid investigators but also to scientists in other fields who wish to learn of the newest results regarding viroids and viroid diseases. Beltsville, Maryland T. O. Diener

9 Contents Viroid Abbreviations..., xxi Introduction T. O. Diener I. Organisms, Viruses, and Viroids II. The Biochemical Significance of Viroids... 3 III. The Possible Evolutionary Significance of Viroids IV. References... 5 I. General Section Chapter 1 Biological Properties T. O. Diener I. Introduction II. Symptomatology A. Macroscopic Symptoms B. Cytopathic Effects C. Biochemical Disturbances III. Ecology and Epidemiology A. Origin of Viroid Diseases B. Environmental Factors C. Natural Transmission D. Economic Importance and Control Measures IV. Experimental Biology A. Experimental Transmission..., B. Experimental Host Range ix

10 x CONTENTS C. Propagation D. Identification E. Quantitation F. Purification G. Diagnostic Procedures H. Interaction with Other Pathogens V. References Chapter 2 Physical-Chemical Properties: Molecular Structure (Primary and Secondary) Paul Keese and Robert H. Symons I. Introduction II. Purification of Viroids A. Preparation of Plant Extracts B. Purification III. Sequence Determination of Viroids A. Fingerprint Analysis B. Direct RNA Sequencing C. Primer-Directed Sequence Analysis D. Sequencing of Viroids Using Cloned cdna IV. Structure of Viroids A. Circular Structure of Viroids B. Sequence and Structure of Viroids C. Structural Domains of Viroids D. Structure of ASBV V. Conclusion VI. References Chapter 3 Physical-Chemical Properties: Structure Formation Detlev Riesner I. Introduction II. Experimental Analysis A. Optical Melting Curves B. Calorimetry C. Electron Microscopy D. Gel Electrophoresis E. Kinetics F. Influence of Ionic Strength and Other Solvent Conditions

11 CONTENTS n III. Theoretical Analysis A. Elementary Parameters B. Mechanistic Models IV. Mechanism A. Premelting Regions B. Main Transition and Formation of Stable Hairpins C. Reversibility D. Experiment and Theory V. Structure Formation and Function A. Viroids: A Dynamic Principle B. Premelting and Virulence C. Relevance of Stable Hairpins VI. Addendum VII. References Chapter 4 Viroid Function: Subcellular Location and in Situ Association with Cellular Components Detlev Riesner I. Introduction II. Subcellular Location A. Nuclei B. Other Organelles III. Subnuclear Location A. Chromosomal Network B. Nucleoli C. Nucleolar Nucleosomes IV. Nature of Viroid Complexes A. Ionic Strength Dependence B. Viroid-Binding Proteins V. Reconstitution of Viroid-Host Interactions III A. Nuclei... III B. Nucleoli... III VI. Location of Viroid Intermediates VII. Location and Function VIII. References Chapter 5 Viroid Function: Viroid Replication Heinz L. Sanger I. Introduction II. The Question of Viroid Translation... " 118

12 xii CONTENTS III. Potentially Possible Pathways of Viroid Replication A. Presumed DNA-Directed Viroid Replication B. RNA-Directed Viroid Replication IV. Intermediates and Products of Viroid Replication A. Monomeric Circular Viroid (+) RNA, the "Mature" Viroid Proper B. Oligomeric Linear Viroid ( - ) RNA C. Oligomeric Linear Viroid ( + ) RNA D. Viroid (+). (-) RNA Hybrid Molecules V. Studies on Viroid Replication in Vivo A. Replication in Intact Plants B. Replication in Plant Protoplasts and Cultured Cells C. Replication in Isolated Plant Cell Nuclei VI. Inhibition Studies on Viroid Replication VII. Replication Models A. The Model of Owens and Diener B. The Models of Branch and Robertson C. The Model of Ishikawa etal D. The Model of Hutchins et al VIII. In Vitro Transcription of Viroid RNA with Purified Polymerases A. Transcription with DNA-Dependent Plant RNA Polymerases B. Transcription with RNA-Dependent Plant RNA Polymerases IX. Viroid Replication as Initiated by Cloned Viroid DNA A. Infectivity of Cloned Double-Stranded Viroid DNA B. Infectivity of Cloned Single-Stranded Viroid DNA C. Viroid-Related RNA Transcripts in E. coli X. In Vitro Synthesis of Viroid RNA with RNA Transcription Systems A. Viroid Synthesis with Bacterial RNA Polymerase/Promoter Systems B. Viroid Synthesis with Bacteriophage RNA Polymerase/Promoter Systems XI. The Processing of Viroid RNAs A. Interconversion of Monomeric Circular and Linear Viroid Molecules in Vitro B. Cleavage of Oligomeric Viroids into Monomers C. Perspectives XII. Structural Requirements for the Replicability of Viroids XIII. Structural Requirements for the Processing of Viroid RNA XIV. Conclusions XV. References

13 CONTENTS xiii Chapter 6 Viroid Function: Molecular Biology of Viroid-Host Interactions Robert A. Owens and Rosemarie W. Hammond I. Viroid Pathogenesis-A Structure/Function Paradigm A. Current Models for Viroid Pathogenesis B. Possible Mechanisms for Disease Induction C. Possible Relationships between Viroid Structure and Function II. Site-Specific Mutagenesis of Infectious cdnas A. Minimal Requirements for cdna Infectivity B. Site-Specific Mutagenesis of PSTV and CEV cdnas C. Construction of Chimeric Viroid cdnas D. Characterization of Mutant Viroids III. Viroid Transcripts as Substrates for RNA Recombination.,. 182 IV. Concluding Remarks... " 184 V. References Chapter 7 Possible Viroid Origin: Viroids, Virusoids, and Group I Introns Gail Dinter-Gottlieb I. Introduction II. Types of Introns III. Viroids as Introns IV. Viroids and the Self-Splicing Intron of Tetrahymena V. Discussion and Digressions VI. References Chapter 8 Possible Viroid Origin: Encapsidated Viroidlike RNA R. I. B. Francki I. Introduction II. Viruses That Encapsidate Viroidlike RNAs III. Are Viroidlike RNAs Satellite RNAs? IV. The Dependence of Viroidlike RNA on Viral RNA V. Structure of Viroidlike RNA VI. Replication of Viroidlike RNA A. In Vivo Studies B. In Vitro Studies C. How Is Viroidlike RNA Synthesized?

14 xiv CONTENTS VII. Possible Relationships of Viroidlike RNAs to Viroids VIII. References II. Special Section Chapter 9 Potato Spindle Tuber T. O. Diener I. Historical II. Geographic Distribution III. Symptomatology IV. Field Transmission and Spread V. Economic Losses VI. HostRange VII. Strains A. Unmottled Curly Dwarf Strain B. Mild Strains VIII. Experimental Transmission IX. Diagnosis A. Bioassay B. Polyacrylamide Gel Electrophoresis C. Molecular Probes X. Interaction with Other Pathogens..., XI. Purification XII. Physical-Chemical Properties XIII. References Chapter 10 Citrus Exocortis Patricia Broadbent and S. M. Garnsey I. Field Symptomatology II. Geographic Distribution III. Host Range IV. Importance of Exocortis V. Strains VI. Transmission A. Transmission by Grafting B. Mechanical Transmission C. Transmission by Vectors D. Transmission through Seed E. Transmission by Dodder

15 CONTENTS xv VII. Detection A. Indicator Plants B. Biochemical Methods of Detection VIII. Cytopathic Effects in Host IX. Control X. Physical-Chemical Properties XI. References Chapter 11 Chrysanthemum Stunt Roger H. Lawson I. Introduction II. Symptomatology A. CSV in Chrysanthemum B. Other Viroids in Chrysanthemum III. Transmission and Spread IV. Host Range V. Diagnosis A. Bioassay B. Polyacrylamide Gel Electrophoresis C. Nucleic Acid Hybridization..., 255 VI. Purification VII. Physical-Chemical Properties VIII. Control Measures..., 257 A. Elimination by Heat Treatment and Meristem-Tip Culture B. Cross-Protection IX. References Chapter 12 Cucumber Pale Fruit T. O. Diener I. Historical II. Geographic Distribution III. Symptomatology IV. Field Transmission and Spread V. Economic Losses VI. Control VII. Purification VIII. Host Range IX. Strains X. References

16 xvi CONTENTS Chapter 13 Coconut Cadang-Cadang fohn W. Randles I. Introduction II. History III. Distribution IV. Symptoms and Host Range V. Epidemiology VI. Economic Losses VII. Diagnosis VIII. Strains IX. Experimental Transmission X. Purification XI. Physical Properties XII. Nucleotide Sequence XIII. Relationship between Viroid Structure and Disease Progress 274 XIV. References Chapter 14 Hop Stunt Eishiro Shikata I. Disease Occurrence II. Symptoms and Damage to Hop Plants III. Host Range and Symptomatology IV. Transmission and Distribution V. Etiology and Purification..., VI. Structure and Function VII. Cucumber and Grapevine Isolates VIII. Diagnosis and Control IX. References Chapter 15 Chrysanthemum Chlorotic Mottle R. Kenneth Horst I. Introduction II. Symptomatology III. Etiology IV. Physical Characteristics

17 CONTENTS xvii V. Control VI. References Chapter 16 Columnea Latent T. O. Diener Chapter 17 Avocado Sunblotch Paul R. Desjardins I. Introduction II. Geographic Distribution and Economic Importance III. Host Range IV. Symptomatology A. Symptomatic Trees B. Symptomless Carrier Trees C. Effect of Light and Temperature V. Strains VI. Recovery Phenomenon A. Development of Symptomless Condition B. Consequences of the Symptomless Carrier Condition VII. Transmission A. Graft Transmission B. Mechanical Transmission C. Seed Transmission D. Pollen Transmission VIII. Mixed Infections with Viruses A. Viruses Involved B. Problems for ASBV Research IX. Isolation and Characterization A. Methods of Isolation and Purification B. Multiple RNA Species C. Nucleotide Sequence X. Ultrastructural Cytology XI. Detection and Control A. Diagnosis B. Viroid Inactivation on Tools C. Use of Symptomless Trees XII. Discussion XIII. References

18 xviii CONTENTS Chapter 18 Tomato Plattta Macho Jorge Galindo A. I. HistoricaL II. Geographic Distribution III. Symptomatology IV. Epidemiology V. Economic Losses VI. Diagnosis... I 318 VII. Strains VIII. Experimental Transmission IX. Purification X. Physical Properties XI. Nucleotide Sequence XII. References Chapter 19 Tomato Apical Stunt B. Walter I. Historicalj Geographic Distribution II. Symptomatology, Epidemiology, and Strains III. Experimental Transmission... ; A. Mechanical Inoculation B. Aphid Transmission IV. Purification A. Polyethylene Glycol Method " B. Rapid Method V. Physical-Chemical Properties VI. Nucleotide Sequence... ; VII. References Chapter 20 Tomato Bunchy Top T. O. Diener I. Symptomatology II. Host Range III. Strains IV. References

19 CONTENTS xix Chapter 21 Burdock Stunt Tien Po and Chen Wei I. Historical II. Geographic Distribution III. Symptomatology IV. Transmission V. Viroid Etiology VI. Purification VII. Some Physical Properties of BSV VIII. The Occurrence of BSV RNA-l and RNA-2 in Separate Plants IX. Ultrastructure of Diseased Leaf Tissues X. Propagation of BSV RNA-l in Tissue Culture XI. Conclusions XII. References Index

20 Viroid Abbreviations ASBV BSV CCCV CCMV CEV CLV CPFV CSV HSV PSTV TASV TBTV TPMV Avocado sun blotch viroid Burdock stunt viroid Coconut cadang-cadang viroid Chrysanthemum chlorotic mottle viroid Citrus exocortis viroid Columnea latent viroid Cucumber pale fruit viroid Chrysanthemum stunt viroid Hop stunt viroid Potato spindle tuber viroid Tomato apical stunt viroid Tomato bunchy top viroid Tomato planta macho viroid xxi