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The Viroids 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 TOGAVIRIDAE AND FLA VIVIRIDAE Edited by Sondra Schlesinger and Milton J. Schlesinger THE VIROIDS Edited by T. O. Diener 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 Library of Congress Cataloging in Publication Data The Viroids. (The Viruses) Includes bibliographies and index. 1. Viroids. I. Diener, T. O. (Theodor Otto), 1921- . II. Series. QR500.V568 1987 576'.6483 87-13017 ISBN-13: 978-1-4612-9035-3 e-ISBN-13: 978-1-4613-1855-2 DOl: 10.1007/978-1-4613-1855-2 © 1987 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. 10013 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 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 Cali­ fornia, Riverside, California 92521 T. O. Diener, Microbiology and Plant Pathology Laboratory, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, Mary­ land 20705 Gail Dinter-Gottlieb, Department of Bioscience and Biotechnology, Drexel University, Philadelphia, Pennsylvania 19104 R. I. B. Francki, Department of Plant Pathology, Waite Agricultural Re­ search 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 Agri­ culture, Orlando, Florida 32803 Rosemarie W. Hammond, Microbiology and Plant Pathology Laboratory, Plant Protection Institute, Beltsville Agricultural Research Center, U.S. Department of Agriculture, Beltsville, Maryland 20705 R. Kenneth Horst, Department of Plant Pathology, Cornell University, Ithaca, New York 14853 Paul Keese, Department of Biochemistry, University of Adelaide, Ade­ laide, 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, Mary­ land 20705 v vi CONTRIBUTORS Robert A. Owens, Microbiology and Plant Pathology Laboratory, Plant Protection Institute, Beltsville Agricultural Research Center, U.S. Department of Agriculture, Beltsville, Maryland 20705 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 Dussel­ dorf, D-4000 Dusseldorf, Federal Republic of Germany Heinz L. Sanger, Max-Planck-Institut fur Biochemie, Abteilung Viroid­ forschung, D-8033 Planegg-Martinsried, Federal Republic of Ger­ many 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 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 fasci­ nating 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 struc­ tural standpoint. Much less is known of the mechanisms of viroid func­ tion, 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 im­ portant beginnings have been made in the elucidation of viroid struc­ ture-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 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. T. O. Diener Beltsville, Maryland Contents Viroid Abbreviations ......................................... , xxi Introduction T. O. Diener I. Organisms, Viruses, and Viroids . 2 II. The Biochemical Significance of Viroids ................... 3 III. The Possible Evolutionary Significance of Viroids. 4 IV. References............................................... 5 I. General Section Chapter 1 Biological Properties T. O. Diener I. Introduction . 9 II. Symptomatology......................................... 10 A. Macroscopic Symptoms . 10 B. Cytopathic Effects. 11 C. Biochemical Disturbances. 13 III. Ecology and Epidemiology. .. .. 16 A. Origin of Viroid Diseases. 16 B. Environmental Factors. 19 C. Natural Transmission. 19 D. Economic Importance and Control Measures... .. 21 IV. Experimental Biology. 22 A. Experimental Transmission ..... , .......... .......... 22 B. Experimental Host Range ............................. 22 ix x CONTENTS C. Propagation . 23 D. Identification......................................... 24 E. Quantitation......................................... 25 F. Purification . 25 G. Diagnostic Procedures ................................ 25 H. Interaction with Other Pathogens. 28 V. References ............................................... 29 Chapter 2 Physical-Chemical Properties: Molecular Structure (Primary and Secondary) Paul Keese and Robert H. Symons I. Introduction . .. 37 II. Purification of Viroids . 37 A. Preparation of Plant Extracts .......................... 38 B. Purification.......................................... 39 III. Sequence Determination of Viroids . 40 A. Fingerprint Analysis. 40 B. Direct RNA Sequencing.. .. .. .. .. .... 41 C. Primer-Directed Sequence Analysis. 42 D. Sequencing of Viroids Using Cloned cDNA. .. ... 43 IV. Structure of Viroids ...................................... 45 A. Circular Structure of Viroids .......................... 45 B. Sequence and Structure of Viroids ..................... 45 C. Structural Domains of Viroids . 49 D. Structure of ASBV . 55 V. Conclusion . 58 VI. References............................................... 59 Chapter 3 Physical-Chemical Properties: Structure Formation Detlev Riesner I. Introduction . 63 II. Experimental Analysis. 64 A. Optical Melting Curves . 64 B. Calorimetry.......................................... 67 C. Electron Microscopy . 69 D. Gel Electrophoresis.

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