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Molecular Plant Virology. Volume I, Virus Structure and Assembly and Nucleic Acid-Protein Interactions PDF

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Molecular Plant Virology Volume I Virus Structure and Assembly and Nucleic Acid-Protein Interactions Editor Jeffrey W. Davies Head Virus Research Department John Innes Institute Norwich United Kingdom Boca Raton London New York CRC Press is an imprint of the Taylor & Francis Group, an informa business First published 1985 by CRC Press Taylor & Francis Group 6000 Broken Sound Parkway NW, Suite 300 Boca Raton, FL 33487-2742 Reissued 2018 by CRC Press © 1985 by CRC Press, Inc. CRC Press is an imprint of Taylor & Francis Group, an Informa business No claim to original U.S. Government works This book contains information obtained from authentic and highly regarded sources. Reasonable efforts have been made to publish reliable data and information, but the author and publisher cannot assume responsibility for the validity of all materials or the consequences of their use. The authors and publishers have attempted to trace the copyright holders of all material reproduced in this publication and apologize to copyright holders if permission to publish in this form has not been obtained. If any copyright material has not been acknowledged please write and let us know so we may rectify in any future reprint. Except as permitted under U.S. Copyright Law, no part of this book may be reprinted, reproduced, transmitted, or utilized in any form by any electronic, mechanical, or other means, now known or hereafter invented, including photocopying, microfilming, and recording, or in any information storage or retrieval system, without written permission from the publishers. For permission to photocopy or use material electronically from this work, please access www.copyright.com (http://www.copyright. com/) or contact the Copyright Clearance Center, Inc. (CCC), 222 Rosewood Drive, Danvers, MA 01923, 978-750-8400. CCC is a not- for-profit organization that provides licenses and registration for a variety of users. For organizations that have been granted a photocopy license by the CCC, a separate system of payment has been arranged. Trademark Notice: Product or corporate names may be trademarks or registered trademarks, and are used only for identification and explanation without intent to infringe. Library of Congress Cataloging in Publication Data Main entry under title: Molecular plant virology. Includes bibliographies and index. Contents: v. 1. Virus structure and assembly and nucleic- acid protein interactions. 1. Plant viruses — Collected works. 2. Molecular biology — Collected works. I. Davies, Jeffrey W. QR351 .M64 1985 576’ .6483 84-9469 ISBN 0-8493-6290-3 (v. 1) A Library of Congress record exists under LC control number: 84009469 Publisher’s Note The publisher has gone to great lengths to ensure the quality of this reprint but points out that some imperfections in the original copies may be apparent. Disclaimer The publisher has made every effort to trace copyright holders and welcomes correspondence from those they have been unable to contact. ISBN 13: 978-1-315-89569-7 (hbk) ISBN 13: 978-1-351-07479-7 (ebk) Visit the Taylor & Francis Web site at http://www.taylorandfrancis.com and the CRC Press Web site at http://www.crcpress.com PREFACE In calling this series Molecular Plant Virology, I had in mind aspects of plant virol- ogy of interest to biochemists, molecular geneticists, biophysicists, genetic engineers, or, collectively, "molecular biologists". At the same time, the intention was to provide up-to-date reviews, by expert contributors, on current research topics in plant virology of interest and referential use to virologists and plant biologists. The selected topics are pitched mainly at a research level, but with sufficient introduction and cross-referenc- ing to enable graduate students to enter this fascinating field and, hopefully, not get lost. Although the volumes are primarily for reference, I encouraged authors to provide readily readable accounts, with, in some cases, interesting historical notes or at times a personal touch. A certain amount of criticism or questioning adds to the flavor.. Molecular biology and virology have run a related course for many years, developing together, merging at times, and gaining from each other. This is not surprising when one considers the nature of virus particles, what we are now learning about their func- tions, and what molecular biology is. At this point a sinking feeling told me I might have to define molecular biology. I decided to go back to the origin and roots of the term. Warren Weaver' states that the first mention, in the 1938 Annual Report of the Rockefeller Foundation, describes " a relatively new field, which may be called molecular biology, in which delicate - modern techniques are being used to investigate ever more minute details of certain life processes". Later,' in a Harvey Lecture, Astbury stated that "Molecular Biology im- plies searching below the large scale manifestations of classical biology for the corre- sponding molecular plan". He went on to say that it was "concerned particularly with the forms of biological molecules and with the evolution, exploitation and ramification of these forms. . . . " He further stated that "Molecular Biology is predominantly 3-dimensional and structural" — but explained that "It must, of necessity, enquire at the same time into genesis and function". Volume I of Molecular Plant Virology reviews aspects of the structure of plant vi- ruses, and development and application to physical techniques such as electron micro- scopy and X-ray crystallography. The structure and assembly of rod-shaped, spherical, and bacilliform virus particles are considered. In the latter case, nucleic acid-protein interaction is emphasized which takes us a step nearer to function. In Volume II, function and molecular plan (strategy) are the key words but still in relation to structure, albeit nucleic acid sequence rather than particle structure. Here again we see new and different techniques having remarkable influence. Early events in infection are discussed, followed by gene expression and replication of RNA and DNA viruses. These two "structure and function" volumes are being published almost concurrently. In the near future we will, hopefully, see the "exploitation", in the form of genetic manipulation with plant viruses and the use of plant virus sequences in the construction of gene vectors. The "ramifications" of the study of structure, function, and modifi- cation of viruses should lead to a molecular analysis of virus-host relationships, host range and symptom expression, and other plant responses including resistance. This molecular pathology will require, however, a better understanding of the molecular biology of plants, both healthy and infected, a subject which is now rapidly progress- ing.3,4,7 8 Should the reader not be familiar with plant virology, I must recommend as one excellent comprehensive text book, Matthew's Plant Virology,' and for companion reading with this series, recent reports from research meetings, such as those of Cold Spring Harbor' and EMBO or NATO Workshops.5-7 Jeffrey W. Davies Norwich, January 1984 REFERENCES 1. Weaver, W., Molecular biology: origin of the term, Science, 170, 581, 1970. 2. Astbury, W. T., Adventures in Molecular Biology, Harvey Lecture Series, 46, 3, 1950. 3. Hall, T. C. and Davies, J. W., Nucleic Acids in Plants, Vols. I and II, CRC Press, Boca Raton, Florida, 1979. 4. Grierson, D. and Covey, S., Plant Molecular Biology, Blackie Press, Glasgow, 1984. 5. Matthews, R. E. F., Plant Virology, 2nd ed., Academic Press, New York, 1982. 6. Robertson, H. D., Howell, S. H., Zaitlin, M., and Malmberg, R. L., Plant infectious agents: viruses, viroids, virusoids and satellites, Current Comm. Molec. Biol., Cold Spring Harbor Laboratory, New York, 1983. 7. Ciferri, 0. and Dure, III, L., Eds., Structure and Function of Plant Genomes, NATO ASI Series, Plenum Press, New York, 1983. 8. van Vloten-Doting, L., Groot, G. S. P., and Hall, T. C., Molecular Form and Function of the Plant Genome, NATO ASI Series, Plenum Press, New York, 1985. 9. Hirth, L., Richards, K., and Fritig, B., Plant Viruses, Satellites and Viroids: Genome Structure, Expression and Replication, EMBO Workshop, Strasbourg, 1984. THE EDITOR Jeffrey W. Davies, Ph.D., F.L.S., received a B.Sc. (1963) and Ph.D. (1966) at the University of Nottingham where he began his research career with E.C. Cocking on plant protoplasts and plant protein synthesis in cell-free extracts. From 1966 to 1970 he was a faculty member at the University of Edinburgh, in the then new Department of Molecular Biology, headed by M.R. Pollock and W. Hayes. During this time, his research concerned the control of enzyme synthesis and the structure and translation of bacterial RNA. This interest extended to bacteriophages and plant viruses after an EMBO-Fellowship (with L. Bosch) in Leiden, The Netherlands (1970), when he was appointed Assistant Scientist in Paul Kaesberg's Biophysics Laboratory, at the Univer- sity of Wisconsin, Madison. His research there concerned translation and replication of RNA bacteriophages and plant viruses, especially brome mosaic virus. In 1976, Dr. Davies joined A. van Kammen's Department of Molecular Biology in Wageningen, the Netherlands, where he continued research on the molecular biology of plant viruses. In 1979, he was appointed Head of the Virus Research Department (formerly the ARC Virus Research Unit, Cambridge) now at the John Innes Institute in Norwich. Dr. Davies' current interests include the development of plant viruses as plant gene vectors, and the molecular pathology of plant virus diseases. CONTRIBUTORS M. G. AbouHaidar, Ph.D. E. M. J. Jaspars, D.Sc. Asssociate Professor Senior Staff Member Department of Botany Department of Biochemistry University of Toronto State University of Leiden Toronto, Ontario Leiden, The Netherlands Canada G. P. Lomonossoff, Ph.D. Virus Research Department J. W. Erickson, Ph.D. John Innes Institute Assistant Professor Norwich, United Kingdom Department of Medicine University of Wisconsin M. G. Rossmann, Ph.D. Medical School Hanley Professor of Biological Sciences Mount Sinai Medical Center Purdue University Milwaukee, Wisconsin West Lafayette, Indiana R. W. Horne, Sc. D., Hon. F.R.M.S. T. M. A. Wilson, Ph.D. School of Biological Sciences Virus Research Department University of East Anglia John Innes Institute Norwich, United Kingdom Norwich, United Kingdom TABLE OF CONTENTS Volume I VIRUS STRUCTURE AND ASSEMBLY AND NUCLEIC ACID- PROTEIN INTERACTIONS Chapter 1 The Development and Application of Electron Microscopy to the Structure of Isolated Plant Viruses (cid:9) 1 R. W. Home Chapter 2 Structure and in Vitro Assembly of Tobacco Mosaic Virus (cid:9) 43 G. P. Lomonossoff and T. M. A. Wilson Chapter 3 Structure and in Vitro Assembly of Papaya Mosaic Virus (cid:9) 85 M. G. AbouHaidar and J. W. Erickson Chapter 4 Structure and in Vitro Assembly of Southern Bean Mosaic Virus, in Relation to That of Other Small Spherical Plant Viruses (cid:9) 123 M. G. Rossman Chapter 5 Interaction of Alfalfa Mosaic Virus Nucleic Acid and Protein (cid:9) 155 E. M. J. Jaspars Index (cid:9) 223 Volume I (cid:9)1 Chapter 1 THE DEVELOPMENT AND APPLICATION OF ELECTRON MICROSCOPY TO THE STRUCTURE OF ISOLATED PLANT VIRUSES R. W. Home TABLE OF CONTENTS I.(cid:9) Introduction (cid:9) 2 II.(cid:9) Development of Electron Microscope Techniques (cid:9) 2 A. Shadow-Casting Method and Replicas (cid:9) 2 B. Thin Sections (cid:9) 4 C. Evaporated Carbon Films (cid:9) 4 D. Positive and Negative Staining Methods (cid:9) 5 III.(cid:9) Symmetry in Virus Architecture Revealed by the Electron Microscope (cid:9)5 IV.(cid:9) Terminology (cid:9) 7 V.(cid:9) The Extraction of Information from Electron Micrographs of Virus Particles (cid:9) 7 A. Photographic Averaging (cid:9) 7 B. Optical Diffraction Methods Applied to Electron Micrographs (cid:9)8 C. Computer Image Reconstruction from Electron Micrographs (cid:9)11 D. The Processing and Analysis of Images by Computer Methods for Modeling Viruses and Other Biological Structures (cid:9) 13 VI.(cid:9) Radiation Damage to the Specimen (cid:9) 15 VII. The Formation of the Crystalline and Paracrystalline Arrays of Plant Viruses (cid:9) 16 VIII. The Application of Electron Microscopy to the Study of Dissociated and Reassembled Products from Plant Viruses (cid:9) 24 IX.(cid:9) The Examination of Isolated Viral Nucleic Acids (cid:9) 26 X.(cid:9) Electron Microscopy of Partially Degraded Virus Particles (cid:9) 30 XI.(cid:9) Electron Microscope Studies of Reassembled Virus Products in Vitro (cid:9)30 A. Isometric Viruses (cid:9) 30 B. Rod and Flexuous Viruses (cid:9) 32 XII. Low Temperature Transmission Electron Microscopy (cid:9) 34 XIII. Abbreviations Used (cid:9) 36 References (cid:9) 38

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