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Comparative Plant Virology, Second Edition, by Roger Hull Revision to Fundamentals of Plant Virology Written by R COMPARATIVE PLANT VIROLOGY SECOND EDITION science & ELSEVIERtechnology books Companion Web Site: http://www.elsevierdirect.com/companions/9780123741547 Comparative Plant Virology, Second Edition, by Roger Hull Revision to Fundamentals of Plant Virology written by R. Matthews Resources for Professors: • Image bank • Virus profiles TOOLS FOR YOUR TEACHING NEEDS ALL textbooks.elsevier.com ACADEMIC PRESS To adopt this book for course use, visit http://textbooks.elsevier.com COMPARATIVE PLANT VIROLOGY SECOND EDITION ROGER HULL Emeritus Fellow Department of Disease and Stress Biology John Innes Centre Norwich, UK AMSTERDAM • BOSTON • HEIDELBERG • LONDON NEW YORK • OXFORD • PARIS • SAN DIEGO SAN FRANCISCO • SINGAPORE • SYDNEY • TOKYO Academic Press is an imprint of Elsevier Cover Credits: BSMV leaf — Mild stripe mosaic; Symptom of BSMV in barley. Image courtesy of A.O. Jackson. BSMV genome: The infectious genome (BSMV) is divided between 3 species of positive sense ssRNA that are designated a, b, and g. Image courtesy of Roger Hull. BSMV particles. Image courtesy of Roger Hull. Diagram showing systemic spread of silencing signal: The signal is generated in the initially infected cell (bottom, left hand) and spreads to about 10–15 adjacent cells where it is amplified. It moves out of the initially infected leaf via the phloem sieve tubes and then spreads throughout systemic leaves being amplified at various times. Image courtesy of Roger Hull. Elsevier Academic Press 30 Corporate Drive, Suite 400, Burlington, MA 01803, USA 525 B Street, Suite 1900, San Diego, California 92101-4495, USA 84 Theobald’s Road, London WC1X 8RR, UK This book is printed on acid-free paper. Copyright # 2009, Elsevier Inc. All rights reserved. No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopy, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permissions may be sought directly from Elsevier’s Science & Technology Rights Department in Oxford, UK: phone: (þ44) 1865 843830, fax: (þ44) 1865 853333, E-mail: [email protected]. You may also complete your request on-line via the Elsevier homepage (http://elsevier.com), by selecting “Customer Support” and then “Obtaining Permissions.” Library of Congress Cataloging-in-Publication Data Hull, Roger, 1937- Comparative plant virology / Roger Hull. – 2nd ed. p. cm. ISBN 978-0-12-374154-7 (hardcover : alk. paper) 1. Plant viruses. I. Title. QR351.H85 2009 579.208–dc22 2008040333 British Library Cataloguing in Publication Data A catalogue record for this book is available from the British Library ISBN 13: 978-0-12-374154-7 For all information on all Elsevier Academic Press publications visit our Web site at www.elsevierdirect.com Printed in China 0910987654321 Contents Preface xiii 1. Effects on Plant Size 26 List of Abbreviations xv 2. Mosaic Patterns and Related Symptoms 26 3. Yellow Diseases 28 4. Leaf Rolling 28 5. Ring Spot Diseases 28 Section I 6. Necrotic Diseases 28 INTRODUCTION TO PLANT 7. Developmental Abnormalities 28 8. Wilting 29 VIRUSES 9. Recovery from Disease 29 10. Genetic Effects 29 C. The Cryptoviruses 29 Chapter 1. What Is a Virus? D. Diseases Caused by Viral Complexes 29 E. Agents Inducing Virus-Like Symptoms 30 I. Introduction 3 V. Histological Changes 30 II. History 3 A. Necrosis 30 III. Definition of a Virus 9 B. Hypoplasia 30 A. How Viruses Differ from Other Plant C. Hyperplasia 32 Pathogens 9 1. Cell Size 32 B. Are Viruses Alive? 13 2. Cell Division in Differentiated Cells 32 IV. Classification and Nomenclature of Viruses 13 3. Abnormal Division in Cambial Cells 32 A. Virus Classification 13 VI. Cytological Effects 32 B. Families, Genera, and Species 14 A. Effects on Cell Structures 32 C. Naming Viruses (Species) 15 1. Nuclei 32 D. Acronyms or Abbreviations 16 2. Mitochondria 33 E. Plant Virus Classification 17 3. Chloroplasts 33 F. Virus Strains 17 4. Cell Walls 33 G. Use of Virus Names 19 5. Cell Death 34 V. Viruses of Other Kingdoms 20 B. Virus-Induced Structures in the VI. Summary 21 Cytoplasm 34 1. Accumulations of Virus Particles 34 Chapter 2. Overview of Plant Viruses 2. Aggregates of Virus-Encoded Proteins 35 3. Caulimovirus Inclusions 35 I. Introduction 23 C. Why Inclusion Bodies? 37 II. Economic Losses Due to Plant Viruses 24 D. Cytological Structures 37 III. Virus Profiles 24 VII. The Host Range of Viruses 38 IV. Macroscopic Symptoms 25 A. Limitations in Host Range Studies 38 A. Local Symptoms 25 B. Patterns of Host Range 39 B. Systemic Symptoms 26 v vi CONTENTS C. The Determinants of Host Range 39 Chapter 4. Plant Virus Origins and 1. Initial Events 39 Evolution 2. Expression and Replication 39 3. Cell-to-Cell Movement 40 I. Introduction 63 4. Stimulation of Host-Cell Defences 40 II. Virus Evolution 64 VIII. Viruses in Other Kingdoms 40 A. Origins of Viruses 64 IX. Summary 40 B. Virus Variation 65 C. Types of Evolution 65 Chapter 3. Agents That Resemble or Alter 1. Microevolution and Macroevolution 65 Plant Virus Diseases 2. Sequence Divergence or Convergence 67 I. Viroids 43 3. Modular Evolution 67 A. Classification of Viroids 44 4. Sources of Viral Genes 67 B. Pathology of Viroids 44 a. Replicases 67 1. Macroscopic Disease Symptoms 44 b. Proteinases 68 2. Cytopathic Effects 44 c. Coat Proteins 70 3. Location of Viroids in Plants 45 d. Cell-to-Cell Movement Proteins 71 4. Movement in the Plant 45 e. Suppressors of Gene Silencing 71 5. Transmission 45 D. Selection Pressures for Evolution 71 6. Epidemiology 45 1. Adaptation to Niches 71 C. Properties of Viroid RNAs 45 2. Maximising the Variation 71 1. Sequence and Structure 45 3. Controlling the Variation 72 2. Replication 47 a. Muller’s Ratchet 73 3. Recombination Between Viroids 49 b. Muller’s Ratchet and Plant 4. Interference Between Viroids 49 Viruses 73 D. Molecular Basis for Biological Activity 50 4. Role of Selection Pressure 73 E. Diagnostic Procedures for Viroids 50 5. Selection Pressure by Host II. Phytoplasma 50 Plants 74 III. Satellite Viruses and Satellite RNAs 51 E. Timeline for Evolution 74 A. Satellite Plant Viruses (A-type) 52 1. Nonconstant Rates of Evolution 74 B. Satellite RNAs (satRNAs) 53 2. Estimated Rates of Evolution 74 1. Large Satellite RNAs (B-type) 53 III. Evidence for Virus Evolution 75 2. Small Linear Satellite RNAs (C-type) 53 A. Geminiviruses 75 3. Small Circular Satellite RNAs (D-type) 54 B. Closteroviruses 75 4. Satellite-Like RNAs 55 C. Luteoviruses 75 a. A Satellite RNA of Groundnut Rosette IV. Coevolution of Viruses with Their Hosts and Virus (GRV) 55 Vectors 80 b. Ancillary RNAs of Beet Necrotic Yellow V. Viruses of Other Kingdoms 80 Vein Virus (BNYVV) 56 VI. Summary 80 5. The Molecular Basis for Symptom Modulation 56 C. Satellite DNAs 57 D. Discussion 58 Section II IV. Defective and Defective Interfering Nucleic Acids 58 WHAT IS A VIRUS MADE OF? A. Group 1: Single Deletion D RNAs 60 B. Group 2: Multiple Deletion D and DI RNAs 60 Chapter 5. Architecture and Assembly of C. Defective DNAs Associated with DNA Virus Particles Viruses 60 V. Viruses of Other Kingdoms 60 I. Introduction 85 VI. Summary 61 II. Methods 86 CONTENTS vii A. Chemical and Biochemical Studies 86 VI. More Complex Isometric Viruses 101 B. Methods for Studying Size and Fine Structure VII. Enveloped Viruses 101 of Viruses 86 VIII. Assembly of Icosahedral Viruses 102 1. Hydrodynamic Measurements 86 A. Bromoviruses 102 2. Electron Microscopy 87 B. RNA Selection During Assembly of Plant 3. X-Ray Crystallography 87 Reoviruses 102 4. Neutron Small-Angle Scattering 87 IX. General Considerations 103 5. Atomic Force Microscopy 87 X. Viruses of Other Kingdoms 104 6. Mass Spectrometry 88 XI. Summary 104 7. Serological Methods 88 8. Stabilising Bonds 88 Chapter 6. Plant Viral Genomes III. Architecture of Rod-Shaped Viruses 88 A. Introduction 88 I. Introduction 105 B. Structure of TMV 89 II. General Properties of Plant Viral 1. General Features 89 Genomes 105 2. Virus Structure 90 A. Information Content 106 C. Assembly of TMV 92 B. Economy in the Use of Genomic Nucleic 1. Properties of the Coat Protein 92 Acids 106 2. Assembly of TMV Coat Protein 92 C. The Functions of Viral Gene Products 107 3. Assembly of the TMV Rod 92 1. Functional Proteins 107 a. Assembly in vitro 92 a. Proteins That Initiate Infection 107 b. Assembly in vivo 94 b. Proteins That Replicate the Viral IV. Architecture of Isometric Viruses 94 Genome 108 A. Introduction 94 c. Proteins That Process Viral Gene B. Possible Icosahedra 94 Products 108 C. Clustering of Subunits 97 d. Proteins That Facilitate Viral Movement D. Quasiequivalence 97 Through the Host 109 V. Small Icosahedral Viruses 97 e. Overcoming Host Defence Systems 109 A. Subunit Structure 97 f. Proteins That Facilitate the Host to Host B. Virion Structure 98 Movement of Viruses 109 1. T ¼ 1 Particles 98 D. Nucleic Acids 109 2. Other Particles Based on T ¼ 1 1. Multipartite Genomes 109 Symmetry 98 2. Nucleic Acid Structures 109 a. Bacilliform Particles Based on T ¼ 1 3. Noncoding Regions 109 Symmetry 98 a. End-Group Structures 109 b. Geminiviruses 99 b. 50 and 30 Noncoding Regions 112 3. T ¼ 3 Particles 99 c. Intergenic Regions 112 a. Bacilliform Particles Based on T ¼ 3 III. Plant Viral Genome Organisation 112 Symmetry 100 A. Structure of the Genome 112 b. Pseudo T ¼ 3 Symmetry 100 B. Recognising Activities of Viral 4. T ¼ 7 Particles 100 Genes 114 C. The Arrangement of Nucleic Acid Within 1. Location of Spontaneous or Artificially Icosahedral Viruses 100 Induced Mutations 114 1. RNA Structure 100 2.
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