Multiplication of RNA Plant Viruses. C.L. Mandahar

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2 Multiplication of RNA Plant Viruses C.L. Mandahar

3 MULTIPLICATION OF RNA PLANT VIRUSES

4 Multiplication of RNA Plant Viruses by C. L. MANDAHAR Botany Department, Panjab University, Chandigarh, India

5 A C.I.P. Catalogue record for this book is available from the Library of Congress. ISBN X (HB) ISBN (HB) ISBN ( e-book) ISBN (e-book) Published by Springer, P.O. Box 17, 3300 AA Dordrecht, The Netherlands. Figure on the front cover is reproduced from the The Journal of Cell Biology, November 1999, Vol. 147(5), p by copyright permission of The Rockefeller University Press, New York, USA Printed on acid-free paper All Rights Reserved 2006 Springer No part of this work 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, with the exception of any material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Printed in the Netherlands.

6 Photograph on the Front Cover The figure on the front cover presents a model to describe infection and replication of Tobacco mosaic virus (TMV) in Y2 tobacco protoplasts. Following introduction of virus to the cell, viral RNA is transported to the perinuclear endoplasmic reticulum (ER) on elements of the protein cytoskeleton, most likely microtubules (Fig. 1). The result ultimately leads to production of virus-specific proteins including viral replicase (R), and viral RNA (vrna) in ER associated virus replication complexes. The ERassociated nascent viral RNAs function as mrnas for the synthesis of movement protein (MP) that remains associated with the replication complexes (Fig. 2). Changes in different regions of TMV RNA-dependent RNA polymerase (RdRp/polymerase/ replicase) may alter cell-to-cell virus movement (Hirashima and Watanabe, 2001); in fact, the polymerase protein has been implicated in movement of TMV and Cucumber mosaic virus (CMV) in infected plants (Deom et al., 1997; Hirashima and Watanabe, 2001, 2003; Choi et al. 2005). Thus, both TMV MP and replicase are likely involved in TMV movement within and between cells. The MP remains associated with virus replication complexes (Kawakami et al., 2004) that comprise large ER-derived structures (Fig. 3), which can be regarded as replication complexes. Formation and anchoring of large virus replication complexes is stabilized by MP and microfilament (MF) interactions (Fig. 3). Actin microfilaments and other cytoskeletal elements transport vrna-mp complexes to the periphery of the cell to initiate cell-to-cell spread or toward other cellular sites where MP is degraded (Fig. 4). In late stages of infection in isolated protoplasts, vrna and MP are localized in hair-like structures that protrude from the surface of the cell through plasma membrane (Fig. 5). These protrusions may be related to desmotubules. Alternatively, they may be a consequence of cell damage, which results in the extrusion of ER through the plasma membrane. Thus, at least two types of ER appear to be involved in TMV infection; one type is involved in vrna replication and does not require the presence of MP while the second type corresponds to the filamentous protrusions that may be involved in intercellular spread of the virus and requires functional MP. Notes 1. The figure is reproduced from Más and Beachy The Journal of Cell Biology November 1999, Vol. 147(5), p , by copyright permission of The Rockefeller University Press, New York, USA. 2. Kawakami, S., Watanabe, Y., and Beachy, R. N Tobacco mosaic virus spreads cell-to-cell as intact replication complexes. Proc. Natl. Acad. Sci. USA 101: For other references, please see Chapter 5. RNA-Dependent RNA Polymerases and Replicases.

7 CONTENTS List of Tables Preface Acknowledgments xv xvii xix 1. Introduction I. Positive-Sense RNA Viruses 1 1 II. Putative Life/Replication Cycle of Plant Viruses 2 A. Core Promoters 7 B. Replication Complexes 8 C. Switches 8 III. cis-acting and trans-acting Viral Nucleotide Sequences A. cis-acting Sequences Internal Control Regions (Internal cis-acting Sequences) Role of cis Factors 3. cis-acting Sequences in Brome Mosaic Bromovirus RNAs B. trans-acting Viral RNA Nucleotide Sequences 14 IV. Host Gene Shut-off and Hijacking of Host Cellular Machinery by Viruses 15 A. Mechanisms of Shut-off 17 V. Classification and Nomenclature 19 A. Classification 19 B. Nomenclature 21 VI. Abbreviations 22 A. Plant Viruses 22 B. Other Abbreviations 23 VII. References Positive-Sense Viral RNA 29 I. Virus Genome 29 II. 5`-End 34 A. Cap or Cap-Like Structure 1. Mechanisms of Cap Formation a. Co-transcriptional Capping 36 b. Cap Snatching 39

8 viii Contents 2. Functions of Cap and Cap-Like Structure B. Genome-Linked Protein Functions 42 III. 3` -End 44 A. trna-like Structure Structure Aminoacylation Pseudoknot 4. Functions a. Role in Transcription (Negative-Strand RNA Synthesis) 51 b. Role in Viral RNA Replication 52 c. Roles of Pseudoknot 54 d. Other Functions B. Poly(A) Tail C. Repair Mechanism of 3` -End of Viral RNA 56 IV. Viral Genes 58 A. Genes of Positive-Sense RNA Viruses 58 V. Functions of Viral RNA 62 VI. References Infection by and Uncoating of Virus Particles 71 I. Infection 71 A. Entry of Virus Particle/Genome into a Cell 71 B. Cell-Infecting Unit 72 C. Nucleo-Cytoplasmic Shuttling 73 II. Uncoating of Virus Particles 75 A. Uncoating 76 B. Site(s) of Uncoating Extracellular Sites Intracellular Sites 78 C. Mechanism(s) of Uncoating Role of Ca 2+ Divalent Cations Role of ph Co-translational and Co-replicational Mechanisms 80

9 Contents ix D. Direction of Uncoating 82 III. References Replication of Plus-Sense Viral RNA 87 I. Introduction 87 II. Models of Viral RNA Replication 90 III. Negative-Strand RNA Synthesis 92 A. Model of Negative-Strand RNA Synthesis IV. Double-Stranded Forms of Replicative RNAs 96 A. Replicative Form RNA 97 B. Replicative Intermediate RNA 97 C. Double-Stranded RNAs as Artifacts 98 V. Synthesis of Progeny Positive-Strand RNA 98 VI. Asymmetry in Negative-Strand and Positive-Strand Progeny RNA 99 Synthesis VII. Time Course of Viral RNA, Viral Protein and Virus Particle Synthesis 100 VIII. Replication Promoters, Enhancers and Repressors 101 IX. Template Selection by Cognate Viral Replicases 104 X. Capsid Protein and Viral RNA Replication 105 A. Functions of Capsid Protein Alfalfa mosaic alfavirus a. Functions of Capsid Protein Bound to Inoculum Viral RNAs 107 b. Functions of Capsid Protein Expressed from Viral RNAs 3 and c. Switch Other Plant Viruses 111 XI. References RNA-Dependent RNA Polymerases and Replicases 119 I. Introduction 119 A. Time Course of Replicase Production 123 B. Isolation and Purification of Viral Replicases 124 II. Plant Viral Polymerases 125 III. Specificity 129

10 x Contents A. Specificity of Viral Polymerase Action Host Factors and Viral Polymerase Specificity 129 B. Absence of Specificity of Viral Polymerase Action 130 IV. Structure 131 A. Conserved Domains 131 B. Shape and Structure 132 C. Miscellaneous 133 V. Functions 134 A. Replication of Viral RNA Binding of Replicase and Role of cis-acting Elements B. Transcription of Viral RNA C. Recombination of Viral RNA 138 D. Evolution of Plant Viruses 139 E. Miscellaneous Functions 140 VI. Classification 141 VII. References Helicases 151 I. Introduction 151 A. Occurrence 152 B. Characteristics of Viral RNA Helicases 154 C. Nucleoside Triphosphate Connection 155 II. Classification 157 A. Relationship between Helicase Superfamilies III. Structure IV. Functions V. References Proteinases 167 I. Introduction 167 A. Classification Chymotrypsin-Like Cysteine and Serine Proteinases Papain-Like Cysteine Proteinases 172

11 Contents xi II. Serine and Serine-Like Proteinases 172 A. Family Potyviridae P1 Proteinase NIa Proteinase 174 B. Family Comoviridae Comovirus Proteinase Nepovirus Proteinase 177 a. Proteolytic Processing 177 b. Genome-Linked Protein (VPg) 179 C. Family Sequiviridae 179 D. Putative Serine Proteolytic Activities 180 E. Conclusions 180 III. Papain-like Cysteine Proteinases A. Main Papain-Like Cysteine Proteinases B. Leader Proteinases/Papain-Like Leader Proteinases Potyviruses Closteroviruses 185 IV. Aspartic Proteinases 186 V. Functions of Proteinases 187 VI. References Subgenomic RNAs 195 I. Introduction 195 A. 5`-Coterminal Subgenomic RNAs 199 B. 3`-Coterminal Subgenomic RNAs 200 II. Mechanisms of Subgenomic RNA Synthesis 202 A. Transcription or Promotion Mechanism 202 B. Termination Mechanism 204 C. Mechanism in Citrus tristeza closterovirus 204 D. Post-transcriptional Mechanism 205 III. Replication of Subgenomic RNA 205 IV. Subgenomic RNA Promoters 206 A. Structure and Recognition by Viral Polymerase 209 B. Subgenomic RNA Promoters of Some Plant Viruses 210 C. Location 212 D. Role 214

12 xii Contents V. Subgenomic RNAs of Some Plant Viruses 214 VI. Expression of Subgenomic RNAs 216 VII. Functions of Subgenomic RNAs 217 A. Temporal Regulation of Gene Expression 217 B. Role in Translation 218 C. Role in Infectivity 218 VIII. References Gene Expression 223 I. Introduction 223 A. Translation Initiation Factors Translation Initiation Factors and Plant Viruses II. Canonical Translation A. Translation Initiation 1. Aberrant Translation Initiation a. Leaky Scanning 228 b. Ribosomal Shunting and Internal Translation Initiation Scanning 230 B. Elongation Step of Translation 230 C. Termination of Translation D. Interference by Viral RNAs E. Translation of Viral RNAs 232 III. Translation Strategies of Viral RNAs 234 A. Regulation of Gene Expression at the Level of Genome Segments B. Regulation of Gene Expression at Transcription Level C. Regulation of Gene Expression at Translational Level Regulation of Gene Expression at Translation Initiation Level 237 a. Factors Affecting Translation Initiation 237 b. Unconventional Translation Initiation Regulation of Gene Expression at Translation Elongation Level (Frameshifting) 242 a. Types of Frameshifting Regulation Gene Expression at Translation Termination (Readthrough) 246 a. Readthrough Mechanisms 248 b. Functions of Readthrough Mechanism Regulation of Gene Expression at Post-translational Level (Proteolytic Processing of Polyproteins) 250

13 Contents xiii IV. Cap-Independent Translation 251 A. Cap-Independent Translation Enhancer (CITE) at 3` -End of Viral RNA 1. Functions of 3-CITE ` Domain 255 B. Cap-Independent Translation Enhancer at 5`-End of Viral RNA 256 C. Internal Ribosome Entry Sites (IRES) Translation Mechanism Advantages of IRES D. Plant Viruses Showing Cap-Independent Translation Plant Viruses Lacking Both 5` -Cap Structure and 3`-Poly(A) Tail 2. Plant Viruses Lacking 5`-Cap Structure but 3`-Poly(A) Tail Present 3. Plant Viruses Lacking 3`-Poly(A) Tail but 5`-Cap Structure Present 260 E. Conclusions 261 V. References Assembly of Virus Particles 271 I. Introduction 271 II. Assembly of Rod-Like Virus Particles 272 A. Tobacco mosaic tobamovirus Assembly of Capsid Protein in vitro Assembly of Virus Particles in vitro 274 a. Nucleation (Assembly Initiation) 275 b. Elongation Mechanism 277 c. Conclusions Assembly of Virus Particles in vivo 278 B. Assembly of Other Rod-Like Viruses 279 III. Assembly of Flexuous Virus Particles 280 IV. Assembly of Icosahedral Virus Particles 282 A. Southern bean mosaic sobemovirus, Tomato bushy stunt tombusvirus, and Satellite tobacco necrosis virus 283 B. Alfalfa mosaic alfamovirus 285 C. Bromoviruses Brome mosaic bromovirus 287 a. Polymorphic Capsids 288 b. Capsid Protein-RNA Interactions Cowpea chlorotic mottle bromovirus 291 D. Other Spherical Plant Viruses 291

14 xiv Contents V. Specificity of Virus Assembly 292 VI. Conclusions 294 VII. References Host Factors and Virus Multiplication 299 I. Introduction 299 II. Host Proteins and Membranes 299 III. Functions of Cellular Factors 302 IV. Sites of Viral RNA Replication 304 A. Cytoplasm Cytoplasmic Inclusions (Viroplasms) Endoplasmic Reticulum 305 B. Chloroplasts 307 C. Other Cellular Organelles 307 V. Replication Complexes 309 A. Replication Complex of Brome mosaic bromovirus 311 B. Replication Complex of Cucumber mosaic virus 313 C. Replication Complex of Tobacco mosaic virus 313 D. Replication Complex of Cucumber necrosis tombusvirus 315 E. Replication Complexes of Other Plant Viruses 316 F. Structure of Replication Complexes 316 VI. Membrane-Targeting and Anchoring of Replication Complexes 318 VII. Vesiculation 319 A. Functions of Vesicles 321 B. Viral Signals Inducing Formation of Vesicles 322 VIII. References Subject Index

15 S. No. LIST OF TABLES Heading Page No. 1 Characteristics of single-stranded positive-sense RNA genomes of plant viruses 32 2 Genes of positive-sense RNA genomes of plant viruses 59 3 Classification, lineage and mode of expression of RNA-dependent RNA polymerases of families and genera of positive-sense RNA plant viruses RNA-dependent RNA polymerases of some positive sense RNA plant viruses Plant viruses belonging to different helicase superfamilies and lineages Plant virus groups and genera encoding different types of demonstrated or putative proteinases Polyprotein precursors, cleavage products and proteinases of some positive-sense RNA plant viruses Positive-sense RNA plant viruses that produce subgenomic RNAs Positive sense RNA plant viruses showing frameshifting mechanism Positive-sense RNA plant viruses showing readthrough mechanism Proteins of host plants of Arabidopsis thaliana and of Saccharomyces cerevisiae that interact with viral RNAs or RdRps subunits of plant alpha-like plant viruses 301 xv