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Regulation of Gene Expression in Animal Viruses NATO ASI Series Advanced Science Institutes Series A series presenting the results of activities sponsored by the NATO Science Committee, which aims at the dissemination of advanced scientific and technological knowledge, with a view to strengthening links between scientific communities. The series is published by an international board of publishers in conjunction with the NATO Scientific Affairs Division A Life Sciences Plenum Publishing Corporation B Physics New York and London C Mathematical and Physical Sciences Kluwer Academic Publishers D Behavioral and Social Sciences Dordrecht, Boston, and London E Applied Sciences F Computer and Systems Sciences Springer-Verlag G Ecological Sciences Berlin, Heidelberg, New York, London, H Cell Biology Paris, Tokyo, Hong Kong, and Barcelona I Global Environmental Change Recent Volumes in this Series Volume 234—Development of the Central Nervous System in Vertebrates edited by S. C. Sharma and A. 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Godfrey, and Enrico Mugnaini Volume 240—Regulation of Gene Expression in Animal Viruses edited by Luis Carrasco, Nahum Sonenberg, and Eckard Wimmer Series A: Life Sciences Regulation of Gene Expression in Animal Viruses Edited by Luis Carrasco Universidad Autönoma de Madrid Madrid, Spain Nahum Sonenberg McGill University Montreal, Canada and Eckard Wimmer State University of New York at Stony Brook Stony Brook, New York Springer Science+Business Media, LLC Proceedings of a NATO Advanced Study Institute on Regulation of Gene Expression in Animal Viruses, held May 30-June 8, 1992, in Mallorca, Spain NATO-PCO-DATA BASE The electronic index to the NATO ASI Series provides full bibliographical references (with keywords and/or abstracts) to more than 30,000 contributions from international scientists published in all sections of the NATO ASI Series. Access to the NATO-PCO-DATA BASE is possible in two ways: —via online FILE 128 (NATO-PCO-DATA BASE) hosted by ESRIN, Via Galileo Galilei, I-00044 Frascati, Italy —via CD-ROM "NATO-PCO-DATA BASE" with user-friendly retrieval software in English, French, and German (©WTV GmbH and DATAWARE Technologies, Inc. 1989) The CD-ROM can be ordered through any member of the Board of Publishers or through NATO-PCO, Overijse, Belgium. Library of Congress Cataloging in Publication Data Regulation of gene expression in animal viruses / edited by Luis Carrasco, Na hum Son en berg, and Eckard Wimmer. p. cm.—(NATO ASI series. Series A, Life sciences; v. 240) "Proceedings of a NATO Advanced Study Institute on Regulation of Gene Expression in Animal Viruses, held May 30-June 8,1992, in Mallorca, Spain"—T.p. verso. Includes bibliographical reference and index. ISBN 978-1-4613-6271-5 ISBN 978-1-4615-2928-6 (eBook) DOI 10.1007/978-1-4615-2928-6 1. Viral genetics—Congresses. 2. Genetic regulation—Congresses. I. Carrasco, Luis, 1949- II. Sonenberg, Nahum. III. Wimmer, Eckard. IV. North Atlantic Treaty Organization. Scientific Affairs Division. V. NATO Advanced Study Institute on Regulation of Gene Expression in Animal Viruses (1992: Palma, Spain) VI. Series. [DNLM: 1. Gene Expression Regulation, Viral—congresses. 2. Genes, Viral—congresses. QW160 R344 1992] QR456.R44 1993 576'.6484-<Jc20 DNLM/DLC 92-48456 for Library of Congress CIP ISBN 978-1-4613-6271-5 © 1993 Springer Science+Business Media New York Originally published by Plenum Press in 1993 Softcover reprint of the hardcover 1st edition 1993 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 PREFACE Viruses, being obligatory parasites of their host cells, rely on a vast supply of cellular components for their replication, regardless of whether infection leads to cell death or to the state of persistence. Animal viruses are providing scientists with relatively simple models to study the molecular biology of genome replication and gene expression. Whereas viruses use, in general, pathways of macromolecular biosynthesis common to the host cell, they have a cunning ability to adopt unusual mechanisms of gene expression and gene replication, provided these special pathways offer an advantage in competition for cellular resources. Any study of viral gene expression and replication is likely to lead also to new insights in cellular metabolism. The discoveries of cis-acting regulatory elements in transcription, the phenomenon of splicing of pre mRNA, and cap-dependent and cap-independent initiation of translation may be cited as examples. In addition, animal virus genomes contain elements and encode proteins that are very useful for the design of vectors for gene cloning and expression in mammalian cells. Apart from the basic interest in their biology, viruses have gained notoriety, of course, because they are pathogens. Human animal viruses may cause diseases ranging from the deadly (AIDS) to the benign (common cold). All studies on animal viruses potentially lead to the development of tools for their control, be it through prevention by immunization or treatment with antiviral drugs. Finally, viruses have yielded invaluable reagents in molecular biology as, for example, the vaccinia virus vector for the expression of foreign genes. This volume contains contrubutions from the faculty of a NATO Advanced Study Institute. The articles summarize the subjects presented at a meeting entitled "The Regulation of Gene Expression in Animal Viruses" that took place in Mallorca, Spain, in May/June, 1992; they convey, in the opinion of the editors, an unabated excitement about basic research in animal virology. v The aim of the Mallorca meeting was to gather scientists and students interested in different animal viruses. Many aspects of molecular virology and concepts of viral pathogenesis were discussed: virus structure at the atomic level, gene expression of DNA viruses, molecular biology and gene variation of viruses containing reverse transcriptase, gene expression and pathogenicity of RNA viruses with double- and single-stranded RNA genomes. This overview is far from complete but it summarizes important topics of a rapidly moving field in biological sciences that has had, and will continue to have, an enormous impact on diverse disciplines such as basic cell biology and human health care. June, 1992 Luis Carrasco Nahum Sonenberg Eckard Wimmer vi CONTENTS Structure ofa human rhinovirus complexed with its receptor molecule ............... 1 Norman H. Olson, Prasanna R. Kolatkar, Marcos A. Oliveira, R. Holland Cheng, Jeffrey M. Greve, Alan McClelland, Timothy S. Baker, and Michael G. Rossmann Cascade regulation of vaccinia virus gene expression .......................................... 13 Bernard Moss Regulation of alpha and gamma gene expression in cells infected with herpes simplex viruses ................................................................................ 25 D. Spector, F.C. Purves, R.W. King, and B. Roizman Transcriptional activation by the adenovirus EIA proteins ............................... .43 Brian A. Lewis and Thomas Shenk Mechanisms regulating nucleocapsid formation of the hepatitis B viruses .......................................................................................................... 49 Ralf Bartenschlager and Heinz Schaller Transcriptional activation by the hepatitis B virus X protein ............................. 67 Robert Lucito and Robert J. Schneider Regulation of human immunodeficiency virus structural protein expression ..................................................................................................... 81 and virion formation Hans-Georg KraussIich Transcription factors of the ETS family: The example ofC-ETSl ....................... 93 Kay Macleod, Bernard Vandebunder, and Dominique Stehelin Infectious influenza viruses from eDNA-derived RNA: reverse genetics .......... 107 Adolfo Garcia-Sastre and Peter Palese Structure and function of the vesicular stomatitis virus RNA- dependent RNA polymerase ...................................................................... 115 Sailen Barik, Adrienne Takacs, Tapas Das, David Sleat, and Amiya K. Banerjee vii RNA Synthesis and mRNA Editing in Paramyxovirus Infections ..................... 125 Joseph Curran, Thierry Pelet, Jean-Philippe Jacques, and Daniel Kolakofsky Antigenic variation of human respiratory syncytial virus G Glycoprotein: Genetic mechanisms and evolutionary significance ................................................................................................. 141 Jose A. Melero, Paloma Rueda, and Blanca Garcia-Barreno Translation regulation by reovirus structural proteins ...................................... 151 Aaron J. Shatkin, Ramona M. Lloyd, Laurie S. Seliger, and Lucia Tillotson The regulation of coronavirus gene expression ................................................... 163 Stuart G. Siddell Interaction of initiation factors and capsid protein with the cap structure of chimaeric MRNAS containing the 5' untranslated regions of the RNAS of semliki forest virus .............................................. 171 Gerda Berben-Bloemheuvel and Harry O. Voorma Aspects of the molecular biology of poliovirus replication .................................. 189 James Harber and Eckard Wimmer 3CD Cleavage of the poliovirus PI precursor: a model for complex proteinase/substrate interactions ............................................................. 225 Wade S. Blair, Xiaoyu Li, and Bert L. Semler Studies on the mechanism of internal initiation of translation on poliovirus RNA ........................................................................................... 245 Karen Meerovitch and Nahum Sonenberg Picornavirus Variation .......................................................................................... 255 Esteban Domingo, Cristina Escarmis, Encarnaci6n Martinez-Salas, Montserrat Martin, Mauricio G. Mateu, and Miguel A. Martinez Modification of membrane permeability by animal viruses ............................... 283 Luis Carrasco, Luis,per.e.z, Alicia Irurzun, Juan Lama, Francisco Martinez-Abarca, Pedro Rodriguez, Rosario Guinea, Jose Luis Castrillo, Miguel Angel Sanz and ~ Jose Ayala Poliovirus neurovirulence and its attenuation .................................................... 305 Vadim I. Agol Index ....................................................................................................................... 323 viii STRUCTURE OF A HUMAN RHINOVIRUS COMPLEXED WITH ITS RECEPI'OR MOLECULE Norman H. Olson!, Prasanna R. Kolatkar!, Marcos A. Oliveira!, R. Holland Cheng!, Jeffrey M. Greve2, Alan McClelland2,3, Timothy S. Baker! and Michael G. Rossmann!,4 !Department of Biological Sciences Purdue University West Lafayette, Indiana 47907-1392, USA 2Institute for Molecular Biologicals Miles INC. 400 Morgan Lane West Haven, Connecticut 06516-4175, USA 3Present address: Genetic Therapy INC. 19 Firstfield Road Gaithersburg, Maryland, 20878, USA 4To whom correspondence should be addressed. INTRODUCTION Human rhinoviruses are one of the major causes of the common cold. They, like other picornaviruses, are icosahedral assemblies of 60 protomers that envelope a single, positive-sense strand of RNA. Each protomer consists of four polypeptides, VP1 -VP4. The three external viral proteins (VP1 - VP3) each have an approximate molecular weight of 30,000 and a similar folding topology (Rossmann et ai., 1985; Hogle et ai., 1985). The external viral radius is -150 A and the total molecular weig-ht is roughly 8.5 x 106. A surface depression, or canyon, that is about 12 A deep and 12 - 15 A wide, encircles each pentagonal vertex (Fig. 1C). Residues lining the canyon are more conserved than other surface residues among rhinovirus serotypes3. The most variable surface residues are at the sites of attachment of neutralizing antibodies (Rossmann et ai., 1985; Sherry and Ruecker, 1985; Sherry et ai., 1986). It has been proposed that the cellular receptor molecule recognized by the virus binds to conserved residues in the canyon, thus escaping neutralization by host antibodies that are too big to penetrate into that region. This hypothesis (Rossmann et ai., 1985; Rossmann, 1989) is supported by site-directed mutagenesis of residues lining the canyon which alters the ability of the virus to attach to HeLa cell membranes (Colonno et ai., 1988). Regulation of Gene Expression in Animal Viruses, Edited by L. Carrasco et al., Plenum Press. New York, 1993 Figure 1. Cryoelectron microscopy of HRV16 particles and their complex with D1D2. (A) Native HRV16. (B) HRV16:D1D2 complex. D1D2 molecules (the two amino terminal domains of ICAM-l) are seen edge-on at the periphery of the virions (large arrow), or end-on in projection (small arrow). Cryoelectron microscopy was performed essentially as described by Cheng et al. (1992) with images recorded at a nominal magnification of 49,OOOX and with an electron dose of -20e-/A2. (C) Schematic diagram of HRV showing the icosahedral symmetry, subunit organization and canyon (shaded). Thick lines encircle five protomers ofVP1, VP2, and VP3. The fourth viral protein, VP4, is inside the capsid. (D) Stereoview of the reconstruction of the HRV16:D1D2 complex, viewed along an icosahedral twofold axis in approximately the same orientation as in (C). Sixty D1D2 molecules are bound to symmetry-equivalent position at the twelve canyon regions on the virion. The reconstruction was modified to correct for defocus and amplitude contrast effects present in the original micrographs (R.H. Cheng, manuscript submitted). (E) Shaded-surface view of HRV14, computed from the atomic structure (Rossmann et al., 1985), truncated to 2o·A resolution. The triangular outline of one icosahedral asymmetric unit corresponding to that in (C) is indicated. Also, conformational changes in the floor of the canyon, produced by certain antiviral agents that bind into a pocket beneath the canyon floor, inhibit viral attachment to cellular membranes (Pevear et al., 1985). Conservation of the viral attachment site inside a surface depression has been observed for Mengo (Kim et al., 1990) and influenza virus (Weis et al., 1988; Colman et al., 1983). There are well over 100 rhinovirus serotypes, which can be divided into roughly two groups according to the cellular receptor they recognize (Abraham and Colonno, 1984; Uncapher et al., 1991). The structures of human rhinovirus 14 (HRV14) (Rossmann et al., 1985), which belongs to the major group of serotypes, and of HRV1A (Kim et ai., 1989), which belongs to 2
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