List of titles Already published Cell Differentiation J. M. Ashworth Functions of Biological Membranes M. Davies Cellular Development D. Garrod Brain Biochemistry H. S. Bachelard Immunochemistry M. W. Steward The Selectivity of Drugs A. Albert Biomechanics R. McN. Alexander Molecular Virology T. H. Pennington, D. A. Ritchie Hormone Action A. Malkinson Cellular Recognition M. F. Greaves Cytogenetics of Man and other Animals A. McDermott RNA Biosynthesis R. H. Burdon Protein Biosynthesis A. E. Smith Biological Energy Conservation C. Jones Control of Enzyme Activity P. Cohen Metabolic Regulation R. Denton, C. I. Pogson Plant Cytogenetics D. M. Moore Population Genetics L. M. Cook Membrane Biogenesis J. Haslam Insect Biochemistry H. H. Rees A Biochemical Approach to Nutrition R. A. Freedland, S. Briggs Enzyme Kinetics P. C. Engel Polysaccharide Shapes D. A. Rees Human Genetics J. H. Edwards Cellular Degradative Processes R. T. Dean Transport Phenomena in Plants D. A. Baker Human Evolution B. A. Wood In preparation The Cell Cycle S. Shall Microbial Metabolism H. Dalton Bacterial Taxonomy D. Jones, M. Goodfellow Metal Ions in Biology P. M. Harrison, R. Hoare Photobiology K. Poff Muscle R. M. Simmons Xenobiotics D. V. Parke Biochemical Systematics J. H. Harborne Biological Oscillations A. Robertson Motility of Living Cells P. Cappuccinelli Isoenzymes in Biology R. Taylor, R. Rider Cloning DNA Molecules D. M. Glover Invertebrate Nervous Systems G. Lunt New editions Biochemical Genetics (2nd edition) R. A. Woods OUTLINE STUDIES IN BIOLOGY Editor's Foreword The student of biological science in his fmal years as an undergraduate and his first years as a graduate is expected to gain some familiarity with current research at the frontiers of his discipline. New research work is published in a perplexing diversity of publications and is inevitably concerned with the minutiae of the subject. The sheer number of research journals and papers also causes confusion and difficulties of assimilation. Review articles usually presuppose a background knowledge of the field and are inevitably rather restricted in scope. There is thus a need for short but authoritative introductions to those areas of modern biological research which are either dealt with in standard introductory textbooks or are not dealt with in sufficient detail to enable the student to go on from them to read scholarly reviews with profit. This series of books is designed to satisfy this need. The authors have been asked to produce a brief outline of their subject assuming that their readers will have read and remembered much of a standard introductory textbook of biology. This outline then sets out to provide by building on this basis, the conceptual framework within which modern research work is progressing and aims to give the reader an indication of the problems, both conceptual and practical, which must be overcome if progress is to be maintained. We hope that students will go on to read the more detailed reviews and articles to which reference is made with a greater insight and understanding of how they fit into the overall scheme of modern research effort and may thus be helped to choose where to make their own contribution to this effort. These books are guidebooks, not textbooks. Modern research pays scant regard for the academic divisions into which biological teaching and introductory textbooks must, to a certain extent, be divided. We have thus concentrated in this series on providing guides to those areas which fall between, or which involve, several different academic disciplines. It is here that the gap between the textbook and the research paper is widest and where the need for guidance is greatest. In so doing we hope to have extended or supplemented but not supplanted main texts, and to have given students assistance in seeing how modern biological research is progressing, while at the same time providing a foundation for self help in the achievement of successful examination results. J. M. Ashworth, Professor of Biology, University of Essex. Molecular Virology T. H. Pennington Professor ofB acteriology University of Aberdeen and D. A. Ritchie Professor of Genetics University of Liverpool LONDON CHAPMAN AND HALL A Halsted Press Book JOHN WILEY & SONS, INC., NEW YORK First published in 1975 by Chapman and Hall Ltd 11 New Fetter Lane, London EC4P 4EE Reprinted 1979 © 1975 T. H. Pennington and R. A. Ritchie Typeset by Preface Ltd, Salisbury, Wilts and London, Colchester and Beccles ISBN 978-0-412-12590-4 ISBN 978-94-010-9532-7 (eBook) DOl 10.1007/978-94-010-9532-7 This paperback edition is sold subject to the condition that it shall not, by way of trade or otherwise, be lent, re-sold, hired out, or otherwise circulated without the publisher's prior consent in any form of binding or cover other than than in which it is published and without a similar condition including this condition being imposed on the subsequent purchaser. All rights reserved. No part of this book may be reprinted, or repro duced or utilized in any form or by any electronic, mechanical or other means, now known or hereafter invented, including photocopying and recording, or in any information storage and retrieval system, without permission in writing from the Publisher. Distributed in the U.S.A. by Halsted Press, a Division of John Wiley & Sons, Inc. New York Library of Consress Cataloging in Publication Data Pennington, T H Molecular virology. (Outline studies in biology) Bibliography: p. Includes index. 1. Virology. I. Ritchie, D. A., Joint author. II. Title. [DNLM: 1. Viruses. 2. Molecular biology. Qw160 P414m] Qr360.P46 576'.64 75-22112 ISBN-13: 978-0-412-12590-4 Contents 1 Introduction page 7 1.1 Historical development of molecular virology 7 1.2 What is a virus? 8 1.3 Titration of viruses 8 1.4 Virus-host interactions 9 2 The virion 11 2.1 Principles of virion construction 11 2.2 Special features of virion anatomy 11 2.2.1 Particles with cubic symmetry 11 2.2.2 Filamentous viruses with helical symmetry 13 2.2.3 Viruses with a lipid-containing membrane containing virus-induced proteins (envelope) 13 2.2.4 Tailed bacteriophages 14 2.2.5 Poxviruses 15 2.3 Viral nucleic acids 15 2.4 The virion: function 18 2.4.1 Transmission of infection 18 2.4.2 Initiation of infection 18 2.4.3 Adsorption 18 2.4.4 Entry 19 2.4.5 Functions of the virion after entry - virion enzymes 19 3 The virus-infected cell 22 3.1 Transcription and translation in the virus-infected cell 22 3.1.1 Double-stranded DNA viruses (Group I) 22 3.1.2 Single-stranded DNA viruses (Group II) 28 3.1.3 Double-stranded RNA viruses (Group III) 29 3.1.4 Single-stranded RNA viruses whose mRNA is identical in base sequence to virion RNA (Group IV) 29 3.1.5 Single-stranded RNA viruses, genome complementary in sequence to mRNA (Group V) 31 3.1.6 Single-stranded RNA genome with a DNA intermediate in their growth (Group VI) 32 3.2 Post-translational modification of proteins 32 3.3 Genome replication 32 3.3.1 Replication of DNA genomes 32 3.3.2 Replication of RNA genomes 37 3.4 Virus assembly 38 3.5 Virus release 40 3.6 Temperate phage and lysogeny 41 3.6.1 The nature of prophage 41 3.6.2 The control of lysogeny 42 4 Virus genetics 44 4.1 Mutations 44 4.1.1 Specific mutations 44 4.1.2 General systems 45 4.2 Functional or complementation analysis 46 4.3 Fundamental studies in recombination 47 4.4 Chromosome mapping 48 4.4.1 Genetic maps 49 4.4.2 Physical maps and their relationship to genetic maps 49 4.5 Genetic recombination 51 5 Tumour virology 54 5.1 What is a tumour? 54 5.2 Causation of tumours 54 5.3 Papovaviruses 54 5.3.1 Transformation by polyoma virus and SV40 56 5.4 RNA tumour viruses 58 5.4.1 General properties 58 5.4.2 Growth and transformation 59 5.4.3 Reverse transcriptase 60 5.4.4 Genetics of RNA tumour viruses 61 5.5 Comparison of transformation by DNA and RNA tumour viruses; oncogene theory 62 Suggestions for further reading 63 Index 64 1 Introduction 1.1 Historical development of molecular virology of effort on a limited number of phages, Viruses have occupied a central position in notably the Escherichia coli phages T2 and T4. molecular biology ever since its development as At the same time Lwoff and his colleagues were an independent discipline. Indeed, molecular studying phage A, a temperate phage of E. coli, biology itselflargely developed out of the work which was to lead to equally fundamental pioneer studies of Delbriick, Luria and Hershey, observations on the regulation of macro who realized, in the late 1930's, that bacterial molecular synthesis. viruses (bacteriophages, often abbreviated to The study of animal and plant viruses has its phages) had properties which made them origins in the latter half of the 19th century uniquely suitable as a model system for an and was largely initiated by workers in medical, attack on one of the then outstanding problems veterinary and agricultural disciplines. Many of of biology, the definition of the gene in their practical successes owe little to molecular physical and chemical terms. The favourable biology, stemming instead from those properties of these viruses include the rapidity approaches successful in combating other of their growth, their ease of assay, and the parasites, such as vector control and the availability of easily scored genetic markers. breeding of resistant varieties of plants. The Taken together, this means that quantitative introduction of new tissue culture techniques in genetic experiments can be done very qUickly. the early 1950's was, however, an event The small size ofviruses also suggested that crucial in the development of animal virology, their structure would be simple, which, in turn, both as an applied subject and as a branch of led to the belief that this kind of system would molecular biology. The development by be suitable for biochemical and physiological Dulbecco of a simplified assay for the titration studies. of animal viruses based on the standard plaque During the next two decades a small group assay method used with phage was another of phage workers uncovered a series of funda crucial event at this time. mental principles which laid the foundations of The development of animal virology owes modern virology and which had far-reaching much to concepts derived from phage studies effects on biological research in general. These and, to a lesser extent, plant viruses. However, studies established the basic pattern of virus in recent years many important features of replication, confirmed the identification of the animal viruses have been described which have nucleic acid molecule as the genetic material, no bacteriophage parallels. These include and led to fundamental advances in the the phenomenon of virion maturation by bud understanding of gene structure. An important ding from cell transformation and reverse factor during this period was the concentration transcription. 7 1.2 What is a virus? genomes, and these groups are further sub A recent defInition of the term virus (Luria and divided into viruses with single-and double Darnell, 1%8) runs 'Viruses are entities whose stranded genomes. genome is an element of nucleic acid, either Three major groups of viruses can be DNA or RNA, which reproduces inside living distinguished on the basis of host specificity; cells and uses their synthetic machinery to viruses of bacteria and blue-green algae, plant direct the synthesis of specialized particles, the viruses, and animal viruses. Many members of virions, which contain the viral genome and these groups show specialized features con transfer it to other cells'. nected with the problem of gaining entry into Viruses differ from other obligate intra and replicating in their particular host cells. A cellular parasites (such as Rickettsiae, and the good example of features restricted to one of Psittacosis group of organisms) in several these groups is the complex structure that fundamental respects, including: many bacteriophages have evolved to overcome (1) Virus particles (virions) contain only one the problem of introducing their nucleic acids type of nucleic acid: this can be either DNA or into their hosts through the barrier of the RNA. tough, rigid, bacterial cell wall. Animal viruses (2) Virus-specified proteins are synthesized do not encounter such a barrier and plant using host ribosomes. viruses enter cells in different ways. (3) Viruses multiply by independent synthesis of their constituent parts which are 1.3 Titration of viruses then assembled to reconstitute new virus Quantitative analysis demands methods for the particles, rather than by growth and division. determination of the numbers of virus particles Virus particles consist essentially of nucleic in a sample. Many methods are available. Some acid (the virus genome) surrounded by a of these assay virus particles directly e.g. protein coat. The function of the coat is to electron microscopy and haem agglutination of protect the nucleic acid from the harsh extra red blood cells, whereas others measure the cellular environment, to facilitate its entry into infectious titre of a virus stock. These two host cells, and, in many animal viruses, to play types of method may not give the same titre an important role in the initiation of virus since not all virions may be infectious. For macromolecular synthesis during the early part phages there is generally a one to one corres of infection. The structure of virus particles pondence between physical and infectious varies enormously in complexity. Many plant particles; for animal viruses the infectious titre viruses, for example, contain a single small is usually lower than the number of particles. A RNA molecule packaged in a coat made up of typical phage assay involves mixing a suitable many identical copies of a single protein, dilution of virus (e.g. containing 100-200 whereas some animal virus particles have coats infectious particles) with a concentrated made up of multiple copies of at least 30 suspension of bacteria (about 108 cells) sus different proteins surrounding an extremely pended in molten agar held at 45°C. This long DNA molecule. Likewise the size of virus mixture is poured over the surface of a petri particles also varies considerably from one type plate containing solidified nutrient agar, to to another. A starting point in most schemes of form a thin layer which soon hardens, thus virus classification is the chemical nature of the immobilizing the phage and bacteria. The plate virus genome; thus viruses are grouped into is incubated to permit multiplication of the those with DNA genomes and those with RNA bacteria which forms a confluent film of cells 8 over the agar surface, except where an in molecular synthesis and some even cause the fectious phage particle has been deposited. At breakdown of host components to provide this site the virus infects a cell and multiplies building blocks for their own synthesis. within it. The crop of a hundred or so progeny Productive infections of cells without cell death liberated from this cell infect adjacent bacteria do occur, however. The viruses causing this which in tum produce further virus. Thus a type of infection have evolved methods of local chain-reaction develops which after a few virion release which do not cause irreversible hours is visible as a clearing in the otherwise cell damage. Many animal viruses, for example, dense lawn of confluent bacteria. This clear are released from the cell membrane by a zone is known as a plaque. By counting the budding process, during which the virus number of plaques a direct estimate of the incorporates a small piece of modified cell number of infectious virus particles is obtained. membrane as one of its structural components. The plaque assay for animal viruses developed This type of infection is compatible not only by Dulbecco is basically similar. Virus is added with cell survival but also with simultaneous to a sheet of tissue culture cells growing in growth of the infected cell and virus produc liquid medium on the flat bottom of a dish. tion. Mter allowing the virus to adsorb to the cells, a In chronological order the events which take layer of molten agar containing nutrient place during the virus growth cycle are: medium is poured over the cells and allowed to (l) Adsorption of the virion to the cell harden. This prevents free diffusion of virus surface. through the medium. As with the phage assay, (2) Entry of the virus nucleic acid (bacterio local areas of virus growth, each starting from phages) or whole or part of the virion (animal one infected cell, are produced in the cell sheet. viruses) into the cell. As cell death rather than cell lysis is the (3) Transcription and translation of viral common end result of animal virus infections, mRNA from the virus genome. plaques are usually detected by staining with (4) Genome replication. dyes which are only taken up by living cells; the (5) Assembly of progeny virions and their plaques stand out as colourless areas against a release from the cell. stained background ofuninfected cells. The whole process is known as the virus growth cycle. The growth cycles of bacterio 1.4 Virus-host interactions phages are usually short, being measured in Cell death is a common end result of virus minutes, whereas animal viruses have much infection. Many bacteriophages, for example, longer growth cycles (Fig. 1.1). This is probably only escape from the host after cell lysis, and related to the faster metabolic processes found these viruses have evolved special mechanisms in bacteria, which, of course, have much shorter to break down the cell wall and membrane growth cycles than eukaryotic cells. when virus growth is completed. Cells infected Not all virus infections lead to progeny with many animal viruses do not lyse at the end production. Some of the reasons for this are of the virus growth period, and a contributory self-evident, including host resistance (host factor to their death is that during infection virus relationships are often highly specific, e.g. these viruses selectively and irreversibly tum off poliovirus will not infect non-primate cells host DNA, RNA and protein synthesis in favour because they lack surface receptors for virus of their own macromolecular synthesis. Many adsorption). In other situations, however, the bacteriophages also turn off host macro- virus genome may enter the cell and remain 9 100 000 Poliovirus 10000 -'.8 . 1000 Vaccinia virus c: o Adenovirus '': 100 :> 10 20 40 Minutes (T4) ! , , , , 5 10 15 , , , 2,0 Hours (others) Time after infection Fig 1,1 Growth curves of animal and bacterial viruses. there, sometimes for many cell generations, many DNA viruses this may happen during the without concomitant virus production. The course of a productive infection. Rarely, and classical example of this type of host-virus usually only under special conditions in the interaction is the lysogeny of bacteria by laboratory, integration of the DNA of these bacteriophages. Here, after infection, the virus viruses may be accompanied by striking changes DNA inserts itself into and becomes covalently in cell morphology and growth patterns linked to the bacterial chromosome. An (transformation); such cells may cause tumours efficient mechanism under virus control then in susceptible hosts (Chapter 5). Many types of ensures that this situation is maintained until RNA tumour virus, however, transform cells certain environmental conditions occur, when efficiently and continue to grow in the trans the virus genome is excised from the host formed cells. The genome of these cells contain chromosome and virion production and cell covalently linked DNA copies of the RNA virus lysis occur. genome. Latency as exhibited by herpiviruses is Many animal viruses can also integrate their another example of the long-term association nucleic acid into the host cell genome. With of virus and host cell. 10