RNA Genetics

Volume II: Retroviruses, Viroids, and RNA Recombination

Esteban Domingo

• Publisher: CRC Press
• Year: 2018
• ISBN:
  9781351093330
• Edition: 1
• Topic: Biowissenschaften
• Subtopic: Mikrobiologie

This book describes the basic features of virus replication, and points out how these features lead into the diverse biologies and genetics of the various viruses.

Reverse Transcribing Viruses and Retrotransposons

Chapter 1

REPLICATION OF RETROVIRUS GENOMES

John M. Coffin

TABLE OF CONTENTS

I.	Introduction
II.	Overview and Statement of the Problem
III.	The Virion
IV.	The Genome
V.	Replication
	A.	Initial Events
	B.	Integration
	C.	Expression
	D.	RNA Processing
	E.	Protein Synthesis and Processing
	F.	Transactivation
VI.	Consequences of Retrovirus Replication
	A.	Transformation and Oncogenes
	B.	Cytopathic Interactions
VII.	Evolution and Genetics
References

I. INTRODUCTION

The study of retroviruses has proven to be a remarkably fruitful endeavor. Although regarded for many years as curiosities of little direct relevance, no one would presently dispute the importance of these agents to modern biology. Retroviruses are now universally recognized as important human and animal pathogens, as valuable models for carcinogenesis, and as paradigms for a mechanism of information transfer that has apparently been a strong force in modeling eukaryotic genomes. There is little reason to doubt that continued study of the basic molecular biology of these fascinating viruses will continue to yield large dividends in our understanding of fundamental processes of practical importance and intellectual appeal.

At first glance, retrovirus replication seems dauntingly complex, replete with jumps and other contortions involving a variety of enzymatic activities and unusual DNA and RNA structures. In this brief chapter, it is my intention to try to convince the reader that much of the complex phenomenology of these viruses follows in a straightforward way from a few basic principles, and that once these principles are understood, one can (with only a little guidance from prior knowledge) reconstruct much of the life cycle and genetics of the viruses.

Retroviruses are unique among vertebrate viruses in many respects. Of all viruses, they have the most intimate association with the host cell, using systems preexisting within the normal cell to accomplish all but the initial steps of the replication cycle, inserting their genetic information into the cell genome to form an irreversible lifetime association — one in which by far the most common outcome is that the cell becomes a producer of new virions, but is otherwise not significantly altered in its physiology. Indeed, alone among eukaryotic viruses, retrovirus infection can span generations, being passed on as endogenous proviruses following infection of the germline. The exceptions to this general rule, although dramatic, are rare. Human immunodeficiency virus (HIV) and the related lentiviruses cause disease as a consequence of the killing of specific target cells, yet the viruses can persist and replicate in the infected individuals for years without significant pathogenic effect. Another exception is found in the prototypic retrovirus isolates — the oncogene-containing viruses — which readily induce malignant transformation in appropriate infected target cells. Although the transforming viruses were the first and most intensively studied members of the family, and have been crucial to understanding the molecular basis of cancer, they are in fact the consequence of uncommon aberrations in the virus replication cycle. They thus represent evanescent phenomena which, if not provided with a good home in the laboratory, do not survive for long in nature.

Like other important biological aspects, the rich variety of retrovirus-host cell interactions — from benign to cytopathic to transforming — follows in a fairly direct way from their unique mode of replication. It is the intention of this chapter not only to describe the basic features of virus replication, but also to point out how these features lead into the diverse biologies and genetics of the various viruses. For more detailed information (and more complete references) the reader is encouraged to consult a number of recent reviews (References 1 to 4).

II. OVERVIEW AND STATEMENT OF THE PROBLEM

If one were to design a virus that follows the retrovirus lifestyle, i.e., to have a replication intermediate which sufficiently resembles a cellular gene that new genomes and virus can be synthesized using only the machinery of the normal host, one would have to consider a number of specific constraints.

1. Since the host cells do not have the means of making RNA copies from RNA templates or short DNA copies from DNA templates, the virus would have to use RNA polymerase for genome and mRNA synthesis. This condition necessitates a replicative intermediate of DNA and a genome of RNA. We will call the DNA replication intermediate the provirus.

2. The provirus should be associated with the cell in a stable, heritable fashion. While one could imagine episomal structures that might have this property (and have apparently been achieved by some DNA viruses), this can probably not be accomplished using host cell systems alone. More straightforward is to have the provirus become covalently associated with the cell genome so that it is replicated along with the cell DNA and regularly passed to progeny cells. Thus, the virus need only provide for the integration step, and the cell will take care of the rest automatically.

3. The integrated provirus must resemble a cellular gene. It must contain signals for initiation of RNA synthesis by cellular RNA polymerase II at appropriate times and rates; the transcripts must contain signals for their own processing into genome and mRNA; and the mRNAs must contain signals for translation into virion proteins. The necessity of transcriptional signals in the provirus creates the fundamental paradox of retrovirology: some of these signals (e.g., promoters) must reside in DNA outside of the region to be copied. Yet the region to be copied will become new genomes which must pass these signals to the next generation of infected cells. How can a virus provide replication signals outside its own genome? A solution is to arrange the process of proviral DNA synthesis so that sequences important for providing transcriptional control signals are present once in the genome, but duplicated in the provirus so that one copy can be used to direct the current round of replication while the unused copy provides genetic continuity into the next round. The duplicated sequence found at each end of the provirus and known as the long terminal repeat (LTR) is thus characteristic of all proviruses.

4. The RNA transcripts must serve multiple roles: as genomes and as mRNAs for internal structural and membrane proteins and enzymes. Except under exceptional circumstances, eukaryotic mRNAs apparently cannot be translated into multiple primary products. Special strategies therefore are required to obtain the variety of viral products needed. A variety of strategies are used by all retroviruses to obtain the necessary range of expression.

5. The infected cell must survive infection and remain in sufficiently good health to continue dividing and live out its normal life span. Thus, the virus infection must not be extremely virulent. There are several aspects to this constraint. First, the expression of the provirus must be limited to an extent which does not efficiently interfere with normal cell functions. Second, the number of proviruses must not be permitted to expand beyond the point that the cell can tolerate. Third, the exit of virus from the infected cell must not require irreparable damage to the cell membrane. The level expression of proviruses is often regulated in interesting (and poorly understood) ways; for example, it can be restricted to specific differentiation states or be made responsible to specific extracellular stimuli (such as hormonal signals), or to proteins encoded by the virus itself. Additionally, with most retroviruses, there seems to be a mechanism strictly limiting the accumulation of additional proviruses by the infected cell. Finally, all retroviruses are enveloped and released by budding — a mechanism that both provides the virus with a protective envelope derived from the cell membrane and permits release of virions without punching holes in the cell membrane.

6. An early step in virus replication must be the copying of the viral genome RNA into the DNA molecule which, after integration, will become the provirus. The uninfected cell, however, does not seem to contain the enzymatic machinery necessary for these reactions. These must be provided by...

Table of contents

• Cover
• Title Page
• Copyright Page
• Table of Contents
• REVERSE TRANSCRIBING VIRUSES AND RETROTRANSPOSONS
• REPLICATION OF VIROIDS AND SATELLITES
• RECOMBINATION IN RNA GENOMES
• INDEX