Jane Flint - Principles of Virology, Volume 1

8 Explain why no infectious viruses are observed in the cell culture medium during the latent phase of a onestep growth curve.

9 You infect a plate of one million cells at an MOI of 100. The particle-to-PFU ratio for this virus is 1,000. How many total virus particles did you add to the cells?

Introduction

Genome Principles and the Baltimore System

Structure and Complexity of Viral Genomes DNA Genomes RNA Genomes

What Do Viral Genomes Look Like?

Coding Strategies

What Can Viral Sequences Tell Us?

The “Big and Small” of Viral Genomes: Does Size Matter?

The Origin of Viral Genomes

Genetic Analysis of Viruses Classical Genetic Methods Engineering Mutations into Viral Genomes Engineering Viral Genomes: Viral Vectors

Perspectives

References

Study Questions

Virocentricity with Eugene Koonin http://bit.ly/Virology_Twiv275

CRISPR-Cas immune systems https://www.microbe.tv/twim/twim-184/

… everywhere an interplay between nucleic acids and proteins; a spinning wheel in which the thread makes the spindle and the spindle the thread.

ERWIN CHARGAFF, 1955

Earth abounds with uncountable numbers of viruses of great diversity. However, because taxonomists have devised methods of classifying viruses, the number of identifiable groups is manageable ( Chapter 1). One of the contributions of molecular biology has been a detailed analysis of the genetic material of representatives of major virus families. From these studies emerged the principle that the viral genomeis the nucleic acid-based repository of the information needed to build, reproduce, and transmit a virus ( Box 3.1). These analyses also revealed that the thousands of distinct viruses defined by classical taxonomic methods can be organized into seven groups, based on the structures of their genomes.

A universal function of viral genomes is to specify proteins. However, none of these genomes encode the complete machinery needed to carry out protein synthesis. Consequently, one important principle is that all viral genomes must be copied to produce messenger RNAs (mRNAs) that can be read by host ribosomes. Literally, all viruses are parasites of their host cells’ translation system.

A second principle is that there is unity in diversity: evolution has led to the formation of only seven major types of viral genome. The Baltimore classification system integrates these two principles to construct an elegant molecular algorithm for virologists ( Fig. 3.1). When the bewildering array of viruses is classified by this system, we find seven pathways to mRNA. The value of the Baltimore system is that by knowing only the nature of the viral genome, one can deduce the basic steps that must take place to produce mRNA. Perhaps more pragmatically, the system simplifies comprehension of the extraordinary reproduction cycles of viruses.

The Baltimore system omits the second universal function of viral genomes, to serve as a template for synthesis of progeny genomes. Nevertheless, there is also a finite number of nucleic acid-copying strategies, each with unique primer, template, and termination requirements. We shall combine this principle with that embodied in the Baltimore system to define seven strategies based on mRNA synthesis andgenome replication. The Baltimore system has stood the test of time: despite the discovery of multitudes of viral genome sequences, they all fall into one of the seven classes.

Replication and mRNA synthesis present no obvious challenges for most viruses with DNA genomes, as all cells use DNA-based mechanisms. In contrast, animal cells possess no known systems to copy viral RNA templates and to produce mRNA from them. For RNA viruses to propagate, their RNA genomes must, by definition, encode a nucleic acid polymerase.

Despite the simplicity of expression strategies, the composition and structures of viral genomes are far more varied than those seen in the entire archaeal, bacterial, or eukaryotic domains. Nearly every possible method for encoding information in nucleic acid can be found in viruses. Viral genomes can be

DNA or RNA

DNA with short segments of RNA

DNA or RNA with covalently attached protein

single-stranded (+) strand, (–) strand, or ambisense ( Box 3.2)

double stranded

linear

circular

segmented

gapped

The genomes of viruses range from the extraordinarily small (<2 kb) to the extraordinarily large (>2,500 kbp); the diversity in size likely provides advantages in the niches in which particular viruses exist.

Viral genomes specify some, but never all, of the proteins needed to complete the viral reproductive cycle.

That only seven viral genome replication strategies exist for all known viruses implies unity in viral diversity.

Some genomes can enter the reproduction cycle upon entry into a target cell, whereas others require prior repair or synthesis of viral gene products before replication can proceed.

Although the details of replication differ, all viruses with RNA genomes must encode either an RNA-dependent RNA polymerase to synthesize RNA from an RNA template or a reverse transcriptase to convert viral RNA to DNA.

The information encoded in viral genomes is optimized by a variety of mechanisms; the smaller the genome, the greater the compression of genetic information.

The genome sequence of a virus is at best a biological “parts list” and tells us little about how the virus interacts with its host.

Technical advances allowing the introduction of mutations into any viral gene or genome sequence are responsible for much of what we know about viruses.

Gene products and regulatory signals required for

replication of the genome

efficient expression of the genome

assembly and packaging of the genome

regulation and timing of the reproduction cycle

modulation of host defenses

spread to other cells and hosts

Information notcontained in viral genomes:

genes encoding a complete protein synthesis machine (e.g., no ribosomal RNA and no ribosomal or translation proteins)

genes encoding proteins of membrane biosynthesis

telomeres (to maintain genomes) or centromeres (to ensure segregation of genomes)

this list becomes shorter with each new edition of this textbook!

Figure 3.1 The Baltimore classification. All viruses must produce mRNA that can be translated by cellular ribosomes. This classification system traces the pathways from viral genomes to mRNA for the seven classes of viral genomes.

The seven strategies for expression and replication of viral genomes are illustrated in Fig. 3.2to 3.8. In some cases, genomes can enter the replication cycle directly, but in others, genomes must first be repaired, and viral gene products that participate in the replication cycle must first be synthesized. Examples of specific viruses in each class are provided.