Jane Flint - Principles of Virology, Volume 1

Figure 3.6Structure and expression of viral single-stranded (+) RNA genomes. (A)Synthesis of genomes, mRNA, and protein. (B)Genome configurations. UTR, untranslated region; VP g, virion protein, genome linked.

There are more different types of (+) strand RNA viruses than any other, and 38 families have been recognized [not counting (+) strand RNA viruses with DNA intermediates]. These genomes are linear and may be single molecules (non-segmented) or segmented, depending on the family. The families Arteriviridae , Astroviridae , Caliciviridae , Coronaviridae , Flaviviridae , Hepeviridae , Nodaviridae , Picornaviridae , and Togaviridae include viruses that infect vertebrates. (+) strand RNA genomes usually can be translated directly into protein by host ribosomes. The genome is replicated in two steps. The (+) strand genome is first copied into a full-length (–) strand, and the (–) strand is then copied into full-length (+) strand genomes. In some cases, a subgenomic mRNA is produced.

Members of four virus families are (+) strand RNA viruses with a DNA intermediate; those viruses within Retroviridae infect vertebrates. In contrast to other (+) strand RNA viruses, the (+) strand RNA genome of retroviruses is converted to a dsDNA intermediate by viral RNA-dependent DNA polymerase (reverse transcriptase). Following integration into host DNA, the viral DNA then serves as the template for viral mRNA and genome RNA synthesis by cellular enzymes.

Viruses with (–) strand RNA genomes are found in 19 families. These genomes are linear and may be single molecules (nonsegmented; some viruses with this configuration have been classified in the order Mononegavirales ) or segmented. Viruses of this type that can infect vertebrates include members of the Arenaviridae , Bornaviridae , Filoviridae , Hantaviridae , Orthomyxoviridae , Paramyxoviridae , Pneumoviridae , and Rhabdoviridae families. Unlike (+) strand RNA, (–) strand RNA genomes cannot be translated directly into protein but must be first copied to make (+) strand mRNA. There are no enzymes in the cell that can make mRNAs from the RNA genomes of (–) strand RNA viruses. These virus particles therefore contain virus-encoded RNA-dependent RNA polymerases. The genome is also the template for the synthesis of full-length (+) strands, which, in turn, are copied to produce (–) strand genomes.

Figure 3.7Structure and expression of viral single-stranded (+) RNA genomes with a DNA intermediate. (A)Synthesis of genomes, mRNA, and protein. (B)Genome configuration.

Figure 3.8 Structure and expression of viral single-stranded (–) RNA genomes. (A)Synthesis of genomes, mRNA, and protein. The icon represents an orthomyxovirus particle. (B and C)Genome configurations.

The genomes of certain (–) strand RNA viruses (e.g., members of the Arenaviridae and Bunyaviridae ) are ambisense: they contain both (+) and (–) strand information on a single strand of RNA ( Fig. 3.8C). The (+) sense information in the genome is translated upon entry of the viral RNA into cells. Replication of the RNA genome yields additional (+) sense sequences, which are then translated.

Some small RNA and DNA genomes enter cells from virus particles as naked molecules of nucleic acid, whereas others are always associated with specialized nucleic acid-binding proteins or enzymes. A fundamental difference between the genomes of viruses and those of their hosts is that although viral genomes are often covered with proteins, they are usually not bound by histones in the virus particle (polyomaviral and papillomaviral genomes are exceptions). However, it is likely that all viral DNAs become coated with histones shortly after they enter the nucleus.

While viral genomes are all nucleic acids, they should notbe thought of as one-dimensional structures. Virology textbooks (this one included) often draw genomes as straight, one-dimensional lines, but this notation is for illustrative purposes only; physical reality is certain to be dramatically different. Genomes have the potential to adopt amazing secondary and tertiary structures in which nucleotides may engage in long-distance interactions ( Fig. 3.9).

The sequences and structures near the ends of viral genomes are often indispensable for replication. For example, the DNA sequences at the ends of parvovirus genomes form T-shaped structures that are required for priming during DNA synthesis. Proteins covalently attached to 5′ ends, inverted and tandem repeats, and bound tRNAs may also participate in the replication of RNA and DNA genomes. Secondary RNA structures may facilitate translation (the internal ribosome entry site [IRES] of picornavirus genomes) and genome packaging (the structured packaging signal of retroviral genomes, [ Fig. 3.9]).

Figure 3.9 Genome structures in cartoons and in real life. (A)Linear representation of a picornavirus RNA genome. UTR, untranslated region. (B)Long-distance RNA-RNA interactions in a tombusvirus RNA genome. The 4,252-nucleotide viral genome is shown with secondary RNA structures at the 5′ and 3′ ends. Sequences that base-pair are shown in blue (required for RNA frameshifting) and red (required to bring ribosomes from the 3′ end to the 5′ end). Courtesy of Anne Simon, University of Maryland. (C)Schematic representation of RNA secondary-structure elements in the human immunodeficiency virus type 1 5′ leader, including the core packaging signal. (D)NMR structure of the RNA shown in C, without elements colored black. Courtesy of Paul Bieniasz, Rockefeller University.

The compact genome of most viruses renders the “one gene, one mRNA” dogma inaccurate. Extraordinary tactics for information retrieval, such as the production of multiple subgenomic mRNAs, alternative mRNA splicing, RNA editing, and nested transcription units ( Fig. 3.10), allow the production of multiple proteins from a single viral genome. Further expansion of the coding capacity of the viral genome is achieved by posttranscriptional mechanisms, such as polyprotein synthesis, leaky scanning, suppression of termination, and ribosomal frameshifting. In general, the smaller the genome, the greater the compression of genetic information.

Knowledge about the physical nature of genomes and coding strategies was first obtained by the study of the nucleic acids of viruses. Indeed, DNA sequencing technology was perfected on viral genomes. The first genome of any kind to be sequenced was that of the Escherichia coli bacteriophage MS2, a linear ssRNA of 3,569 nucleotides. dsDNA genomes of larger viruses, such as herpesviruses and poxviruses (vaccinia virus), were sequenced completely by the 1990s. Since then, high-throughput sequencing has revolutionized the biological sciences, allowing rapid determination of genome sequences from clinical and environmental samples. Organand tissue-specific viromes of many organisms have been determined. In one study, over 186 host species representing the phylogenetic diversity of vertebrates, including lancelets (chordates, but considered invertebrates), jawless fish, cartilaginous fish, ray-finned fish, amphibians, and reptiles, all ancestral to birds and mammals, were sampled. RNA was extracted from multiple organs and subjected to high-throughput sequencing. Among 806 billion bases that were read, 214 new viral genomes were identified. The results show that in vertebrates other than birds and mammals, RNA viruses are more numerous and diverse than suspected. Every viral family or genus of bird and mammal viruses is also represented in viruses of amphibians, reptiles, or fish. Arenaviruses, filoviruses, and hantaviruses were found for the first time in aquatic vertebrates. The genomes of some fish viruses have now expanded so that their phylogenetic diversity is larger than in mammalian viruses. New relatives of influenza viruses were found in hagfish, amphibians, and ray-finned fish. As of this writing, the complete sequences of >8,000 different viral genomes have been determined. Published viral genome sequences can be found at http://www.ncbi.nlm.nih.gov/genome/viruses/.