Principles of Virology. Jane Flint
Newly synthesized mRNAs are encapsidated and then copied to produce dsRNAs.
Figure 3.4 Structure and expression of viral single-stranded DNA genomes. (A) Synthesis of genomes, mRNA, and protein. (B and C) Genome configurations.
Figure 3.5 Structure and expression of viral double-stranded RNA genomes. (A) Synthesis of genomes, mRNA, and protein. (B) Genome configuration.
BACKGROUND
RNA synthesis in cells
There are no known host cell enzymes that can copy the genomes of RNA viruses. However, at least one enzyme, RNA polymerase II, can copy an RNA template. The 1.7-kb circular, ssRNA genome of hepatitis delta satellite virus is copied by RNA polymerase II to form multimeric RNAs (see the figure). How RNA polymerase II, an enzyme that produces pre-mRNAs from DNA templates, is reprogrammed to copy a circular RNA template is not known.
Hepatitis delta satellite (–) strand genome RNA is copied by RNA polymerase II at the indicated position. The polymerase passes the poly(A) signal (purple box) and the self-cleavage domain (red circle). For more information, see Fig. 6.25 Redrawn from Taylor JM. 1999. Curr Top Microbiol Immunol 239:107–122, with permission.
Figure 3.6 Structure and expression of viral single-stranded (+) RNA genomes. (A) Synthesis of genomes, mRNA, and protein. (B) Genome configurations. UTR, untranslated region; VPg, virion protein, genome linked.
(+) Strand RNA (Fig. 3.6)
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.
(+) Strand RNA with a DNA Intermediate (Fig. 3.7)
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.
(–) Strand RNA (Fig. 3.8)
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 3.7 Structure 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.
What Do Viral Genomes Look Like?
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 not be 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]).