Members of two virus families, Caulimoviridae and He- padnaviridae, have a gapped DNA genome. The Hepadnaviridae include viruses that infect vertebrates. As the gapped DNA genome is partially double stranded, the gaps must be filled to produce perfect duplexes. This repair process must precede mRNA synthesis because the host RNA polymerase can transcribe only fully dsDNA. The unusual gapped DNA genome is produced from an RNA template by a virus-encoded enzyme, reverse transcriptase.
Single-Stranded DNA (ssDNA) (Fig. 3.4)
Thirteen families of viruses containing ssDNA genomes have been recognized; the families Anelloviridae, Circoviridae, Genomoviridae, and Parvoviridae include viruses that infect vertebrates. ssDNA must be copied into mRNA before proteins can be produced. However, RNA can be made only from a dsDNA template, whatever the sense of the ssDNA. Consequently, DNA synthesis must precede mRNA production in the replication cycles of these viruses. All synthesis of viral DNA is catalyzed by cellular DNA polymerases.
Figure 3.2 Structure and expression of viral double-stranded DNA genomes. (A) Synthesis of genomes, mRNA (shown as green line in yellow box), and protein (shown as brown line). The icon represents a polyomavirus particle. (B to E) Genome configurations. Ori, origin of replication; ITR, inverted terminal repeat; TP, terminal protein; L, long region; S, short region; UL and US, long and short unique regions; IRL, internal repeat sequence, long region; IRS, internal repeat sequence, short region; TRL, terminal repeat sequence, long region; TRS, terminal repeat sequence, short region; OriL, origin of replication of the long region; OriS, origin of replication of the short region.
Figure 3.3 Structure and expression of viral gapped, circular, double-stranded DNA genomes. (A) Synthesis of genome, mRNA, and protein. (B) Configuration of the hepadnavirus genome.
RNA Genomes
Cells have no RNA-dependent RNA polymerases that can replicate the genomes of RNA viruses or make mRNA from RNA templates (Box 3.3). One solution to this problem is that RNA virus genomes encode RNA-dependent RNA polymerases that produce RNA from RNA templates. The other solution, exemplified by retrovirus genomes, is reverse transcription of the genome to dsDNA, which can be transcribed by host RNA polymerase.
dsRNA (Fig. 3.5)
There are twelve families of viruses with linear dsRNA genomes. The number of dsRNA segments in the virus particle may be 1 (Totiviridae, Hypoviridae, and Endornaviridae, viruses of fungi, protozoa, and plants); 2 (Partitiviridae, Birnaviridae, and Megabirnaviridae, viruses of fungi, plants, insects, fish, and chickens); 3 (Cystoviridae, viruses of Pseudomonas bacteria); 4 (Chrysoviridae, viruses of fungi); or 10 to 12 (Reoviridae, viruses of protozoa, fungi, invertebrates, plants, and vertebrates). While dsRNA contains a (+) strand, it cannot be translated to synthesize viral proteins as part of a duplex. The (–) strand of the genomic dsRNA is first copied into mRNAs by a viral RNA-dependent RNA polymerase. 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