Taxonomic Structure of the Family
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Metaviridae |
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Genus |
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Genus |
Morphology of particles is relatively poorly characterized and capsomeric symmetry is unknown. Members include species which produce primarily or exclusively intracellular particles (e.g., Saccharomyces cerevisiae Ty3 virus, SceTy3V) so that collections of particles are heterogeneous with respect to stage of maturation. These intracellular particles will be referred to as virus-like particles (VLPs). Extracellular particles are enveloped with ovoid cores and will be referred to as virions (e.g., Drosophila melanogaster gypsy virus, DmeGypV). Elements which generate VLPs or virions will be referred to collectively in this chapter as retrotransposons.
Physicochemical and Physical Properties
Physical properties differ for virions and VLPs.
The genomes of retrotransposons in this family are positive strand RNAs. The genomic RNA is polyadenylated at the 3-end; a cap structure has not yet been described, but may be presumed, given similarities of member elements with retroviruses. In addition to the RNA genome, some cellular RNAs may be randomly associated with particles including specific tRNAs in the case of elements replication of which is primed by tRNAs. Particle fractions from cells are heterogeneous with respect to maturation and so are associated with intermediates and products of reverse transcription in addition to genomic RNA.
Proteins present in characterized VLPs include a major structural or capsid protein (CP), an aspartate protease (PR), reverse transcriptase containing an RNase H domain (RT-RH), and integrase (IN). For most elements, these proteins are not yet characterized, but are predicted based on similarity of the protein sequence of the protein encoded by the internal domain. In most cases, the CP is not markedly similar to retroviral CP. VLPs of some retrotransposons in this family contain protein with the metal finger characteristic of nucleocapsid (NC) of retroviruses. Viruses of the genus Errantivirus are distinguished by the presence of processed envelope proteins that apparently correspond to retroviral transmembrane (TM) and surface (SU) proteins.
In the case of members which generate virions, the virion membrane appears to be derived from the membrane of the host cell.
Carbohydrates have not been characterized, although their presence is inferred from sensitivity of the DmeGypV envelope precursor protein to digestion with endoglycosidase F.
Genome Organization and Replication
The integrated form of these retrotransposons is composed of long terminal repeats (LTRs) flanking a central unique domain (Fig. 1). The length of elements ranges from 4 kbp to more than 10 kbp. The LTRs are from 77 nts in the case of Bombyx mori mag virus (BmoMagV) to greater than 2 kbp in length, in the cases of Drosophila virilis Ulysses virus (DviUllV) and Tribolium castaneum Woot virus (TcaWooV). Chromosomal copies of the elements are flanked by short direct repeats of sequence derived from the insertion site. The length of the repeat is characteristic of the element and ranges from 4 to 6 bp. The internal domain contains one to three ORFs. The 3-end of the second ORF can extend into the downstream LTR as in the case of SceTy3V. In all cases, the order of domains encoded in the ORFs is inferred to be: 5-CA-(NC where present)-PR-RT-RH-IN-ENV-3. Where characterized, envelope proteins are encoded downstream of the second ORF by spliced mRNAs. These ORFs are referred to differently for different elements and in this discussion, will be generally referred to as gag, pol and env. Thus elements may have one gag-pol ORF, two (gag and pol) or three (gag, pol and env) ORFs. The group with the latter organization clusters phylogenetically (Fig. 2) as well as functionally and thus is supported as a separate genus.
Transcription of the genomic RNA is initiated in the upstream LTR and terminates at a position downstream of that site in the downstream LTR. This divides the long terminal repeats into regions represented uniquely in the 5-end of the genomic RNA (U5), uniquely in the 3-end of the genomic RNA (U3) or repeated at the 5 and 3-ends (R). Thus, the LTRs are comprised of U3-R-U5 regions analogous to those found in integrated retroviruses. By analogy with retroviruses, these species may carry two copies of the RNA genome per virion or particle; however, this has not yet been demonstrated and dimerization functions have not yet been characterized.
Genomic RNA is translated into proteins required for particle structure, polyprotein maturation, reverse transcription and integration. Intracellular particle preparations show that particle fractions are comprised predominantly of species derived from the upstream portion of the ORF or where two or three ORFs are present from first ORF. Where two ORFs occur, they overlap and the second ORF is translated as a fusion protein of the first and second ORF translation products. The mechanism of frameshifting is not uniform among the member elements. In case of SpoTf1V, the most completely characterized retrotransposon of this family containing one ORF, it appears that a polyprotein is produced and later proteolytic events are responsible for a high ratio of major structural proteins to catalytic proteins. Little is actually known about where in the cell particle assembly occurs. PR is required for maturation of viral proteins. Catalytic proteins are PR, RT-RH, and IN. Shortly after production of protein precursors, processed species are observed. Based on similarity of these retrotransposons to retroviruses, it is likely that processing follows, and is dependent upon, intracellular assembly. Particle fractions are associated with genomic RNA and extrachromosomal DNA. RT activity associated with the particulate fraction can be measured by exogenous assays.
Reverse transcription of genomic RNA of known members of this family is primed from either the 5-end of a genomic RNA or from the 3-end of a tRNA in each case, with complementarity overlapping, adjacent to, or just downstream of the U5 region of the genomic transcript. In cases in which the reverse transcription intermediates have been characterized (DmeGypV, SceTy3V, and SpoTf1V), data are consistent with a species representing a minus-strand copy templated from the site of priming up to the 5-end of the genomic RNA. This is a minor species. By analogy with retroviruses, this intermediate is probably transferred to the 3-end of the genomic RNA, where an overlap of the R region minus strand represented in the cDNA and the R region plus strand represented at the 3-end of the genomic RNA, allows transfer of the minus-strand strong stop which then acts to prime copying of the template plus-strand genomic RNA. Plus-strand priming probably occurs, as in retroviruses, from a polypurine tract or related sequence overlapping, adjacent to, or just upstream of the U3 region in the genomic RNA. This is consistent with priming from a site of cleavage by RH. Plus-strand, strong-stop species have been identified for some representatives (DmeGypV and SceTy3V) which are consistent with this position of priming and copying through to the first modified base in the primer tRNA. This family is heterogeneous with respect to the presence of extra terminal nucleotides in the extrachromosomal replicated DNA and with respect to the presence of TG-CA inverted repeats at the ends of the integrated sequence.
Activation of transposition of these elements can cause disruption of host physiology depending on the site of insertion. Several members exhibit preferential patterns of insertion. It is notable that germline activation, which is a feature of some retroviruses, also occurs for some of these elements. In the case of SceTy3V, for example, transcription is induced by mating pheromone and transposition occurs after mating. In the case of DmeGypV, transposition occurs in germline cells.
Like the viruses of the families Pseudoviridae and Hepadnaviridae, the viruses of the family Metaviridae are clearly related to the viruses of the family Retroviridae. All of these families are related by reverse transcription and a viral core structure made up of of Gag-like proteins. Metaviridae, Pseudoviridae and Retroviridae also share the following: a proviral form characterized by LTRs, protease, RNase H and integrase activities essential for multiplication, readthrough-mediated (Gag-Pol) pol gene expression and tRNA primers (in some species).
An important and controversial question is the extent of the relationship of the family Metaviridae to the family Retroviridae. Because the genomic structure of their members is clearly related to, but simpler than that of the viruses of the family Retroviridae (with the notable exception of DmeGypV and a few allied species with three ORFs), many authors who have considered the problem have concluded that the family Metaviridae represents a more primitive group that probably spawned the Retroviridae (presumably by transducing genes encoding ligands for cell-surface receptors). This conclusion makes sense within the context of the enormous diversity of other types of retroelements, which are all clearly phylogenetically related by the presence of RT (see Fig. 4 in the Pseudoviridae chapter), but not all of which encode a virus-like intermediate. An alternative viewpoint that cannot be ruled out, but for which there is less phylogenetic support, is that viruses of the family Metaviridae represent degenerate forms of the members of the family Retroviridae.
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