Taxonomic Structure of the Family
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Pseudoviridae |
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Genus |
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Genus |
These retroelements are often referred to as LTR-retrotransposons of the Ty1-copia family. Most authors refer to the particles that these elements produce as virus-like particles (VLPs) because they do not display infectivity according to the traditional virological definition. However, there is good evidence that these particles are essential and direct intermediates in the life cycle of these elements. We use the term “virion” here to conform to the usage in this volume.
The morphology of virus particles of members of the family Pseudoviridae is poorly known and variable. For example, Saccharomyces cerevisiae Ty1 virus (SceTy1V) and Drosophila melanogaster copia virus (DmeCopV) both make similar looking particles but SceTy1V particles are cytoplasmic whereas those of DmeCopV are nuclear. The typical mean radius is 30-40 nm. The virion is ovoid to spheroid, often with electron-dense centers. There is no envelope.
Unknown for most elements in the family, several icosahedral symmetry forms, including T = 3 and T = 4, have been reported for SceTy1V 1-381 mutant (Fig. 1).
Physicochemical and Physical Properties
In most systems, virions are only very crudely characterized biochemically.
The major virion RNA molecule consist of an LTR-to-LTR transcript of ~ 5-6 kb. Most elements package a host-derived primer tRNA in addition. This transcript encodes one to two ORFs in most elements, encoding equivalents of retroviral gag and pol; the second expressed at lower levels than the first. There is RNA, as well as various DNA forms (intermediates) in the virion preparation. The RNA is 5 to 8 kb, positive sense, capped and polyadenylated; the DNA is 5.5 to 9 kbp long. The linear ssRNA is in virions, and the linear dsDNA “provirus” is integrated in the genome.
Both gag and gag-pol primary translation products are processed by the appropriate retrotransposon protease. The known gag-encoded proteins include analogs of retroviral capsid (CP) nucleocapsid (NC) although the latter is only present in a subset of these elements. The known Pol-encoded proteins include the protease (PR), integrase (IN), and reverse transcriptase/RNase H (RT-RH). All of these proteins appear to be required for replication.
Genome Organization and Replication
The DNA form of the genome consists of two LTRs flanking a central coding region. The LTR sequences can be divided into three segments called U3, R and U5 based on the relationship between the termini of the RNA form and the DNA form (Fig. 2). The U3 region is unique to the 3-end of the RNA , the R region is repeated in the RNA and the U5 region is unique to the 5-end of the RNA. 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 is typically 5 bp. In all cases, the order of domains encoded in the ORFs is inferred to be: 5-CP-(NC where present)-PR-IN-RT-RH-3. This is one key characteristic that distinguishes members of the family Pseudoviridae from members of the families Metaviridae and Retroviridae (in which the IN domain lies downstream of RT-RH).
The virion-associated RT-RH mediates the conversion of the LTR to LTR transcript into a full-length nucleic acid duplex containing full-length LTR sequences in the form of dsDNA. This DNA is then integrated into host DNA by the IN protein, where it becomes a part of the host genome and can persist there, essentially indefinitely. The integrated form (equivalent to the retroviral provirus) is then transcribed by host RNA polymerase II to generate new retrotransposon RNAs. In most elements, the reverse transcription and integration processes closely mimic the replication of retroviral RNA, but there are some important exceptions.
Members of the family Pseudoviridae are commonly referred to as LTR retrotransposons of the SceTy1V/DmeCopV family. They form an intrinsic and significant part of the genome of many eukaryotic species, especially plants. For most of these elements, the virion is known to be an essential part of their multiplication cycle, but is not likely to be infectious in the traditional virological sense, under normal conditions.
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