106 and the sedimentation coefficient is estimated at ~ 200-300S for wild type and ~ 115S for 1-381 mutant. The virions are sensitive to high temperature (65°C).
|
Type Species |
(SceTy1V) |
Virions are ovoid to spheroid, strictly intracellular particles, sometimes observed as paracrystalline clusters in the cytoplasm in yeast cells. Particles are quite heterodisperse structurally. However, the C-terminal deletion mutant containing residues 1-381 of the gag protein is less heterodisperse than the wild-type and cryo-electron micrographs of these particles reveal a beautiful surface structure with icosahedral symmetry (Fig. 1). The mean radius of the virions is 20-30 nm for wild type and 20 nm for the much better characterized and more uniform 1-381 mutant. The virions are not enveloped. The total Mr is estimated at 14 106 and the sedimentation coefficient is estimated at ~ 200-300S for wild type and ~ 115S for 1-381 mutant. The virions are sensitive to high temperature (65°C).
The major virion RNA species consist of an LTR-to-LTR transcript of 5.6 kb. SceTy1V packages host-derived primer tRNAiMet in addition. SceTy1V particles contain more than one (probably two, by analogy with retroviruses) RNA molecules. This transcript encodes two overlapping ORFs, gag and pol; the second expressed as the result of a +1 frameshift relative to the first. The major nucleic acid forms are RNA in VLP, as well as various DNA forms (intermediates) in VLP preparations, and finally, after integration is complete, the integrated DNA “provirus”. The genome size for SceTy1V is RNA-5.6 kb; DNA-5.9 kb. There is linear ssRNA in virion, and the provirus (integrated) consists of dsDNA.
The known gag-encoded proteins are capsid (CP) and a short C-terminal peptide (the latter is only inferred to exist and has not been directly observed). No recognizable NC peptide has been identified. The known pol-encoded proteins are a protease (PR), integrase (IN), and reverse transcriptase/RNase H (RT). All of these proteins appear to be required for replication.
Genome Organization and Replication
The DNA form of the SceTy1V genome consists of two 335 bp LTRs largely flanking a central coding region, although SceTy1V is unusual in that gag initiates within the U5 region of the 5
-LTR (Fig. 2). The LTR sequences can be divided into three segments called U3, R and U5. The U3 region is unique to the 3-end of the RNA, the R region is repeated in the RNA and the the U5 region is unique to the 5-end of the RNA. SceTy1V encodes a 5.6 kb ssRNA with two ORFs. The first ORF is gag and encodes the major CP as well as a small C-terminal peptide; these two proteins are proteolytically derived from the gag primary translation product. The second ORF, which overlaps gag in the +1 frame, is pol and encodes protease (PR), integrase (IN), and reverse transcriptase/RNAse H (RT-RH). All of these pol proteins are derived by proteolysis of the gag-pol precursor by the Ty1 PR. The gag-pol precursor is expressed by an inefficient programmed frameshift that occurs within the sequence CUU AGG C (the indicated codon boundaries represent the gag frame), which is necessary and sufficient to specify the +1 frameshift. A minor shorter transcript of ~ 2.2 kb is reported to be 5 coterminal with the major transcript, but has not been fully characterized. A second minor transcript is reported to be 3 coterminal with the major transcript and is most clearly observed in yeast strains with spt3 mutations. These spt3 mutations eliminate or greatly reduce the abundance of the full-length transcript.
The initial step in replication is transcription of SceTy1V to generate the full-length RNA described above. This RNA is encapsidated in the cytoplasm in a precursor particle consisting of unprocessed gag and gag-pol proteins. Action of the SceTy1V PR then converts this into a mature virus particle. It is thought that this somehow activates the reverse transcription process.
The first step in the reverse transcription process is the extension of the tRNAiMet primer, which binds to the (-) strand primer binding site [(-)PBS in Fig. 4] in the full-length RNA. The product of this extension is referred to as (-) strand strong stop DNA or (-) ssDNA by analogy with retroviruses. The (-) ssDNA is transferred to the 3-end of the full-length RNA, where it can be further extended to generate a nearly full-length (-) strand DNA. Priming of the plus strand initiates at the (+) PBS1 (also sometimes referred to as PPT1 for polypurine tract 1) but the mechanism of this priming and the exact nature of the primer have not yet been determined. Extension yields a product, (+) ssDNA that corresponds to the similarly named retroviral intermediate. Transfer of (+) ssDNA to the left end of the (-) strand DNA sets up a primer-template that can be extended in principle, to generate full-length duplex DNA. However, studies indicate that the (+) strand is not continuous because a second priming event occuring near the middle of the molecule at a site called (+) PBS2 results in a discontinuity in the middle of the plus strand. We will refer to this final product of reverse transcription as the dsDNA form, although some experiments suggest that in many of these molecules there may be stretches of RNA rather than DNA in the (+) strand. The dsDNA is imported into the cell nucleus by an unknown mechanism.
The full length dsDNA is a substrate for the SceTy1V IN, which inserts the dsDNA into a chromosomal target site, in the process generating a 5 bp target site duplication of the host target site DNA. Sequences located upstream of polIII-transcribed genes represent strongly preferred targets for such SceTy1V integration in vivo.
Retrotransposon SceTy1V is probably best thought of as a genome parasite of Saccharomyces cerevisiae. In typical wild strains of this yeast, 3-15 copies of SceTy1V are found per haploid genome, whereas in typical laboratory isolates, there are 25-40 copies. In addition to this, the genome contains several hundred solo-LTRs (not associated with a central coding region) or fragments thereof. It appears to be restricted to this host species and to very closely related species of Saccharomyces, but is absent from more distant species of Saccharomyces. However, those species are likely to harbor related elements. Transmission is likely to be exclusively vertical, and horizontally through conjugation. SceTy1V and/or the closely related species, SceTy2V, has been found in virtually all isolates of S. cerevisiae, isolated from all over the world. No cytopathic effects have been reported. Some strains are reported to contain very large numbers of SceTy1V virus particles and be otherwise normal in every way.
List of Species Demarcation Criteria in the Genus
In general, elements inhabiting different host species are considered different species because they have diverged (through vertical descent from a common ancestor) at least as much as the host species themselves (probably more so, due to the error-prone mechanism of replication). However, there are instances in the Pseudoviridae and Metaviridae in which one finds two closely related elements inhabiting the same host species, e.g., SceTy1V and SceTy2V of S. cerevisiae. In these elements, the RT amino acid sequences are quite similar. Although, the capsid-encoding sequences have diverged significantly (e.g., less than 50% amino acid sequence identity) their DNA sequences fail to cross hybridize. The question then arises whether these represent different species or more subtle variants. We have considered such elements separate species if at least one of the major coding regions (e.g., capsid) is less than 50% identical to the reference amino acid sequence. For example, SceTy1V and SceTy2V Gag amino acid sequences are 49% identical.
Official virus species names are in italics. Tentative virus species names, alternative names ( ), strains or serotypes are not italicized. Virus names, genome sequence accession numbers [ ], and assigned abbreviations ( ) are:
|
Arabidopsis thaliana Ta1 virus |
[X13291] |
(AthTa1V) |
|
Hordeum vulgare BARE-1 virus |
[Z17327] |
(HvuBar1V) |
|
Nicotiana tabacum Tnt1 virus |
[X13777] |
(NtaTnt1V) |
|
Nicotiana tabacum Tto1 virus |
[D83003] |
(NtaTto1V) |
|
Physarum polycephalum Tp1 virus |
[X53558] |
(PpoTp1V) |
|
Saccharomyces cerevisiae Ty1 virus |
[M18706] |
(SceTy1V) |
|
Saccharomyces cerevisiae Ty2 virus |
[M19542] |
(SceTy2V) |
|
Saccharomyces cerevisiae Ty4 virus |
[X67284] |
(SceTy4V) |
|
Solanum tuberosum Tst1 virus |
[X52387] |
(StuTst1V) |
|
Triticum aestivum WIS-2 virus |
[X63184; X57168 (LTR)] |
(TaeWis2V) |
|
Zea mays Hopscotch virus |
[U12626] |
(ZmaHopV) |
Tentative Species in the Genus
None reported.
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