The species assigned to the genus Metavirus encode Gag and Pol proteins. However, this genus is now known to also include distinct lineages of viruses showing high divergence and polyphyletic relationships to each other.
SceTy3V forms spherical, but irregular, intracellular virus-like particles (VLPs) of about 50 nm in diameter. These are observed as clusters or as individual particles in the cytoplasm of cells expressing high levels of SceTy3V RNA.
Physicochemical and physical properties
VLPs sediment as a heterodispersed population of around 156S. The major particle-associated RNA is a 5.2 kb, polyadenylated RNA.
Mature proteins include capsid (CP, 26 kDa), nucleocapsid (NC, 15 kDa), protease (PR, 15 kDa), reverse transcriptase-ribonuclease H (RT-RH, 58 kDa) and integrase (INT, 61 kDa).
Genome organization and replication
The integrated provirus of Saccharomyces cerevisiae Ty3 virus (SceTy3V) is 5.4 kbp and consists of an internal region flanked by two LTRs each of 340 bp. The 5.4 kb RNA contains two ORFs - gag and pol - which overlap in the +1 frame. The primer binding site (PBS) is complementary to tRNAMet. Insertions of SceTy3V are flanked by 5 bp direct repeats derived from duplication of the insertion site following the cleavage and repair. SceTy3V is transcribed into a 5.2 kb genomic RNA, which is translated into Gag and Gag-Pol polyproteins. The tRNAMet PBS has its 5′-end two nt downstream of the junction of the 5′-LTR with the internal domain. The full-length SceTy3V DNA molecule is 2 bp longer at each end than the integrated molecule, consistent with predictions based on the positions of the priming sequences. Two nucleotides are removed from each 3′-end prior to integration. SceTy3V integrates within one or two nucleotides of the transcription initiation site of genes transcribed by RNA polymerase III.
SceTy3V transcription is induced by pheromone signal transduction. Although proteins are produced in cells undergoing signalling, DNA is not made in cells arrested in G1 phase of the cell cycle. Consequently, it is most likely that in natural populations, transposition only occurs after the fusion of mating cells to form diploids.
Species demarcation criteria
Members of different species in the genus Metavirus have less than 50% identity in their Gag proteins. For example, although Drosophila melanogaster Mdg virus (DmeMdg1V) and Drosophila melanogaster 412 virus (Dme412V) are both present in Drosophila melanogaster and constitute a phylogenetic clade, their Gag protein sequences are only 39% identical. On the other hand, some metaviruses such as Drosophila buzzatii Osvaldo virus (DbuOsvV) and Arabidopsis thaliana Athila virus (AthAthV) carry an ORF for a potential env-like gene, although these two viruses show polyphyletic relationships to each other or to errantiviruses. Moreover, phylogenetic analysis of RT or other protein domains shows that neither DbuOsvV or AthAthV cluster with metaviruses that lack the env gene. In terms of genome architecture, metaviruses may present genome organizations different from that of SceTy3V. For example, Schizosaccaromyces pombe Tf1 virus (SpoTf1V) encodes a single long Gag-Pol protein which is processed by a mechanism dependent on the SpoTf1V PR protein. Some other current members of the genus Metavirus (namely, those belonging to the chromovirus clade) are also distinguished from SceTy3V by aspects of the replication priming. For example, SpoTf1V forms an RNA structure involving 89 bases at the 5′-end of the RNA, which is processed by RH to cleave within the structure between nt 11 and 12 from the 5′-end. This cleavage allows self-priming of SpoTf1V RT from the 3′-end of the 11 nt fragment annealed immediately downstream of the 5′-LTR. Other chromoviruses present a similar self-priming mechanism (Esnault and Levin 2015, Butler et al., 2001).