Figure 1 (Left) Reconstruction of the atomic resolution structure of the Saccharomyces cerevisiae virus L-A (ScV-L-A) virion. (Center) Schematic representation of a T=1 capsid structure. (Right) The ScV-L-A particle viewed down an icosahedral two-fold axis with the Cα positions traced. Red Gag molecules contact the three-fold axes, but not the two-fold or five-fold axes. Purple molecules surround the five-fold axes and contact the two-fold axes. Thus, two kinds of Gag molecules with identical covalent structure are in distinct environments in the viral particle.
Figure 2 Cryo-electron microscopic reconstruction of Saccharomyces cerevisiae virus L-A (ScV-L-A) at 16 Å resolution. The view shown is along a five-fold axis of the icosahedral particles. The virions show the “T=2” symmetry found in the cores of all dsRNA viruses.
Figure 3 Genome organization of Saccharomyces cerevisiae virus L-A (ScV-L-A). The virion-associated RNA polymerase catalyzes in vitro end-to-end transcription of dsRNA by a conservative mechanism to produce mRNA for CP. In the case of ScV-L-A, all of the positive strand transcripts are extruded from the particles. The positive strand of satellite RNA M1, or deletion mutants of L-A or M1, on the other hand, often remain within the particle where they are replicated to produce two or more dsRNA molecules per particle (headful replication). The positive ssRNA of ScV-L-A is the molecule encapsidated to form progeny virus particles. The encapsidation signal on ScV-L-A or M1 positive sense ssRNA is a 24 nt stem-loop sequence located 400 nt from the 3’ end in each case. The Gag protein must be acetylated (by the cellular Mak3p) for assembly and packaging to proceed. These particles have a replicase activity that synthesizes the negative strand on the positive strand template to produce dsRNA, thus completing the replication cycle. Replication requires an internal site overlapping the packaging signal, and a specific 3’-end sequence and secondary/tertiary structure. Virions accumulate in the cytoplasm.
Figure 4 Negative contrast electron micrograph of an isolate of Helminthosporium victoriae virus 190S, the type member of the genus Victorivirus.
Figure 5 Genome organization of Helminthosporium victoriae virus 190S. The genomic plus strand includes two large, overlapping ORFs, with the 5’ one (ORF1) encoding the CP and the 3’ one (ORF2) encoding the RdRp. The stop codon of ORF1 overlaps the start codon of ORF2 in the tetranucleotide sequence AUGA.
Figure 6 Negative contrast electron micrograph of particles of an isolate of Giardia lamblia virus. TMV (rod-shaped) is included as an internal size marker. The bar represents 100 nm.
Figure 7 Negative contrast electron micrograph of particles of an isolate of Leishmania RNA virus 1 - 1. The bar represents 100 nm.
Figure 8 Genome organization of Leishmania RNA virus 1 - 1 (LRV-1-1).
Figure 9 Phylogenetic relationships among members of the family Totiviridae. A Bayesian tree was derived from the RdRp ORF amino acid sequences of each analyzed virus. The multiple sequence alignment was generated using MUSCLE v3.7 without Gblocks curation; the phylogenetic tree was generated using MrBayes v3.1.2 (10,000 generations with sampling every 100 and first 100 generations discarded); and the tree was rendered using TreeDyn v198.3. All four steps were performed using the “à la carte” option at www.phylogeny.fr/ with other default settings. The tree was refined for presentation using FigTree v1.3.1 obtained from http://tree.bio.ed.ac.uk/software/figtree/. The tree is rooted on outgroup virus HvV145S (Helminthosporium victoriae virus 145S; GenBank accession no. YP_052858) from the family Chrysoviridae, and the scale bar indicates the number of substitutions per position in the alignment. Approved and probable members of the family Totiviridae included in the tree are (GenBank accession no. in parenthesis): ScV-L-A, Saccharomyces cerevisiae virus L-A (NP_620495.1); ScV-L-BC, Saccharomyces cerevisiae virus L-BC (NP_042581.1); UmV-H1, Ustilago maydis virus H1 (NC_003823.1); HvV190S, Helminthosporium victoriae virus 190S (AAB94791.2); MoV1, Magnaporthe oryzae virus 1 (YP_122352.1); HmV1-17, SsRV1, Sphaeropsis sapinea RNA virus 1 (NP_047558.1); Helicobasidium mompa totivirus 1-17 (NP_898833.1); CmRV, Coniothyrium minitans RNA virus (YP_392467.1); EfV1, Epichloe festucae virus 1 (CAK02788.1); GaRV-L1, Gremmeniella abietina RNA virus L1 (AAK11656.1); SsRV2, Sphaeropsis sapinea RNA virus 2 (NP_047560.1); LRV1-1, Leishmania RNA virus 1 - 1 (NP_041191.1); LRV2-1, Leishmania RNA virus 2 - 1 (NP_043465.1); TVV1-1, Trichomonas vaginalis virus 1-1 (AAA62868.1); TVV2-1, Trichomonas vaginalis virus 2-1 (AAF29445.1); TVV3-1, Trichomonas vaginalis virus 3-1 (NP_659390.1); EbRV1, Eimeria brunetti RNA virus 1 (NP_108651.1); GLV, Giardia lamblia virus (NP_620070.1); and IMNV, penaeid shrimp infectious myonecrosis virus (YP_529549.1). Viruses are clustered and labeled as follows: genus Totivirus (cyan), genus Victorivirus (orange), genus Leishmaniavirus (green), proposed new genus of Trichomonas viruses (magenta), and genus Giardiavirus (brown). Probable family members EbRV1 and IMNV are indicated in gray.