Figure 1 (Top panel) On the left a diagrammatic representation of Sindbis virus (SINV). The knobs on the surface represent the external portions of the E1+E2 heterodimers. The heterodimers associate to form trimers. The 240 heterodimers and 240 copies of SINV capsid proteins are arranged in an icosahedral lattice with a T = 4 symmetry (from Harrison, 1990). On the upper right; thin section of peletted particles of Semliki forest virus (SFV) (Courtesy of Prasad, B.V.V.). On the lower right, negative contrast electron micrograph of particles of SFV (Courtesy of von Bonsdorff, C.H.) The bars represent 100 nm. (Lower panel) Surface-shaded representations of a particle of Ross River virus (RRV). On the left is an intact virion as viewed along a threefold axis. It was determined from cryo-electron microscopy and image reconstruction (Cheng, Kuhn, Olson, Rossmann, Choi, Smith and Baker, 1995). The virus surface is predominantly composed of the envelope glycoproteins E1 and E2 which form trimers (E1+E2)3 that appear as spike-like projections. Large openings surrounding the threefold spikes reveal the underlying lipid bilayer. Small openings are also observed along the fivefold axes and even smaller ones are found at the base of each spike. A portion of the outer glycoprotein layer and the underlying lipid bilayer has been removed in the center image revealing the inner nucleocapsid core. The polar head groups of the membrane are shown as distinct layers separating the outer glycoproteins from the inner nucleocapsid core. The image on the right is the nucleocapsid core showing the pentameric and hexameric capsomeres. 240 copies of the nucleocapsid protein together with the genome RNA form a T = 4 icosahedron. (Courtesy of R. Kuhn.)
Figure 2 Togavirus genomic coding strategies. Shown are comparative schematic representations of the alphavirus and rubivirus genomic RNAs with untranslated regions represented as solid black lines and ORFs as open boxes (NS-ORF = nonstructural protein ORF; S-ORF = structural protein ORF). Within each ORF, the coding sequences for the proteins processed from the translation product of the ORF are delineated. The asterisk between nsP3 and nsP4 in the alphavirus NS-ORF indicates the stop codon present in some alphaviruses that must be translationally readthrough to produce a precursor containing nsP4. Additionally, within the NS-ORF’s, the locations of motifs associated with the following activities are indicated: (MT) methyl transferase, (P) protease, (H) helicase, (X) unknown function, and (R) replicase. The sequences encompassed by the subgenomic RNA (sgRNA) are also shown. The scale at the top of the diagram is in kilobases. (Courtesy of T. Frey.)
Figure 3 Genome organization, translation, transcription and replication strategies of Sindbis virus (SINV). The regions of the 11.7 kb genomic RNA and 26S subgenomic mRNA (dark lines) that code respectively for the nonstructural (nsP) and structural proteins (dark boxes) are shown. Replication and transcription are indicated by thick arrows. The gray line is the replicative intermediate that is also the template for the sgRNA. E3 is a structural protein in some alphaviruses (not present in Rubella virus (RUBV)). Initiation codons are indicated by (*), termination codons by (†) and ($) (the latter is readthrough to produce P1234, hence nsP4). Dark triangles represent nsP2 protease activity. (Adapted from Strauss and Strauss, 1983.)
Figure 4 Unrooted phylogenetic tree of 23 alphaviruses generated from E1 amino acid sequences using the neighbor-joining method and drawn using the FITCH distance algorithm implemented in the PHYLIP software package. Numbers adjacent to nodes indicate bootstrap support values exceeding 50% for defined groups to the right. (Courtesy of A. Powers and S. Weaver.)
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