Читать книгу Principles of Virology - Jane Flint, S. Jane Flint - Страница 186

In the simplest arrangement, the nucleic acid makes direct contact with the protein(s) that forms the protective shell of the virus particle. Proteins on the inner surfaces of the icosahedral capsids of many small RNA viruses interact with the viral genome. As we have seen, the interior surface of the poliovirus capsid can be described in detail. Nevertheless, we possess no structural information about the arrangement of the RNA genome, for the nucleic acid is not visible in the X-ray structure. However, the genome of the porcine picornavirus Seneca Valley virus has been visualized by this method (albeit at low resolution) (Fig. 4.19A). Much of the RNA genome forms an outer layer in which it makes extensive contact with the inner surface of the capsid. Highly ordered RNA genomes are also present in T = 3 nodaviruses, such as Flock house virus, in which an outer decahedral cage of ordered RNA surrounds additional rings (Fig 4.19B). More recently, higher-resolution views (sufficient to observe some bases in the RNA!) of a small viral RNA genome have been obtained using cryo-EM reconstruction without imposition of any symmetry (Box 4.7). This approach is likely to be more widely applicable.

Use of the same protein or proteins both to condense the genome and to build a capsid allows efficient utilization of limited genetic capacity. It is therefore an advantageous arrangement for viruses with small genomes. However, this mode of genome packing is also characteristic of some larger viruses, notably rotaviruses and herpesviruses. The genome of rotaviruses comprises 11 segments of double-stranded RNA located within the innermost of the three protein shells of the particle. Remarkably, as much as 80% of the RNA genome appears highly ordered within the core, with strong elements of icosahedral symmetry (Fig. 4.19B).

One of the most surprising properties of the large herpesviral capsid is the absence of internal proteins associated with viral DNA: despite intense efforts, no such core proteins have been identified, and the viral genome has not yet been visualized. In contrast, cryo-EM has allowed visualization of the large, double-stranded DNA genome of bacteriophage T4, which is organized in closely apposed, concentric layers (Fig. 4.20A). This arrangement illustrates graphically the remarkably dense packing needed to accommodate such large viral DNA genomes in closed structures of fixed dimensions. This type of organization must require neutralization of the negative charges of the sugar-phosphate backbone. Neutralization might be accomplished by proteins that form the inner surface of the capsid, or by the incorporation of small, basic peptides made by the host cell, such as spermine and spermidine.

Figure 4.19 Ordered RNA genomes in small and large icosahedral virus particles. (A) The 20-Å X-ray crystal structure of the picornavirus Seneca Valley virus viewed down a twofold axis of icosahedral symmetry, showing the density ascribed to the RNA genome (brown). The structural proteins are colored as in Fig. 4.12 and 4.13: VP1 (blue), VP2 (green), VP3 (red), and VP4 (yellow). (B) Outer layer of the double-stranded, segmented RNA genome of the rotavirus bluetongue virus observed at 6.5-Å resolution by X-ray crystallography of viral cores. The electron density of this layer of RNA (green) from maps averaged between two closely related serotypes is shown with A-form duplex RNA modeled into the rods of density. These RNA spirals represent some 80% of the >19-kbp genome. Reprinted from Gouet P et al. 1999. Cell 97:-481–490, with permission. Courtesy of D.I. Stuart, University of Oxford.