Principles of Virology. Jane Flint

with icosahedral symmetry, the positions of pentamers determine the geometry of cones. However, in cones, pentamers are present only in the terminal caps. The human immunodeficiency virus type 1 cones formed in vitro and isolated from mature virions can be modeled as a fullerene cone assembling on a curved hexagonal lattice with five pentamers (red) at the narrow end of the cone, as shown in the expanded view. The wide end would be closed by an additional 7 pentamers (because 12 pentamers are required to form a closed structure from a hexagonal lattice). (C) The fullerene cone model was subsequently confirmed and refined by cryo-EM of helical tubes of CA at higher resolution, molecular dynamics simulations, and cryo-EM of cores purified from and within virus particles. Shown is an example of computational slices of perfect fullerene cones observed within virus particles, with cryoelectron tomographic models superimposed. The C-terminal domains of CA molecules are shown in gray, the N-terminal domains of CA pentamers in blue, and those of CA hexamers colored according to the quality of their alignment, from red (low) to green (high). From Mattei S. 2017. Science 354:1434–1437, with permission. Courtesy of J. Briggs, European Molecular Biology Laboratory, Heidelberg, Germany.

       Li S, Hill CP, Sundquist WI, Finch JT. 2000. Image reconstructions of helical assemblies of the HIV-1 CA protein. Nature 407:409–413.

       Zhao G, Perilla JR, Yufenyuy EL, Meng X, Chen B, Ning J, Ahn J, Gronenborn AM, Schulten K, Aiken C, Zhang P. 2013. Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics. Nature 497:643–646.

       Mattei S, Glass B, Hagen WJH, Kräusslich H-G, Briggs JAG. 2016. The structure and flexibility of conical HIV-1 capsids determined within intact virions. Science 354:1434–1437.

Other Capsid Architectures

As noted previously, capsids with icosahedral or helical symmetry are characteristic of the majority of virus particles described to date. Nevertheless, these architectures are not universal, and the capsids of even some relatively small viruses can be constructed according to an alternative design. This property is exemplified by the capsids of some retroviruses.

The capsid of all retroviruses surrounds a nucleoprotein that contains the diploid (+) strand RNA genome. The capsid is surrounded by the viral matrix (M) protein, which is encased in the viral envelope. However, retroviral capsids may be spherical, cylindrical, or conical, the shape exhibited by capsids of human immunodeficiency virus type 1 and other lentiviruses (Fig. 4.18A and B). These capsids are built from a single capsid (CA) protein, which can form both pentamers and hexamers. The odd appearance of the human immunodeficiency virus type 1 capsid might suggest that it represents an exception to the geometric rules that dictate the viral architectures described in previous sections. However, this is not the case: this capsid can be described by a fullerene cone model that combines principles of both icosahedral and helical symmetry. In this model (Box 4.6), which has been confirmed by cryo-electron tomography of intact virus particles, a closed structure is formed using 12 pentamers, just as in an icosahedral capsid. However, pentamers are not spaced at regular intervals throughout the structure. Rather, they are restricted to the terminal caps and separated by spirals (a variant of helical symmetry) of CA hexamers that form the body of the cone.

Packaging the Nucleic Acid Genome

      A definitive property of a virion is the presence of a nucleic acid genome. Incorporation of the genome requires its discrimination from a large population of cellular nucleic acid. This packaging process is described in Chapter 13. The volumes of closed capsids are finite. Consequently, accommodation of viral genomes necessitates a high degree of condensation and compaction. A simple analogy illustrates vividly the scale of this problem; packing of the ~150-kbp DNA genome of herpes simplex virus type 1 into the viral capsid is equivalent to stuffing some 10 ft of 22 American gauge wire (diameter, 0.644 mm) into a tennis ball. Such confinement of the genome can result in high internal pressure, equivalent to that generated in locomotive steam engines, some 18 and 25 atm within herpes simplex virus type 1 and phage capsids, respectively. Such pressure provides the force that powers ejection of DNA genomes. Packaging of nucleic acids is an intrinsically unfavorable process because of the highly constrained conformation imposed on the genome. In some cases, the force required to achieve packaging is provided, at least in part, by specialized viral proteins that harness the energy released by hydrolysis of ATP to drive the insertion of DNA. In many others, the binding of viral RNA or DNA genomes to capsid proteins appears to provide sufficient energy. The latter interactions also help to neutralize the negative charge of the sugar-phosphate backbone, a prerequisite for close juxtaposition of genome sequences.

      We possess relatively little information about the organization of genomes within viral particles: nucleic acids or protein-nucleic acid assemblies are not visible in the majority of high-resolution structural studies reported. This limitation indicates that the genomes or internal structures lack the symmetry of the capsid, do not adopt the same conformation in every viral particle, or both. Nevertheless, three mechanisms for condensing and organizing nucleic acid molecules within capsids can be distinguished and are described in the following sections.

Direct Contact of the Genome with a Protein Shell

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