Virus Structure

To form an infectious particle, a virus must overcome two fundamental problems:

1. To assemble the particle utilizing only the information available from the components which make up the particle itself (capsid + genome).
2. Virus particles form regular geometric shapes, even though the proteins from which they are made are irregularly shaped.

In 1957, Fraenkel-Conrat & Williams showed that when mixtures of purified tobacco mosaic virus (TMV) RNA & coat protein were incubated together, virus particles formed. The discovery that virus particles could form spontaneously from purified subunits without any extraneous information indicated that the particle was in the free energy minimum state & was therefore the favoured structure of the components. This stability is an important feature of the virus particle.

Although some viruses are very fragile & are essentially unable to survive outside the protected host cell environment, many are able to persist for long periods, in some cases for years.

Helical capsids

Closer examination of the TMV particle by X-ray crystallography reveals that the structure of the capsid actually consists of a helix rather than a pile of stacked disks.

A helix can be defined mathematically by two parameters:

• amplitude (diameter)   &
• pitch (the distance covered by each complete turn of the helix)

TMV particles are rigid, rod-like structures, but some helical viruses demonstrate considerable flexibility & longer helical virus particles are often seen to be curved or bent. Flexibility is important attribute since long helical particles are subject to damage from shear forces & the ability to bend reduces the chance of breakage.

The fact that helical symmetry is a useful way of arranging a single protein subunit to form a particle is confirmed by the large number of different types of virus which have evolved with this capsid arrangement.

Icosahedral (isometric) capsids:

In the 1950s, Brenner & Horne (among others) developed sophisticated techniques which enabled them to use electron microscopy to reveal many of the fine details of the structure of virus particles. One of the most useful techniques proved to be the use of electron-dense dyes such as phosphotungstic acid or uranyl acetate to examine virus particles by negative staining. The small metal ions in such dyes are able to penetrate the minute crevices between the protein subunits in a viral capsid to reveal the fine structure of the particle.

Francis Crick & James Watson (1956), were the first to suggest that virus capsids are composed of numerous identical protein sub-units arranged either in helical or cubic (=icosahedral) symmetry.

In order to construct a capsid from repeated subunits, a virus must 'know the rules' which dictate how these are arranged. For an icosahedron, the rules are based on the rotational symmetry of the solid, which is known as 2-3-5 symmetry:

An axis of two-fold rotational symmetry through the centre of each edge An axis of three-fold rotational symmetry through the centre of each face An axis of five-fold rotational symmetry through the centre of each corner (vertex)

To help you understand this further, you can build your own icosahedral virus particle.

The simplest icosahedral capsids are built up by using 3 identical subunits to form each triangular face, thereby requiring 60 identical subunits to form a complete capsid. A few simple virus particles are constructed in this way, e.g. bacteriophage ØX174:

In most cases, analysis reveals that icosahedral virus capsids contain more than 60 subunits, for the reasons of genetic economy given above. The capsids of picornaviruses provide a good illustration of the construction of icosahedral virus particles (e.g. polioviruses, foot-and-mouth disease virus, rhinoviruses).

Poliovirus

Foot & Mouth Disease Virus (FMDV)

Enveloped viruses

'Naked' virus particles, i.e. those in which the capsid proteins are exposed to the external environment are produced from infected cells at the end of the replicative cycle when the cell dies, breaks down & lyses, releasing the virions which have been built up internally. This simple strategy has drawbacks. In some circumstances it is wasteful, resulting in the premature death of the cell.

Many viruses have devised strategies to exit the infected cell without its total destruction. This presents a difficulty in that all living cells are covered by a membrane composed of a lipid bilayer. The viability of the cell depends on the integrity of this membrane. Viruses leaving the cell must therefore allow this membrane to remain intact & this is achieved by extrusion (budding) of the particle through the membrane, during which process the particle becomes coated in a lipid envelope derived from the host cell membrane & with a similar composition:

The structure underlying the envelope may be based on helical or icosahedral symmetry & may be formed before or as the virus leaves the cell. In the majority of cases, enveloped viruses use cellular membranes as sites allowing them to direct assembly. The formation of the particle inside the cell, maturation & release are in many cases a continuous process.
The site of assembly varies for different viruses. Not all enveloped viruses bud from the cell surface membrane, many viruses use cytoplasmic membranes such as the golgi complex, others such as herpesviruses which replicate in the nucleus may utilize the nuclear membrane. In these cases, the virus is usually extruded into some form of vacuole, in which it is transported to the cell surface & subsequently released.

Envelope Proteins:

• Matrix Proteins: These are internal virion proteins whose function is effectively to link the internal nucleocapsid assembly

• Glycoproteins: These are transmembrane proteins, anchored to the membrane by a hydrophobic domain & can be subdivided into two types, by their function:
  • External Glycoproteins - Anchored in the envelope by a single transmembrane domain. Most of the structure of the protein is on the outside of the membrane, with a relatively short internal tail. Often individual monomers associate to form the 'spikes' visible on the surface of many enveloped viruses in the electron microscope. Such proteins are the major antigens of enveloped viruses.

  • Transport Channels - This class of proteins contains multiple hydrophobic transmembrane domains, forming a protein-lined channel through the envelope, which enables the virus to alter the permeability of the membrane, e.g. ion-channels.

Complex Virus Structures

However, there are many viruses whose structure is more complex. In these cases, although the general principles of symmetry already described are often used to build part of the virus shell (this term being appropriate here since such viruses often consist of several layers of protein & lipid), the larger & more complex viruses cannot be simply defined by a mathematical equation as can a simple helix or icosahedron.

Because of the complexity of some of these viruses, they have defied attempts to determine detailed atomic structures using the techniques described earlier.

Poxviruses:

An example of such a group & the problems of complexity is shown by the members of the poxvirus family. These viruses have oval or 'brick-shaped' particles 200-400nm long. In fact, these particles are so large that they were first observed using high resolution optical microscopes in 1886 & thought at that time to be 'the spores of micrococci'.

The external surface of the virion is ridged in parallel rows, sometimes arranged helically. The particles are extremely complex & have been shown to contain more than 100 different proteins.
Antigenically, poxviruses are very complex, inducing both specific & cross-reacting antibodies - hence ability to vaccinate against one disease with another virus (i.e. the use of vaccinia virus to immunize against smallpox (variola) virus).
Poxviruses & a number of other complex viruses also emphasise the true complexity of some virus - there are at least ten enzymes present in poxvirus particles, mostly concerned with nucleic acid metabolism/genome replication.

Tailed Phages:

In other cases, the particle structure of complex viruses has been much more completely investigated. One of the prime examples of such a group are the tailed phages of Escherichia coli. These viruses have been extensively studied for excellent reasons - they are easy to propagate in bacterial cells & can be obtained in high titres & are easily purified, facilitating biochemical & structural studies.

The head of the particle consists essentially of an icosahedral shell attached via a collar to a contractile, helical tail. At the end of the tail is a plate which functions in attachment to the bacterial host & also in penetration of the bacterial cell wall by virtue of lysozyme-like enzymes associated with the plate. In addition to these structures, thin protein fibres are attached to the plate, which along with the tail plate, are involved in binding to the receptor molecules in the wall of the host cell.

In detail, the structure of these phages is rather more complex than this simple picture, for example, there are several internal proteins & polyamines associated with the genomic DNA in the head & an internal tube structure inside the outer sheath of the helical tail. In the infected bacterial cell, there are separate assembly pathways for the head & tail sections of the particle, which come together at a late stage to make up the virion.

Protein-nucleic acid interactions & genome packaging

• small positively charged ions (Na, Mg, K, etc)
• polyamines
• various nucleic acid-binding proteins

Many viruses with double-stranded DNA genomes have basic histone-like molecules closely associated with the DNA. Some of these are virus-encoded, in other cases, the virus may utilize cellular proteins, e.g. the polyomavirus genome assumes a chromatin-like structure in association with four cellular histone proteins, similar to that of the host cell genome.

The second problem the virus must overcome is to achieve the specificity required to select & encapsidate the virus genome from the large background of cellular nucleic acids. In most cases, by the late stages of virus infection when assembly of virus particles occurs, transcription of cellular genes has been reduced & a large pool of virus genomes have accumulated. The overproduction of viral nucleic acids eases but does not eliminate the problem of specific genome packaging. Therefore, a specific virus-encoded capsid or nucleocapsid protein is required to achieve this end. Hence many viruses, even those with relatively short, compact genomes such as retroviruses & rhabdoviruses encode this type of protein.

The other side of the packaging equation are the specific nucleotide sequences in the genome (the packaging signal) which permit the virus to select genomic nucleic acids from the cellular background. The packaging signal from a number of virus genomes has been identified.

Viruses with segmented genomes face further problems. Not only must they encapsidate only viral nucleic acid & exclude host cell molecules, but they must also attempt to package one of each of the required genome segments. Like many other aspects of virus assembly, the way in which packaging is controlled is not well understood, but the key must lie in the specific molecular interactions between the genome & the capsid. In general, the physical structure of virus genomes within virus particles has been poorly studied.

Virus Receptors - Recognition & Binding

Other interactions of the virus capsid with the host cell:

An example are the nucleocapsid proteins of viruses which replicate in the nucleus of the host cell. These molecules contain within their primary amino acid sequences 'nuclear localization signals' which are responsible for the migration of the virus genome plus its associated proteins into the nucleus where replication can occur.

Virions are not inert structures. Many virus particles contain one or more enzymatic activities, although in most cases these are usually not active outside the biochemical environment of the host cell.

All viruses with negative-sense RNA genomes must carry with them a virus-specific RNA-dependent RNA polymerase since uninfected cells have no mechanism for RNA-dependent RNA polymerization & therefore, genome replication could not occur if this enzyme were not included in the virus particle. The more complex DNA viruses (e.g. herpesviruses & poxviruses) carry a multiplicity of enzymes in the particles, mostly concerned with nucleic acid metabolism in some way.

SUMMARY:

1. To protect the genome

2. To deliver the genome to the appropriate site in the host cell so that it can be replicated.

3. A number of repeated structural motifs found in many different virus groups are evident. The most obvious is the division of many virus structures into those based on helical or icosahedral symmetry.

4. Virus particles are not inert. Many are armed with a variety of enzymes which carry out a range of complex reactions, most frequently concerned with the replication of the genome.

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© MicrobiologyBytes 2007.