MicrobiologyBytes: Introduction to Microbiology: Virus Structure Updated: August 23, 2007 Search

Virus Structure

Detailed notes for these documents can be found in Chapter 2 of Principles of Molecular Virology.

CoverStandard Version: The 4th edition contains new material on virus structure, virus evolution, zoonoses, bushmeat, SARS and bioterrorism, CD-ROM with FLASH animations, virtual interactive tutorials and experiments, self-assessment questions, useful online resources, along with the glossary, classification of subcellular infectious agents and history of virology. (Amazon.co.uk)

Cover Instructors Version: The 4th edition contains new material on virus structure, virus evolution, zoonoses, bushmeat, SARS and bioterrorism, CD-ROM with all the Standard Version content plus all the figures from the book in electronic form and a PowerPoint slide set with complete lecture notes to aid in course preparation. (Amazon.co.uk)

At the simplest level, the function of the outer shells (CAPSID) of a virus particle is to protect the fragile nucleic acid genome from:

  • Physical damage - Shearing by mechanical forces.
  • Chemical damage- UV irradiation (from sunlight) leading to chemical modification.
  • Enzymatic damage - Nucleases derived from dead or leaky cells or deliberately secreted by vertebrates as defence against infection.
The protein subunits in a virus capsid are multiply redundant, i.e. present in many copies per particle. Damage to one or more subunits may render that particular subunit non-functional, but does not destroy the infectivity of the whole particle.

Furthermore, the outer surface of the virus is responsible for recognition of the host cell. Initially, this takes the form of binding of a specific virus-attachment protein to a cellular receptor molecule. However, the capsid also has a role to play in initiating infection by delivering the genome from its protective shell in a form in which it can interact with the host cell.

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.
How do these simple organisms solve these difficulties? The information to answer these problem lie in the rules of symmetry.

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

Tobacco mosaic virus (TMV) is representative of one of the two major structural classes seen in viruses of all types, those with helical symmetry. The simplest way to arrange multiple, identical protein subunits is to use rotational symmetry & to arrange the irregularly shaped proteins around the circumference of a circle to form a disc.
Multiple discs can then be stacked on top of one another to form a cylinder, with the virus genome coated by the protein shell or contained in the hollow centre of the cylinder.

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:

Helices are rather simple structures formed by stacking repeated components with a constant relationship (amplitude & pitch) to one another - note that if this simple constraint is broken a spiral forms rather than a helix - unsuitable for containing a virus genome.

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:

An alternative way of building a virus capsid is to arrange protein subunits in the form of a hollow quasi-spherical structure, enclosing the genome within. The criteria for arranging subunits on the surface of a solid are more complex than those for building a helix.

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:

If the virus particle became covered in a smooth, unbroken lipid bilayer, this would be its undoing. Such a coating is effectively inert, & though effective as a protective layer preventing desiccation of or enzymatic damage to the particle, would not permit recognition of receptor molecules on the host cell. Therefore, viruses modify their lipid envelopes by the synthesis of several classes of proteins which are associated in one of three ways with the envelope:

Complex Virus Structures

The majority of viruses can be fitted into one of the three structural classes outlined above, i.e. those with helical symmetry, icosahedral symmetry or enveloped viruses based on either of these two.

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.

 

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Protein-nucleic acid interactions & genome packaging

In most cases, the linear virus genome when stretched out in solution is at least an order of magnitude longer than the diameter of the capsid.
Folding the genome in order to stuff it into such a confined space is quite a feat of topology, but is compounded by repulsion by the cumulative negative electrostatic charges on the phosphate groups of the nucleotide backbone resulting in the genome resisting being crammed into a small space. Viruses overcome this difficulty by packaging along with the genome a number of positively-charged molecules in order to counteract this negative charge repulsion. These include: Some of these latter proteins are virus-encoded & contain amino acids with basic side-chains such as arginine & lysine which interact with the genome.

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

Cellular receptor molecules used by a number of different viruses from diverse taxonomic groups have now been identified. This is achieved by binding of a specific virus-attachment protein on the outer surface of the virion to a cellular receptor molecule on the outer surface of the host cell. The interaction of viruses with a cellular receptors is a major event in determining the subsequent events in replication & the outcome of infections. It is this interaction which 'activates' extracellular virus particles & initiates the replication cycle.

Other interactions of the virus capsid with the host cell:

The function of the virus capsid is not only to protect the genome, but also to deliver it to a suitable host cell & more specifically, the appropriate compartment of the host cell (in the case of eukaryote hosts) to allow replication to proceed.

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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