Virion Structure

I. Nucleic Acids

The genomic nucleic acid of animal viruses can be double-stranded DNA, single stranded DNA, double stranded RNA, or single stranded RNA. With the exception of the hepadna viruses (Hepatitis B virus) whose genomic DNA is partially single stranded and partially double stranded, a particular virus only has one of these forms of nucleic acid in its virion. Viruses with double- stranded DNA or single-stranded RNA are most abundant. A single family exists which has double stranded RNA as its genome and a single family exists which has single-stranded DNA as its genome.

Properties and considerations of each type of genomic nucleic acid:

Because it is identical to the cell's DNA, viruses with this type of nucleic acid can borrow all of their synthetic enzymes from the cell. Because these enzymes are localized in the nucleus of the cell, all of the DNA viruses except for the poxviruses replicate in the nucleus of the infected cell.

DNA viruses show a great range in complexity- from 3000 nucleotide pairs to 250,000 nucleotide pairs. The simplest of these viruses utilize the cell's DNA synthetic machinery and RNA polymerase. Intermediate to large DNA viruses encode their own DNA polymerase and DNA binding proteins, but still utilize the cell's RNA polymerase. The large DNA viruses also encode some enzymes which can synthesize and modify nucleotide precursors. The poxviruses have the largest repetoire of DNA synthetic enzymes and also encode their own RNA polymerase.

Double-stranded DNA as a molecule is rigid and highly negatively charged (because of the PO4 groups). Because of the rigidity, double-stranded DNA containing animal viruses uniformly have icosahedral nucleocapsids. The DNA is usually coiled and supercoiled into a compact form inside the nucleocapsid. The presence of basic proteins and polycations (spermidine and putrescine) is common. The papovaviruses (SV40) incorporate cell histones which complex the virion DNA into a chromatin-like structure.

Different forms of double-stranded DNA are found:

Circular DNA's held in a circular configuration either by covalent bonding or by the presence of complementary sequences at each end ("sticky ends").

Linear DNA's which often contain terminal or inverted terminal repeats. The linear strands of the Poxvirus DNA are chemically crosslinked. Adenovirus DNA has covalently linked proteins at the 5' terminus of each strand of the genomic DNA

Reasons for these different structures:

          1. Chemical resistance to exonucleases
          2. Circular DNAs retain their supercoil
          3. Completion of the copying of the 3' end of the DNA template during DNA replication

One family of animal viruses, the parvoviruses, has single stranded DNA in their virions. These viruses are extremely simple, having a size of 5000 nucleotides. In the infected cell, the single stranded virion DNA is converted to a double stranded DNA replicative form by cell polymerases. This replicative form is then the template for more single stranded virion DNAs. With the exception of the retrovirus family, the genomic RNA of ss RNA viruses skips any DNA step in its replication cycle and is replicated via a complementary ss RNA intermediate. This step necessitates the availability of an enzyme which can synthesize product RNA from an RNA template (an RNA-dependent-RNA polymerase). Such enzymes are not found in animal cells and thus the virus must encode such enzymes in its genome.

Because RNA viruses are not dependent on cellular enzymatic machinery for replication of their nucleic acid, most families of these viruses replicate entirely in the cytoplasm of the infected cells (the exceptions are the myxoviruses and the retroviruses).

The RNA of 5 ss RNA virus families can be translated directly on ribosomes. These genomes are known as being "plu-sense" or "plus-polarity". Five other ss RNA virus families have a genomic RNA which is complementary to the virus messenger RNA and therefore must be transcribed into messenger RNA during the replication cycle. Such viruses are known as "minus sense" or "minus-polarity" and have virion associated RNA-dependent-RNA-polymerases to accomplish this function. Two families (the bunya and arena viruses) can have genomic RNAs which are both plus and minus sense.

The genomes of some ss RNA aminal viruses are segmented and consist of from 2 to 8 segments (all enclosed in the same virion). Some segmented single stranded RNA viruses of plants (with 2 or 3 segments) have their segments in different virions- these are known as viruses with bipartite or tripartite genomes.

The retroviruses are the unique member of this class of viruses. First, they have a diploid genome- two identical pieces of single stranded RNA in the virion. Second, the virion contains an enzyme (RNA-dependent-DNA polymerase or reverse transcriptase) which uses this RNA as a template for the synthesis of double stranded DNA which integrates into the cell DNA. Copies of the virion RNA are then synthesized by the cell's RNA polymerase.

Structurally, RNA is very flexible and can be fit into a helical as well as icosahedral capsid. The capsid proteins of RNA viruses usually have a basic, electropositive domain which interacts with the RNA and neutralizes its negative charge. Ss RNA can base pair with itself and form a secondary structure. This can be important in gene regulation and virion structure.

Plus-sense RNA viruses tend to have isometric capsids which allow easy escape of the RNA which is then translated on cell ribosomes. Negative-sense RNA viruses all have helical capsids in which the virion RNA is held in an extended form along which the virion associated polymerase can transcribe.

One RNA animal virus family, the reoviruses, has a ds RNA as a genome. These RNAs are segmented (10 to 11 segments) and each segment is short (<2000 nucleotide pairs). The virion of these viruses is icosahedral and contains a transcriptase which synthesizes mRNAs from the genomic template.

The genomes of RNA viruses are limited in size. The largest genome is that of the coronaviruses which is 30,000 nucleotides in length. However, the other families have genomes of between 7000 and 15,000 nucleotides. The reason for this size limitation is that the polymerases which replicate the RNAs of these viruses have no correction or proofreading system as do the DNA polymerases of cells which correct errors made by the polymerases. Polymerases make errors at a rate of between 1 in 104 to 1 in 105. Such errors can cause a fatal mutation. Therefore, the size of an RNA genome is limited by the error rate of its polymerase. Only 1 in 10 virions produced during an infection cycle is infectious. The 9/10 noninfectious particles may contain such mutations. The rapid, polymerase-induced mutation rate inherent in these RNA viruses allows these viruses to evolve rapidly in response to selective pressure (such as antibody reponse) and is responsible for epidemiological phenomena such as antigenic drift.

RNA viruses are thought to be more primitive than DNA viruses. At the beginning of cell life, RNA is thought to have been the original form of nucleic acid. Besides carrying genetic information, RNA can also serve a structural function (as in the ribosomal RNAs) and enzymatic functions have been documented. As cell life progressed, a more stable repository of genetic information (DNA) was evolved, and RNA came to be a labile species which had messenger, structural, and possibly enzymatic functions. Because RNA viruses have enzymes (RNA-dependent-RNA polymerases) which can no longer be found in cells, it is

thought that these viruses evolved at a time when these enzymes were present in cells (before the advent of DNA).

II. Capsids

The are two basic types of capsids: rod-shaped and spherical

The advantages to these types of structure can be explained geometrically. These two types of capsids actually helical and icosahedral in architecture. Because of the geometric nature of these architecture, capsids are termed as having helical or icosahedral "symmetry".

Viruses are simple and have limited genomic coding potential. Capsids are quite large having a minimal molecular weight of 10 X 106 daltons. There is no feasible way for viruses to code for a protein of this size and therefore the capsid is made up of a large number of protein subunits. Again, because of the simplicity of the viral genome, the number of different proteins which can be used is limited and ideally the capsid should consist of multiple copies of a single protein. With a single capsid protein species interacting with other copies of itself, the diversity of protein:protein interactions which hold the capsid together is limited. Therefore, a geometric design in which each protein is in the same interactive environment is favored. The protein:protein interactions which hold the capsid together are hydrophobic interactions and hydrogen bonding.

The helix is the simplest 3-dimensional arrangement which meets these criteria. All helical capsids consist of a single capsid protein. The nucleic acid runs up the center of the helix, providing a structural backbone on which the helix can assemble and determining the length of the capsid. The flexibility of the capsid is determined by the strength of the protein:protein interactions.

 
An icosahedron, a 20-faced solid, also fits these geometric requirements. Up to 60 identical subunits can thus be accommodated in an equivalent environment and the simplest plant viruses have such a structure. The subunits can consist of a single protein, but can also consist of a complex formed by a number proteins. The simple icosahedron limits the size of the capsid. Larger capsids with cubic symmetry have evolved by using larger numbers of subunits forcing these subunits to fit into the resulting "quasi-equivalent" environment. The number of subunits that can be incorporated is determined by the "triangulation number" (1,3,4 etc.). A T=3 capsid will have 180 subunits. Subunits meeting in groups of 6 form hexamers and subunits meeting in groups of five at the 12 vertices form pentamers. In some viruses, notably adenoviruses, different capsid proteins form the hexamers and pentamers.

The subunits of a virion which can be recognized by electron microscopy are called capsomers. Each capsomer consists of from 1 to 6 protein subunits, depending on the virus.

There are advantages and disadvantages to each type of capsid symmetry.

Helical symmetry:

1. Readily self assembles.

2. Maximal nucleic acid-protein interaction

1. Must be completely broken down for nucleic acid release.

2. Maximal surface/volume ratio

3. Contortion of nucleic acid too great to accommodate double stranded nucleic acid

Icosahedral symmetry:

1. Minimum surface/volume ratio

2. Need not disassemble to release nucleic acid

3. Accommodates both single and double stranded nucleic acid

1. Difficult to self assemble. This problem is sometimes overcome by:

    A. Conformational changes of promoters after assembly-often in the form of a proteolytic cleavage

    B. The presence of non-capsid proteins which provide a scaffold on which the capsid is assembled. These "scaffolding proteins" may either be reused or broken down after assembly

In many viruses, the capsid is the virion. Such virions are called "naked" virions. In such virions, the capsid proteins must contain the virus receptors capable of recognizing receptors on the surface of the cell for adsorption, penetration, and entry to occur.

The structures of the capsids of a number of viruses have been solved both by X-ray diffraction analysis of crystals and by cryo-electronmicroscopy. Although viruses conform to geometrical principles, there surfaces are not planar but are decorated with features that resebmle ridges and canyons, as is shown in the following image of poliovirus, a naked, icosahdedral virus:

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Click here for access to a library containing images, some video, of a number of viruses whose capsid structure has been resolved.
 
 III. Envelopes

In a large number of viruses, the capsid is surrounded by a lipid bilayer or envelope. The lipid bilayer is appropriated from the cells membranes and therefore has a lipid content similar to that of the cell membrane from which it was derived. Virion envelopes are obtained by budding of the capsid through cell membranes, surrounding itself with membrane as it buds. Most viruses bud through the cytoplasmic or intracytoplamic membranes (vacuole membranes, Golgi membranes, endoplasmic reticulum membranes). The exception are the Herpes viruses which bud through the nuclear membrane.

Virus envelopes contain no cell proteins, but do contain virus specific proteins. Two general types of virion membrane proteins occur:

Virion glycoproteins have the following functions: