In this article we will discuss about the morphology and components of virions.
Morphology of Virions:
The knowledge about the structure of virions could be gathered mainly by electron microscopy and X-ray diffraction studies. The application of these physical techniques combined with the chemical analyses of the viruses revealed the architectural details of the virions.
Viruses are among the smallest biological agents. The size of virions varies widely. The largest ones, like smallpox-viruses, are almost of the size of the smallest bacteria, like rickettsiae. The smallest ones, like Parvovirus, have diameters of about 20 nm. A comparison of dimensions of some bacteria and viruses is shown in Table 6.1. For convenience the dimensions of bacteria have been given in the same units i.e. nm, though for bacteria the usual unit is µm.
The virions consist of two basic components, a nucleic acid core which constitutes the viral genome and a surrounding protein shell, known as the capsid. The two together forms the nucleocapsid. Many viruses have an additional membranous covering enclosing the nucleocapsid.
It is known as an envelope. A virion without an envelope is called naked. The capsid protects the genome which is either DNA or RNA and gives a definite shape to the virion. In contrast, the envelope is often loose, without a definite shape.
Generally, the virions have two types of morphological symmetry. They are either icosahedral or helical. An icosahedron is a solid-geometrical structure, a polyhedron consisting of 20 equilateral triangles with 12 corners. The helical virions are cylindrical, consisting of a tightly coiled capsid with a central hollow core containing the nucleic acid. Both icosahedral and helical viruses may be naked or enveloped.
Some viruses, like many bacteriophages, are complex and have both types of symmetries in a single virion. Such viruses have an icosahedral head and a cylindrical tail with helical symmetry. Some bacteriophages have more complex structures in having a collar, a tail plate, a tail sheath and tail fibres.
The structures of some virions are diagrammatically drawn in Fig. 6.1:
Components of Virions:
1. The Capsid:
It is the protein shell enclosing the viral genome. The nucleic acid together with some associated basic proteins forms the core of the virion. The relatively small genomes of the viruses cannot make many proteins. Therefore the viruses cannot afford too many proteins for building the capsid.
The capsid of tobacco mosaic virus, for example, contains only a single polypeptide. In the icosahedral viruses, the capsid is made from one to several polypeptides. The polypeptides fold to form the basic structural unit of the capsid, known as a protomer.
The protomers may associate with each other to form a capsomer. In icosahedral viruses five protomers form a pentameric capsomer, or six protomers are associated to form a hexameric capsomer. In a single virion, both pentameric and hexameric capsomers are present to give the characteristic shape and size to the virion. The number of total capsomers is characteristic for the particular virus. Thus, herpes virus has 162 capsomers and adenoviruses have 252 capsomers (Fig. 6.2).
In helical viruses, the capsomers are linked to each other to form a long chain which folds into a helix with a hollow core through which the nucleic acid molecule passes. Each helical virus has a fixed diameter and its length is determined by the size of the nucleic acid. For example, TMV has a diameter of 15 to 18 nm and a length of 300 nm. Its genome which is a single-stranded RNA has 6,000 nucleotides.
The RNA molecule lies in a groove within the hollow core of the helical capsid consisting of a single kind of protomers. The capsid polypeptide of TMV contains 158 amino acid residues coded by only 474 nucleotides out of the total 6,000 nucleotides present in TMV RNA genome.
A model of the TMV based on X-ray diffraction studies made by klug and caspar is diagrammatically represented in Fig. 6.2:
2. The Envelope:
In some viruses the nucleocapsid is enclosed by an envelope. The envelope consists of lipids and proteins, and the latter is sometimes covalently linked to carbohydrates. The envelope lipids and carbohydrates generally originate from the cytoplasmic or nuclear membrane of the host cell.
The envelope proteins are usually specified by the viral genome. Because of the fluidity of the lipids, envelopes are flexible and form a loose covering. The enveloped viruses may, therefore, assume different shapes (pleomorphic).
Depending on the virus, the carbohydrate-protein complexes (glycoproteins) may form projections on the outer surface of the envelope. These projections are called spikes or peplomers. The spikes have definite size and they are distributed evenly at definite intervals. The influenza virus has an enveloped virion with spikes. The spikes are 10 nm high and are at a distance of 8 nm from each other. The spikes of influenza virus have enzymatic activities of two kinds.
Some spikes having haemagglutinin activity help in attachment to RBCs of host cells causing haemagglutination. Other spikes have neuraminidase activity which probably helps in gaining entry into the host cell. Neuraminidase can cleave sialic acid residues of carbohydrates found on the surface of many types of human cells.
The structure of sialic acid is shown in Fig. 6.3:
3. Viral Nucleic Acids (Genome):
The most important constituent of a virus is its nucleic acid. It encodes the genetic information for synthesis of viral proteins. The genome consists of either DNA or RNA. Its size varies widely ranging between only 100 codons in very small viruses and 100,000 codons in large viruses. For example, polyoma virus has only 4-5 genes, while X-phage has 46 genes, herpes virus has 150 genes and smallpox virus has 240 genes.
The nucleic acid, DNA or RNA may be single-stranded (ss) or double-stranded (ds) depending on the virus. On the basis of nucleic acids, viruses can be classified into four categories, viz. ss-RNA viruses, ds-RNA viruses, ss-DNA viruses and ds-DNA viruses. These categories are present in all the three major groups, like animal, plant and bacterial viruses.
However, the occurrence of the four categories of genomes in these three groups is not uniform. For example, majority of plant viruses are ss-RNA viruses. Similarly, majority of bacteriophages have ds-DNA genome. Most of the mycophages have ds-RNA.
Examples of some viruses with their genome constitution and genome size are shown in Table 6.2:
Another important feature of nucleic acids in viruses is that they may be linear or circular. Majority of animal DNA viruses have a linear molecule, whether the DNA is single- or double- stranded. Sometimes, the terminal nucleotides of either ss-DNA or ds-DNA are complementary e.g. in ss-DNA of parvovirus or ds-DNA of adenovirus.
The complementary ends of such molecules help in formation of a circular molecule. The ds-DNA of λ-phage is also a linear molecule with 12-nucleotide long single-stranded cohesive ends which help in circularization. Some bacteriophages, like T-even coliphages e.g. T1, T3 etc. have an unnatural base, 5-methyl cytosine and coliphage T4 has 5-hydroxymethyl cytosine.
The structures of these unnatural bases are shown in Fig. 6.4:
Some plant viruses have circular ds-RNA. But animal RNA viruses have generally linear molecules. The RNA in some viruses occurs in several segments. For example, the ss-RNA of influenza virus is divided in eight segments.
Another interesting feature of ss-RNA viruses is that, in some, the viral RNA can directly act as m-RNA e.g. in the picorna viruses like poliovirus. Such viral RNA is designated as positive (+) strand. In other ss-RNA viruses, like influenza virus or mumps virus, the viral RNA is first transcribed into a complementary RNA with the help of a virion-borne transcriptase.
The complementary RNA then acts as messenger directing protein synthesis. In this case the virion RNA is designated as minus (-)-strand. If the viral RNA is segmented as in influenza virus, each segment is transcribed into a separate m-RNA.
The situation in the retroviruses which also have ss-RNA as virion nucleic acid is quite different from other RNA viruses. In retroviruses, such as HIV (human immunodeficiency virus), the RNA present in the virions acts as a template for synthesis of a complementary DNA (c-DNA) strand with the help of an RNA-dependent DNA polymerase, commonly known as reverse transcriptase.
The enzyme is present in the virions of HIV. The c-DNA is then converted to a ds-DNA which carries the genetic information of the viral RNA. This DNA then directs viral protein synthesis by the usual transcription and translation process exploiting the host biochemical machinery.
4. Other Components of Virions:
The nucleic acid core of virions contains some basic proteins associated with the genome. In some animal viruses, these proteins resemble histones and protamine’s. In bacteriophages, the core proteins are polyamines, like spermine and spermidine. Presumably, these basic core proteins function as stabilizing factors in keeping the loops of polynucleotide chains of DNA or RNA in a compact folded form.
Besides the core proteins, viruses also contain other proteins. Some of these are glycoproteins which form the spikes or peplomers on the envelope. Others are non-glycosylated, like the matrix proteins found in the inner side of the envelope surrounding the nucleocapsid.
Apart from these structural proteins, some viruses contain special enzymes which are not available in the host cells and which are required for completing their life cycle. For example, influenza virus contains an RNA transcriptase which is an RNA-dependent RNA polymerase and is used for synthesizing m-RNA from the ss-RNA of the viral genome.
Similarly, the retroviruses, like HIV, carry reverse transcriptase which synthesizes DNA using the viral RNA as template. Vaccinia viruses contain a DNA transcriptase for synthesizing RNA. Some of the coliphages possess endo-glycosidases which catalyse cleavage of capsular polysaccharides of the host bacteria. Thus, it is evident that many viruses contain besides the capsid proteins, other proteins having either a catalytic or structural function.