B.SC. PART[I] FIRST YEAR BOTONY
LESSION—2
Viruses, Viroids and Prions
VIRUSES
M.
W. Beijerinck, a Dutch
bacteriologist, demonstrated in 1898 that viruses differ from other cellular
organisms. He discovered that the virus of tobacco mosaic disease could be
precipitated from a suspension of alcohol without losing its infectious power
and the fluid was capable of diffusing through agar gel. These characteristics
are not possessed by bacteria or any other living organism. This led Beijerinck
to believe that the fluid itself was living and he put forward the principle of
Contagium vivum fluidum (infectious living fluid). In
the same year, Loeffer and Frosch demonstrated that foot and mouth disease of
cattle is caused by a filtrate apparently free of any bacteria. They concluded
that if the agent of this disease is particulate, it must be smaller than the
diameter of the smallest known bacteria. Nearly 40 years after these
observations, the structure of virus was studied by Wendell M. Stanley, an organic chemist, in 1935. He
showed that the infectious principle of virus could be crystallized and that
the crystals consisted largely of proteins. For many years it was thought that
virus is simply a protein molecule, but later it was discovered that virus
contains a small but constant amount of RNA or DNA in addition to protein. A
virus is therefore, not simply a protein but a nucleoprotein and its infectious
principle is the nucleic acid rather than protein. Stanley was awarded Nobel
prize in 1946 for this discovery.
Subsequently, many already known
diseases like mumps chicken pox and hog cholera, as well as many newly
identified diseases, were found to be caused by filterable agents, i.e.,
viruses. An English scientist, F.W. Twort (1915), and a Canadian, Felix d,
herelle (1917), independently discovered that a virus was capable of dissolving
or lysing bacterial cells. This virus was designated as bacteriophage, i.e., eater of bacteria.
Luria (1953) described viruses as
submicroscopic entities capable of being introduced into specific living cells
and reproducing inside such cells only. According to Andre Lwoff (1966), a
Nobel Laureate French virologist, the most appropriate definition of viruses is
viruses are viruses. Some biologists think that viruses are descendants of
cellular organisms that have become highly specialized as parasites, others
consider that viruses were originally fragments of DNA or RNA broken off from
the nucleic acid of cellular organisms. However, it is now well established
that viruses are obligately parasitic,
self replicating non-cellular organism and essentially composed of a protein
covering surrounding a central nucleic acid molecule (either DNA or RNA). Most of
the modern virologists prefer not to define viruses by any specific definition
but describe them by their various physical, chemical, biological and clinical
properties.
Origin
of Viruses
The origin of viruses has been a subject of
considerable speculation in the scientific community. However there is general
agreement that viruses (phage) probably infected bacteria during the period
when Archaea and Eubacteria were the sole life forms on the earth. Later, when
eukaryotes evolved they were also attacked by viruses. Following three major
theories have been proposed for the origin of viruses.
[I] Theory
of Coevolution
According to this theory viruses
originated in the primordial soup and coevolved with the more complex life
forms (e.g., Archaea and Eubacteria). The earliest self replicating genetic
system was probably composed of RNA. RNA can promote RNA polymerization and
this process was probably accelerated by the proteins present in the primordial
soup. The DNA template is much more effective and originated early in
evolution. RNA then became the messenger between the DNA template and protein
synthesis. Thus the genetic code came into being and permitted orderly
replication. Gradually the early replicative forms became complex and became encased
in a lipid sac; thus it metabolic machinery became separated from the
surrounding environment. Such individual units may have been the ancestor of
the Archaea and Eubacteria. At the same time some replicative forms, composed
mainly of self-replicative nucleic acid surrounded by protein coat, may have
retained simplicity. This entity was the forerunner of the virus. It gradually
evolved acquired the ability to invade and take over the genetic machinery of a
host. Thus there was coevolution of the bacterium and virus.
[II]
Retrograde evolution
This theory is
based on the assumption that viruses originated from such free-living or
parasitic prokaryotes which gradually
lost biosynthetic capacity and genetic information. Eventually the
prokaryotes evolved to simply a group of genes known as virus. It seems
possible that intracellular parasitic microorganisms could have become more and
more dependent on the host cell for readymade metabolites and in the process
last much of its own biosynthetic capacity. The theory proposes intracellular
parasitic bacteria, such as rickettsiae or the chlamydae as the potential
example that could regress to viral state.
[iii] Escaped gene
theory
The theory proposes that pieces of host cell RNA or DNA gained
independence from cellular control and escaped from the cell. Living organisms
make duplicates of their genetic information by initiating replication at a
specific site called the initiation site. The replication cycle ends when a
full complement of the genome is synthesized. If initiation of replication
beings elsewhere on the genome this duplication occurs independent of host
control. A virus that could recognize nucleotide sequences at sites other than
the start site and that carried the proper polymerase could have the capacity
to produce RNA or DNA without interference from normal control mechanisms.
The origin of viruses may have been with episomes (plasmid) or
transposons. These are circular DNA molecules that replicate in cytoplasm and
can be integrated into or excised from various sites in the host chromosome.
Plasmids can also move from cell to cell carrying information such as fertility
or antibiotic resistance. Transposons are bits of DNA present in both
prokaryotic and eukaryotic cells that can move one site in a chromosome to
another site carrying genetic information. The DNA of transposon carries a gene
for synthesis of the reverse transcriptase and transposon elements with such
properties have some similarity to retroviruses. Analysis of nucleotide
sequences in viruses indicates that they are quite equivalent of specific
sequence in the host cell. Evidence accumulated so for strongly supports the
proposal that viruses originated from escaped host nucleic acid.
General Characteristics of Viruses
Viruses are sub-microscopic particles which have been studied in detail
by electron microscope using selective techniques. A simple virus particle
often designated as virion ,consists
of a nucleic acid core of genetic material enclosed within protein coat . The
amount of protein in different viruses varies from 60-95 per cent and the rest
is nucleic acid.
[I]
Size
designated as filterable
viruses (now it has been established that many microbes of bacterial nature are
also capable of passing through such filters, therefore, the word filterable
was subsequently dropped).
M.
W. Beijerinck, a Dutch
bacteriologist, demonstrated in 1898 that viruses differ from other cellular
organisms. He discovered that the virus of tobacco mosaic disease could be
precipitated from a suspension of alcohol without losing its infectious power
and the fluid was capable of diffusing through agar gel. These characteristics
are not possessed by bacteria or any other living organism. This led Beijerinck
to believe that the fluid itself was living and he put forward the principle of
Contagium vivum fluidum (infectious living fluid). In
the same year, Loeffer and Frosch demonstrated that foot and mouth disease of
cattle is caused by a filtrate apparently free of any bacteria. They concluded
that if the agent of this disease is particulate, it must be smaller than the
diameter of the smallest known bacteria. Nearly 40 years after these
observations, the structure of virus was studied by Wendell M. Stanley, an organic chemist, in 1935. He
showed that the infectious principle of virus could be crystallized and that
the crystals consisted largely of proteins. For many years it was thought that
virus is simply a protein molecule, but later it was discovered that virus
contains a small but constant amount of RNA or DNA in addition to protein. A
virus is therefore, not simply a protein but a nucleoprotein and its infectious
principle is the nucleic acid rather than protein. Stanley was awarded Nobel
prize in 1946 for this discovery.
Subsequently, many already known
diseases like mumps chicken pox and hog cholera, as well as many newly
identified diseases, were found to be caused by filterable agents, i.e.,
viruses. An English scientist, F.W. Twort (1915), and a Canadian, Felix d,
herelle (1917), independently discovered that a virus was capable of dissolving
or lysing bacterial cells. This virus was designated as bacteriophage, i.e., eater of bacteria.
Luria (1953) described viruses as
submicroscopic entities capable of being introduced into specific living cells
and reproducing inside such cells only. According to Andre Lwoff (1966), a
Nobel Laureate French virologist, the most appropriate definition of viruses is
viruses are viruses. Some biologists think that viruses are descendants of
cellular organisms that have become highly specialized as parasites, others
consider that viruses were originally fragments of DNA or RNA broken off from
the nucleic acid of cellular organisms. However, it is now well established
that viruses are obligately parasitic,
self replicating non-cellular organism and essentially composed of a protein
covering surrounding a central nucleic acid molecule (either DNA or RNA). Most of
the modern virologists prefer not to define viruses by any specific definition
but describe them by their various physical, chemical, biological and clinical
properties.
Origin
of Viruses
The origin of viruses has been a subject of considerable speculation in the scientific community. However there is general agreement that v viruses (phage) probably infected bacteria during the period when
A rchaea and Eubacteria were the sole life forms on the earth. Later when
eukaryotes evolved they were also attacked by viruses. Following three major
theories have been proposed for the origin of viruses.
[I] Theory
of Coevolution
According to this theory viruses
originated in the primordial soup and coevolved with the more complex life
forms (e.g., Archaea and Eubacteria). The earliest self replicating genetic
system was probably composed of RNA. RNA can promote RNA polymerization and
this process was probably accelerated by the proteins present in the primordial
soup. The DNA template is much more effective and originated early in
evolution. RNA then became the messenger between the DNA template and protein
synthesis. Thus the genetic code came into being and permitted orderly
replication. Gradually the early replicative forms became complex and became encased
in a lipid sac; thus it metabolic machinery became separated from the
surrounding environment. Such individual units may have been the ancestor of
the Archaea and Eubacteria. At the same time some replicative forms, composed
mainly of self-replicative nucleic acid surrounded by protein coat, may have
retained simplicity. This entity was the forerunner of the virus. It gradually
evolved acquired the ability to invade and take over the genetic machinery of a
host. Thus there was coevolution of the bacterium and virus.
[II]
Retrograde evolution
This theory is
based on the assumption that viruses originated from such free-living or
parasitic prokaryotes which gradually
lost biosynthetic capacity and genetic information. Eventually the
prokaryotes evolved to simply a group of genes known as virus. It seems
possible that intracellular parasitic microorganisms could have become more and
more dependent on the host cell for readymade metabolites and in the process
last much of its own biosynthetic capacity. The theory proposes intracellular
parasitic bacteria, such as rickettsiae or the chlamydae as the potential
example that could regress to viral state.
[iii] Escaped gene
theory
The theory proposes that pieces of host cell RNA or DNA gained
independence from cellular control and escaped from the cell. Living organisms
make duplicates of their genetic information by initiating replication at a
specific site called the initiation site. The replication cycle ends when a
full complement of the genome is synthesized. If initiation of replication
beings elsewhere on the genome this duplication occurs independent of host
control. A virus that could recognize nucleotide sequences at sites other than
the start site and that carried the proper polymerase could have the capacity
to produce RNA or DNA without interference from normal control mechanisms.
The origin of viruses may have been with episomes (plasmid) or
transposons. These are circular DNA molecules that replicate in cytoplasm and
can be integrated into or excised from various sites in the host chromosome.
Plasmids can also move from cell to cell carrying information such as fertility
or antibiotic resistance. Transposons are bits of DNA present in both
prokaryotic and eukaryotic cells that can move one site in a chromosome to
another site carrying genetic information. The DNA of transposon carries a gene
for synthesis of the reverse transcriptase and transposon elements with such
properties have some similarity to retroviruses. Analysis of nucleotide
sequences in viruses indicates that they are quite equivalent of specific
sequence in the host cell. Evidence accumulated so for strongly supports the
proposal that viruses originated from escaped host nucleic acid.
General Characteristics of Viruses
Viruses are sub-microscopic particles which have been studied in detail
by electron microscope using selective techniques. A simple virus particle
often designated as virion ,consists
of a nucleic acid core of genetic material enclosed within protein coat . The
amount of protein in different viruses varies from 60-95 per cent and the rest
is nucleic acid.
[I]
Size
Earlier the size of viruses was measured by using the technique of filtration through collodion membrance of known porosity. But now techniques like ultracentrifugation and electron microscopy are employed. Viruses are very small in size, varying over a wide range from 20-350 nm. The largest are the otrhopoxviruses, measuring about 240 nm×300 nm, i.e. , approximately 1/10 the size of a red blood cell. The complex bacteriophages are about 65 nm × 200 nm. Among the smallest viruses known are the enteroviruses, which are less than 30 nm in diameter. The dimensions of some common viruses are shown in Table 1 and Fig. 2.
[II] Nucleic acid
Viruses differ fundamentally from cellular organisms in that they contain only one type of nucleic acid which may be either DNA or RNA. The viruses containing DNA are called Deoxyviruses, where as those having RNA are known as Riboviruses. Viruses vary considerably in the structure of nucleic acids. In general (i) all plant viruses have single stranded RNA, (ii) animal viruses have either single or (rarely) double-stranded RNA or double-stranded DNA, (iii) bacterial viruses contain mostly double-stranded DNA but can also have single stranded DNA or RNA and (iv) most of the insect viruses contain RNA and only a few have DNA. The DNA of some bacterial and animal viruses is circular, but in others it is like RNA. Careful extraction of nucleic acids from viruses
has shown that a virion contains only a single molecule of nucleic acid. The number of nucleotide pairs in a molecules varies from 1,000-250,000 pairs. But the number of pairs in a specific virion is always constant. The amount of nucleic acid depends on the size of virion usually large the size of virion greater is the amount of nucleic acid.
Characteristics of
nucleic acids of some better known plant and animal viruses are given in table
2.
[III] Protein coat
The capsomeres forming the capsid (protein coat) of a virion are of two types___ pentamer, made of five identical monomers, and hexamer, having six monomers. Each monomer is connected with the neighbouring monomers on either side with the help of the bonds. Likewise, the capsomeres are also connected with each other, but the bonds between the capsomeres are weak (Fig. 3A).
In some complex forms
(e.g., influenza and herpes virus) the capsid is covered bty an envelope. It usually consists of some
combination of lipids, protein and carbohydrates. Some animal viruses, which
released from the host call by an extrusion process, get coated by the host
cell’s plasma membrane. This membrane eventually becomes the viral envelope
(Fig 3B).
Envelope of many
viruses have projections called spikes. These are made of carbohydrate-protein
complexes. Viruses attach themselves to the hodt cell by means of spikes. Besides,
the spike characteristic is an important tool for the identification of viruses.
Viruses whose running
are not covered by an envelope , are known an naked or nonenveloped viruese (e.g. , TMV). In such form the
capsid facilitates the attachment of the viruses to the host surface and also
protects the viruses nucleic acid from the nuclease enzymes present in the
biological fluids.
General Morphology of Viruses
Viruses may be classified in to various morphological types
on the basis of the capsid architecture. The structure of capsid and individual
capsomere can be studied by electron microscopy and x-ray crystallography [Figs.
4, 5]. Following are some of the common morphological forms of viruses.
[I]Helical
viruses
These viruses are cylindrical
or rod-like in form and the central nucleic acid strand is called like a
helical spring. The protein subunits (capsomeres) are helically arranged around
the helical spring. The common example of helical viruses are New Castle virus,
Mumps virus Rabies virus and Tobacoo mosaic virus (Fig. 4A).
[II] Polyhedral viruses
In these viruses the
nucleic acid is packed is an unknown manner within a hollow polyhedral head.
They have been classified further into
tetrahedral, octahedral and icosahedral
from depending upon the number of faces. Of these, icosahedral fromis
considered to be the most efficient shape because of packing and bending of
capsomeres in a near spherical from. An icosahedron has 12 corners, 20 triangular
faces and 30 edges (e. g. , Adenovirus, poliovirus; Fig. 4B).
[III] Enveloped viruses
As mentioned earlier,
the capsid of these viruses is covered by an envelope. Such viruses may be
spherical, helical or polyhedral in shape (Fig.4C).
[IV] Complex viruses
Bacterial viruses or
bacteriophages have a complex structure and are called complex viruses. For example T-even bacteriophages have a capsid (head)
to which other structures like a helical tail sheath base plate, tail fibers
and pins are attached. Another example of complex viruses are pox viruses in
which the nucleic acid is surrounded by several coats (Fig. 4D).
Classification and Nomenclature
of viruses
[I] Classification
Classification of viruses has been
problematic due to their ultramicroscopic size, presence of both living and
non-living features and absence of fossil records. Initially, viruses were
classified into the following four groups on the bases of their host range and
clinical, epidemiological and pathological symptoms.
1. Plants Viruses. These viruses infect only plants and depending upon the host
they have been subdivided into bacterial viruses, algal viruses, fungal
viruses, etc.
2.
Invertebrate Viruses. Viruses infecting invertebrates have been included in this group.
3.
Vertebrate Viruses. This group includes viruses infecting animals.
4.
Dual-host Viruses. This group includes those viruses which infect two different hosts mentioned
above.
Holmes (1948) included all viruses in a single order Virales which was included into three
suborders.
1. Phagineae. This suborder includes viruses infecting
bacteria, i.e. , bacteriophage.
2. Phytophagineae. It includes viruses infecting plants.
3. Zoophagineae. It includes viruses infecting animals.
Since viruses
are very different from cellular organisms, it is difficult to classify them
into typical taxonomic categories, viz. , kingdom, phylum etc. International committee on Taxonomy of
viruses (ICTV) has suggested ‘family’ as the highest taxonomic category for
viruses.
Major groups
of viruses are distinguished first by their nucleic acid content as either RNA
or DNA viruses. Subsequent subdivisions are based largely on several other
properties of nucleic acids which are briefly mentioned below.
The RNA viruses can be single-stranded (ssRNA) or
duble-stranded (dsRNA). Most of the RNA viruses are, however, single-stranded.
As most of the eukaryotic cells do not have the enzymes to copy viral RNA
molecules, the RNA viruses must either cary the enzymes or have the genes for
those enzymes as part of their genome. Accordingly two types of single stranded
RNA viruses have been identified__ (i) positive
(+) sence RNA is that which during an infection acts like mRNA and can
be translated by the hosts ribosomes, and (ii) negative (-) sence RNA is the RNA that acts as a
template during transcription to make a complementary (+) sense mRNA after entering the hosts cell.
This strand is translated by host ribosome.
The different
families of RNA viruses are distinguished from one another by their nucleic
acid content, their capsid shape and the presence and absence of an envelope.
Some important human. Animal and plant virus families are given in Table 3.
Like RNA
viruses, the DNA viruses are grouped into families according to their DNA
organization. The double sranded DNA (ds DNA) viruses are further separated on
the basis of the shape of their DNA (linear or circular), their capsid shape,
and the presence or absemce of an envelope. Some important families of DNA
viruses are given in Table 4.
Based on
information obtained from ultracentrifuge and electron microscopic studies,
Lwoff, Horne and Tournier (1962) proposed a system of classification of viruses
(known as LHT system) which was accepted by International Committee for viruses Nomenclature (1966). Their
classification is based upon the following characters: (i) type of nucleic acid, (ii) molecular weight of viruses, (iii)
shape and size of viruses, (iv) symmetry of viruses, (v) number of protein subunits
in a capsid, (vi) diameter of nucleic acid coil, (vii) presence of outer
envelope, (viii) intercellular multiplication, (ix) temperature inactivation of
viruses. (x) method of viral transmission, and (xi) symptoms of viral on the
host plant.
The following
is an outline of Lwoff, Horne and Tournier’s system of classification.
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