VIR30806 - Fundamental and Applied Virology (VIR30806)
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Wageningen University (WUR)
The only summary of Fundamental and Applied Virology on the market! Nice and comprehensive summary about the theory of the course, deduced from the lectures.
VIR30806 - Fundamental and Applied Virology (VIR30806)
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Summary Virology
Lecture 1 Structure and replication of viruses
Viruses are one of the smallest in genome sizes,
especially compared with plants with the smallest being
the MS2 bacteriophage with just four proteins and 3500
bp, and the largest being the Pandora virus with
approximately 2.5 million bp. Viruses are obligate
parasites, this means that they need the presence of a
living host cell, this can be a plant, animal or bacterium.
They need this living host cell for their replication and
their existence. Viruses lack many prerequisites for life,
such as no enzymes for metabolism and no ribosomes,
so absence of de novo protein synthesis. Basically,
viruses are a set of encapsulated genes that can be
transmitted between a defined set of host cells.
Capsid is an arrangement of 180 coat protein molecules
with the small example on the right. A Mimi virus is an
example of a very large virus.
A virophage does not replicate in the virus since there is
no metabolism inside the virus. This small virophage
uses the large Mimi virus as a vehicle to be transported between organisms. The Mimi virus infects
unicellular organisms and replicates together with the Mimi virus in the host cell.
Simian viruses infect monkeys and other primates, there are a lot of simian viruses from 1 to 50. Only
one virus sv-40 is able to cause tumours and therefore is
the only one that anyone has ever heard of. The others
do not cause disease so are not studied. In humans
around 250 viruses have been described, most of which
cause disease. If the simian virus scenario is an accurate
picture of the ratio of disease-causing viruses to harmless
viruses, in humans alone there could be as many as
20,000 viruses.
Approximately 67.7% of DNA sequences floating in our
blood plasma belong to viruses. Approximately 5560
viruses are recognized by taxonomy committee of which
a little more than 1100 plant viruses.
Coat proteins don’t only protect as a shell but also have
important functions (see composition of viruses slide). Some
viruses have an envelope, a lipid membrane, and in this
membrane there are often viral proteins or glycoproteins. In
plant viruses there are not much with an envelope. This can
contain also fusion proteins or binding proteins. On top of the
slide are adenoviruses with no lipid membrane and on the
bottom influenza with a lipid membrane. This virus is
pleomorphic, which means more flexible structure.
,Basic rules of virus architecture, structure and assembly
are the same for all families, although some structures are
more complex than others. Influenza for example has a
recognizable haemagglutinin and neuraminidase
glycoproteins on their envelope.
If the nucleoprotein must be dissociatable to release the
content and infect the host. On the right there are 5 capsid
proteins clustered so this is called a capsomere. A
structural unit is a single coat protein. The viruses that do
not have a envelope the nucleocapsid is the virus particle
and virion is a single virus particle.
The two round virus particle molten together are called
Gemini viruses.
The most basic shape, icosahedral, has 20 triangular phases
each corner of the 5 triangular phases comes together or also
called a pentamer (coat protein). This virus particle has a
triangulation number of 1. That means that you use the 20
triangular phases of the icosahedral. With larger RNA
molecules you need to increase the structure of the virus
particle. The original icosahedral shape remains but it has
been subdivided in this case in four triangles, so in total 4
times 20 is 80, times three is 240 coat protein molecules to
form this t=4 particle. Every virus particle has 12 pentamers
and an increasing number of hexamers (Look at the clip
online).
More complex viruses like Tomato spotted wilt virus has an
envelope and in this envelope there are two glycoproteins.
The classification is based on morphology, physicochemical
properties, genome, sequence, and macromolecules.
No “rules” about virus families that may or may not be present in a given kingdom. For example,
virus families infecting two kingdoms of organisms are: Bunyaviridae (animals and plants),
Partitiviridae (plants and fungi), Reoviridae (animals and plants), Rhabdoviridae (animals and plants),
Phycodnaviridae (protozoa and plants), Picornaviridae (plants and animals), and Totiviridae (protozoa
/ fungi and insects).
,You need a messenger RNA to make a protein, the plus sense RNA viruses can immediately act as a
mRNA. So when a virus like this enters a cell the protein synthesising system can use this virus to
make proteins, but not in DNA viruses. These have to chance into a minus sense DNA viruses. Minus
sense RNA viruses can not serve as a mRNA because a plus sense is needed.
To replicate, a virus must first have a means of placing its genetic material into the host cell (vector).
Once its genetic material is in, the host cell’s normal metabolic processes are subverted by pre-
existing or newly synthesized viral proteins (host shut-off). The host cell, once under viral control, is
reprogrammed to manufacture new viral proteins and genetic material at a dramatic rate. The host
cell provides all of the raw materials to manufacture new viral
particles such as: suitable cellular compartments, amino acids,
nucleotides, and ATP (for energy). Viruses are also well equipped to
evade host cell defences.
Tobacco mosaic virus is a plus sense RNA virus. Plant viruses always
have movement proteins to move through plasmodesma that have
to be modified. This is not in animal viruses. It has an helical
arrangement. Plus-strand RNA virus (see right) RNA is directly
translatable and RNA is directly infectious. If it enters the cell the
RNA is released in the cell and ribosomes step up at the five prime
and can be used as a messenger and translate proteins. The first
protein is involved in replication, it forms the polymerase, is used
instantly for replication of the RNA. Plus sense RNA is copied in minus
sense and this is used to create new plus sense RNA molecules and
are new progeny virus. This is able to form new virus particles. This is
happening in the cytoplasm and not in the nucleus.
The eukaryotic protein synthesizing system features: cellular mRNAs
have a cap (inverted and methylated GTP at the 5'-terminus
[m7G(5')ppp(5')N] and a poly(A) tail at the 3'-terminus, mRNA
contain a single open reading frame (ORF), Translation is
initiated at an AUG start codon. The context of this codon
controls efficiency of translation (Kozak). Also the cap, 5'
untranslated region, the coding region, the 3' untranslated
region and the poly(A) tail all have potential to influence
translational efficiency (look at the clips online).
, Minus sense RNA virus like TSWV is not directly translatable.
The virus can not translate its own polymerase first. Plus sense
do not have polymerase inside their cell because they can
immediately translate it.
DNA virus replication strategies: The virus needs to make
mRNAs that can be translated into protein by the host cell
translation machinery. The virus needs to replicate its
genome. Host enzymes for mRNA synthesis and DNA
replication are nuclear (except for those in mitochondrion)
and so, if a virus is to avail itself of these enzymes, it needs to
enter the nucleus. Production of viral mRNAs and proteins.
Gene expression is divided into early and late phases. Early
genes encode enzymes and regulatory proteins needed to
start viral replication processes. Late genes encode structural
proteins, proteins needed for assembly of the mature virus.
Site of replication is
often at the
membrane of
organelles on the
cytoplasmic side.
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