Retroviruses

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Retroviruses
Cross-sectional schematic diagram of HIV virion.
Each virion expresses 72 glycoprotein
projections composed of gp120 (orange) and gp41
(light blue). Gp41 is a transmembrane molecule
that crosses the lipid bilayer of the envelope.
Gp120 is noncovalently associated with gp41 and
serves as the viral receptor for CD4 on host
cells. The viral envelope also contains some
host-cell membrane proteins such as class I and
class II MHC molecules. Within the envelope is
the viral core, or nucleocapsid, which includes a
layer of a protein called p17 (green) and an
inner layer protein called p24 (yellow). The HIV
genome consists of two copies of ssRNA, which are
associated with two molecules of reverse
transcriptase p64 (light red) and nucleoid
proteins p10, a protease (red), and p32, an
integrase (dark blue).
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SUMMARY There is more genetic diversity among
viruses than in all the rest of the Animal, Plant
Bacterial kingdoms, all of whose genomes
consist of d/s DNA. The expression of virus
genetic information is dependent on the structure
of the genome of the particular virus concerned,
but in every case, the genome must be recognized
expressed using the mechanisms of the host cell.
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Virus Structure
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Link to lots of virus structures
http//web.uct.ac.za/depts/mmi/stannard/linda.html
http//web.uct.ac.za/depts/mmi/stannard/linda.html
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The complex arrangements of macromolecules in the
virus shell are minute marvels of molecular
architecture. Specific requirements of each
type of virus have resulted in a fascinating
apparent diversity of organization and
geometrical design. Nevertheless, there are
certain common features and general principles
of architecture that apply to all viruses.
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In 1956, Crick and Watson proposed on theoretical
considerations and on the basis of rather flimsy
experimental evidence then available,principles
of virus structure that have been amply
confirmed and universally accepted.
They first pointed out that the nucleic acid in
small virions was probably insufficient to code
for more than a few sorts of protein molecules
of limited size. The only reasonable way to
build a protein shell, therefore, was to use the
same type of molecule over and over again, hence
their theory of identical subunits.
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The second part of their proposal concerned the
way in which the subunits must be packed in the
protein shell or capsid. On general grounds it
was expected that subunits would be packed so as
to provide each with an identical environment.
This is possible only if they are packed
symmetrically. Crick and Watson pointed out that
the only way to provide each subunit with an
identical environment was by packing them to fit
some form of CUBIC SYMMETRY. A body with cubic
symmetry possesses a number of axes about which
it may be rotated to give a number of identical
appearances. These predictions were soon
confirmed and it became evident that the
occurrence of icosahedral features in quite
unrelated viruses was not a matter of chance
selection but that icosahedral symmetry is
preferred in virus structure.
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Figure 4.2
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Figure 4.4--helical/rod shaped viruses
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TMV
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To heighten the contrast between viruses and the
background, use is made of electron-dense
"stains". These are usually compounds of heavy
metals of high atomic number, that serve to
scatter the electrons from regions covered with
the stain. If virus particles are coated with
stain (positive staining), fine detail may be
obscured. Negative staining overcomes this
problem by staining the background and leaving
the virus relatively untouched. The negative
stain is molded round the virus particle,
outlining its structure, and is also able to
penetrate between small surface projections and
to delineate them. If there are cavities within
the virus particle that are accessible to the
stain, these will be revealed and some of the
internal structure of the virus may be disclosed.
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Most biological materials show little contrast
with their surroundings unless they are stained.
In the case of light microscopy, contrast can be
enhanced by using colored stains which
selectively absorb certain wavelengths. The
electrons in the electron microscope are absorbed
very little by biological material and contrast
is obtained mainly by electron scattering.
In transmission electron microscopy, only
electrons which pass through the specimen are
involved in the formation of the final image.
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The introduction of NEGATIVE STAINING (Brenner
and Horne, 1959) revolutionized the field of
electron microscopy of viruses. Within just a few
years, much new and exciting information about
the architecture of virus particles was acquired.
Not only were the overall shapes of particles
revealed but also the symmetrical arrangement of
their components. This led to a need for a new
terminology to describe the viral components.
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Negative staining When particles are covered
with stain, components of both top and bottom
surfaces of a three-dimensional structure are
contained in the two-dimensional image. This
superposition can make it difficult to
distinguish fine structures which would
ordinarily be well within the resolution of the
electron microscope. One-sided staining
provides more accurate information about the
organization of capsomers, etc., although these
particles are less well supported and tend to
"collapse", resulting in apparent increase in
size.
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When two surfaces of regularly repeating units
(such as the surface of some virus particles)
are superimposed slightly out of register,
moire pattern artifacts may result which could
lead to false interpretation of particle
ultrastructure.
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Below is an example of rotaviruses stained from
below, and from both sides (top and bottom)

Rotaviruses have a lattice-like
arrangement of capsomers (left), and the large
ring shapes (right) are artifacts produced by
moire effects.
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Rotavirus Rotaviruses infect
the lining of the intestine and cause diarrhoea,
especially in children. Rotavirus particles are
approximately 75nm in diameter. They have
icosahedral symmetry and particles possess two
concentric protein shells, or capsids. The term
"rota", meaning wheel, is derived from the
appearance of the complete double-capsid
particle when viewed by negative staining in a
position where the 5-fold axis of symmetry is
acentric. Apparent spoke-like components are then
visible on one side of the virus particle
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A double-capsid particle is shown on the left,
and the single (inner) capsid on its right. The
arrangement of capsomers on the inner capsid
gives the appearance of a lattice - 5 capsomers
surround a space at each apex (5-fold axis).
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The outer capsid The outer capsid is positioned
upon the virion in such a way that the
capsomeres of each capsid layer coincide
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The inner capsid
A drawing depicts the apparent
arrangement of capsomers on the inner capsid, and
is shown side-by-side with a colorized EM image.
Lines denote the 5-fold axes of symmetry.
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An ICOSAHEDRON is composed of 20 facets, each
an equilateral triangle, and 12 vertices, and
because of the axes of rotational symmetry is
said to have 532 symmetry Axes of Symmetry
There are, in fact, six 5-fold axes of symmetry
passing through the vertices, ten 3-fold axes
extending through each face and fifteen 2-fold
axes passing through the
edges of an icosahedron.
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http//web.uct.ac.za/depts/mmi/stannard/linda.html
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Icosahedral symmetry requires definite numbers of
structure units to complete a shell. In their
discussions, Crick and Watson (1956), thinking
in terms of asymmetrical protein subunits packed
in such a way that each has an identical
environment, pointed out that a virus with 532
symmetry required a multiple of 60 subunits to
cover the surface completely. Each unit would be
related identically and asymmetrically
with its neighbors, and none of the units would
coincide with an axis of symmetry.
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Box 4.3 CPMV
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Box 4.6 Evolutionary relationship deduced from
structure Bacteriophage vs. Adenovirus
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Figure 4.6 Symmetrical/icosohedral viruses
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Box 4.5
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Figure 4.11 SV40
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Figure 4.13
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Box 4.7
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Lwoff, Anderson and Jacob (1959) proposed the
terms "capsid" and "capsomers" to represent,
respectively, the protein shell and the units
comprising it, and the term"virion" to denote the
complete infective virus particle (i.e. a capsid
enclosing the nucleic acid). This terminology was
generally accepted although it later proved to be
inadequate.
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