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Viruses
What is a virus ?
• Viruses are submicroscopic, obligate intracellular
parasites
• Morphologically, virus particle is a protein shell,
in which the viral genome is enclosed
• Virus particles are produced from the assembly of
pre-formed components and do not grow or
undergo division
• Viruses lack the genetic information which
encodes apparatus necessary for the generation of
metabolic energy and for protein synthesis
Origins of Viruses
• How did these become independent genetic entities? The only
absolute requirement is an origin of replication in the nucleic acid.
• Regressive theory: viruses are degenerate forms of intracellular
parasites. The leprosy bacillus, rickettsiae and chlamydia have all
evolved in this direction. Mitochondria and chloroplasts are often
suggested to have been derived from intracellular parasites.
However viruses do not have their own rRNAs or protein synthesis
machinery. Also begs the question of RNA virus evolution ?
• Progressive theory: Cellular RNA and DNA components: Normal
cellular nucleic acids that gained the ability to replicate
autonomously and therefore to evolve. DNA viruses came from
plasmids or transposable elements. They then evolved coat
proteins and transmissibility. Retroviruses derived from
retrotransposons and RNA virus from mRNA.
• Coevolution theory: Viruses coevolved with life – their evolotion
might go all the way back to RNA world!
• All of these could be correct! No compelling reason to think that
RNA viruses have evolved in the same way as DNA viruses
The particle
Common things to all
virus particles:
1. It encloses genomic
nucleic acid
2. It is a polymer,
assembled from one or
few different kinds of
monomers
The nucleocapsid
• Nucleocapsid is the viral nuleic acid,
enclosed in the protein shell
• In case of simple non-enveloped viruses
nucleocaspsid and virus particle is the same
thing
• In enveloped viruses, lipid bilayer of
cellular origin encloses the nucleocapsid
Enveloped and non-enveloped viruses
• Non-enveloped virus
DNA or RNA genome
• Enveloped virus
Matrix protein
Lipid
bilayer
Nucleocapsid
Envelope protein
Two different kinds of
nucleocapsids
• Filamentous
• Icosahedral
The helical geometry of filamentous virus
TMV (Tobacco mosaic virus)
Pitch of
helix
22.8 Å
m=16.3 (subunits per helix turn)
p=1.4Å
(axial rise per
subunit)
The geometry of icosahedral viruses
• Due to geometrical constraints, there are 60
equivalent environments in icosahedron. This means,
that icosahedron can be made of 60 equivalent
subunits
• Most icosahedral viruses, however are made of more
than 60 subunits, making quasi-equvalent contacts.
• The number of subunits is always a certain multiple
of 60, called a triangulation (‘T’) number. For
example, T=3 virus will have 180 subunits, T=7
virus 7x60=420 subunits. Only certain T values are
allowed (1, 3, 4,7, 9, 13, 16,19,21,25...).
T=1 (60 subunits)
T=4 (240 subunits)
T=3 (180 subunits)
The blue triangle represents
one face of icosahedron
Structure of T=3 icosahedral bacteriophage MS2
FG
loops
The three subunits A, B and C are in slighly different conformations. A and C subunits
are clustered around 3- fold axes, forming hexamers, whereas B subunits gather around
5-fold axes, forming pentamers. Note the differnt conformation of FG loops for A, B and
C subunits
The genomes
• I: Double-stranded DNA. Examples: Adenoviruses, Herpesviruses,
Papillomaviruses, Poxiviruses, T4 bacteriophage
Some replicate in the nucleus e.g adenoviruses using cellular proteins.
Poxviruses replicate in the cytoplasm
• II: Single-stranded (+)sense DNA. Examples: phage M13, chicken
anaemia virus, maize streak virus
Replication occurs in the nucleus, involving the formation of a (-)sense
strand, which serves as a template for (+)strand RNA and DNA synthesis.
• III: Double-stranded RNA. Examples: Reoviruses, Rotavirues
These viruses have segmented genomes. Each genome segment is
transcribed separately to produce monocistronic mRNAs.
• IV: Single-stranded (+)sense RNA Examples: Hepatitis A and C,
Small RNA phages, common cold viruses, SARS
a) Polycistronic mRNA e.g. Picornaviruses; Hepatitis A. Genome RNA =
mRNA. Means naked RNA is infectious, no virion particle associated
polymerase. Translation results in the formation of a polyprotein product,
which is subsequently cleaved to form the mature proteins.
b) Complex Transcription e.g. Togaviruses. Two or more rounds of
translation are necessary to produce the genomic RNA.
• V: Single-stranded (-)sense RNA. Examples: Influenza viruses,
Hantaviruses
Must have a virion particle, containing RNA directed RNA polymerase.
a) Segmented e.g. Orthomyxoviruses. First step in replication is
transcription of the (-)sense RNA genome by the virion RNA-dependent
RNA polymerase to produce monocistronic mRNAs, which also serve as
the template for genome replication.
b) Non-segmented e.g. Rhabdoviruses. Replication occurs as above and
monocistronic mRNAs are produced.
• VI: Single-stranded (+)sense RNA with DNA intermediate in lifecycle (Retroviruses). Examples: HIV, Avian leukosis virus
Genome is (+)sense but unique among viruses in that it is DIPLOID, and
does not serve as mRNA, but as a template for reverse transcription.
• VII: Partial double-stranded (gapped) DNA with RNA intermediate
(Hepadnaviruses) Example: Hepatitis B
This group of viruses also relies on reverse transcription, but unlike the
Retroviruses, this occurs inside the virus particle on maturation. On
infection of a new cell, the first event to occur is repair of the gapped
genome, followed by transcription.
Simple and complex genomes and particles
Phage MS2
Genome: linear +ssRNA 3400 nt, 4 ORFs, 4 proteins (A for
receptor binding, C for coat, L for lysis and R for polymerase)
A
C
R
L
Particle: Genome encapsidated in
a single layer coat protein shell
Hepatitis B virus
Genome: partial dsDNA 3200 bp, 4ORFs, 6 proteins
(S, preS for envelope, C for core, P for polymerase and X for
transcription factor)
Particle: Genome with polymerase encapsidated in doublelayer protein shell. The outer shell is composed of multiple
copies of S, M (S+preS2) and L (S+preS1+preS2) proteins
Adenovirus
Genome: linear ds DNA, 35 000 bp, 40 genes
Particle: 10 proteins, single layer
Phage T4: complicated genome & particle
Mimivirus: the biggest known genome and particle
• Genome: 1,181,404 nt, codes for 1262 proteins
• Some proteins are involved in protein synthesis, thus violating one
criterium in a definition of “what is a virus”
• Infects amoebae
Hepatitis B (3,200 bp, 4 proteins)
Adenovirus (35,000 bp, 40 proteins)
T4 phage (173,000 bp, 280 proteins )
Mimivirus (1,180,000 bp, 1262 proteins)
Chlamydia trachomatis (1,040,000 bp, 936 proteins)
Burrelia burgdorferi (1,440,000 bp, 1738 proteins)
E.coli (4,600,000 bp, 4377 proteins)
Electron micrograph of mimivirus particle and
comparison with sizes of other viruses
E.coli
Poxivirus
T4 phage
head
Adenovirus
Hepatitis B
Smallest viruses
The viral life cycle
•Initation phase:
a) Attachment to the host cell receptor (Ig like receptors, cellular
adhesion molecules, membrane transport proteins, oligosaccharides,
etc)
b) Penetration (endocytosis, fusion)
c) Uncoating
Most bacteriophages avoid penetration and uncoating stages by
injecting the viral nucleic acid into the cell
Plant viruses do not use specific receptors and enter the cell either
through insect vectors or mechanically damaged parts of plant
Some viruses initiate direct cell fusing. In this process infected cell
is fused with uninfected.
Initiation phase
Enveloped
virus
Nonenveloped
virus
Movie: animal virus penetration
by fusion
Movie: DNA injection in E.coli
by T4 bacteriophage
The viral life cycle
•
a)
b)
c)
d)
Replication phase
nucleic acid replication
mRNA synthesis
protein expression
assembly
The viral life cycle
• Release phase
a) exit from cell (lysis, exocytosis, budding)
b) maturation (rearrangement of
nucleocapsid, etc)
In enveloped
viruses
assembly can be
coupled to
release
Examples of viral life cycles
• Small RNA phages
• HIV
• Influenza
Initiation phase of small RNA
phages
A protein
Attachment
Bacterial
pili
Transport of
genomic RNA
into cytoplasm
Replication and release
Translation of
viral proteins
Lysis
Coat
Replicase
A
Assembly
Release
HIV
• Retroviridae, Lentivirus (~10 kb diploid
+ssRNA genome)
The life cycle of HIV
HIV maturation
During HIV maturation, structural polyproteins are cleaved in active
units. This causes rearangement of virion structure and makes the
particle infectious.
Influenza virus
• (-)sense segmented
RNA genome
• enveloped, a bit
irregular particle
• 2 types of spike
proteins
(neuraminidase and
hemagglutinin)
• Infects birds and
mammals
Life cycle of influenza virus
Should we be scared of that avian
H5N1 influenza?
• Maybe...
• In 1918 influenza of porcine origin killed around
40, 000, 000 people worldwide
• H5N1 influenza is not easily transmitted to humans and
certainly not from one human to another
• The problem might arise when a chimeric human-avian
virus arises by exchanging genomic RNA segments
• That one could be as lethal as avian and as easily
transmitted as human
• Most probably H5N1 will not become pandemic, but some
day we will certainly see something similar to 1918...
Virus life cycle and antiviral
therapy
• In antiviral therapy, any vital step in viral
life cycle can be blocked
• Frequent targets are viral polymerases (HIV,
herpes, HCV and others)
• Other targets include viral protease (HIV)
amd matrix protein (influenza, blocks
uncoating)
Smaller than virus
Satellites: small RNA molecules, absolutely
dependent on presence of another virus
Type A: an RNA molecule of more than 700 nt,
which encodes its own capsid protein
Type B: an RNA molecule of more than 700 nt,
which encodes a non-structural protein
Type C: a linear RNA of less than 700 nt, which does
not encode any proteins
Type D: a circular RNA of less than 700 nt, which
does not encode any proteins
Several DNA satellites have been described as well
• Satellites often cause different symptoms
than the host virus alone
• Most known satellites are associatet with
plants (satellite tobaco necrosis virus,
satellite panicum mosaic virus, etc)
• Some are dependent on animal viruses – for
example dependoviruses, wich are satellites
of adenoviruses.
Different symptoms of infection by Tobacco
necrosis virus without (left) and with coinfection of Tobacco sattelite necrosis virus
Viroids
• Viroids are very small (200-400 nt) rod-like
RNA molecules with a high degree of
secondary structure
• Viroids do not encode any proteins and
unlike satellites they are not dependent on
the presence of another virus
Structure of viroids
• Conserved central domain is responsible for replication
• Pathogenic or P domain can display similarities with
various cellular RNAs sequences (snRNAs, signal
recognition particle) and therefore interfer with cellular
proceses
• Viroids also have been shown to directly ativate certain
protein kinases
Viroid replication
• Viroids utilize cellular RNA polymerases for their
replication
• Replication is performed by “rolling circle
mechanism”
• The resulting long RNA molecule is cut in pieces
and ligated either autocatalytically or by cellular
factors (depending on a viroid)
• So in a sense, at least some viroids are
ribozymes...
Examples of plants, infected with various viroids
Hepatitis d virus – a chimeric molecule,
half viroid, half satellite
• Viroid like properties
- Rod-like RNA molecule
- Central conserved region
similar to plant viroids
- Rolling circle replication
- Self-cleaving activty
• Satellite like properties
- Encodes a protein, which is
necessary both for
encapsidation and
replication
- Dependent on presence
another virus – HBV
- Genome larger than for
viroids (1640 nt)
Prions
• Chronic, progressive and always fatal
infections of the nervous system
• Infectious agent is protein only, without
presence of any nucleic acid
The main known infections
• Animal
-Scrapie
-Transmissible mink
encelophathy
-Bovine spongiform
encephalophaty
-Feline spongiform
enelophaty
• Human
- Creutzfeldt-Jakob
disease (CJD)
- Gerstmann-Straussler
syndrome
- Kuru
Even yeasts have prions!
Kuru
• A fatal disease, ”laughing death” found in
New Guinea
• Has been shown to be transmitted through
ritual cannibalism
• Certain tribes used to honour their dead
close relatives by eating them
Scrapie
The infectous agent in prion deseases
• PrPc (PrP cellular) is the normal variant of the protein of
unknown function, expressed in nervous tissue
• PrPSc (PrP Scrapie) is the same protein, which has
undergone severe structural rearrangement, forming
unsoluble, b-sheet rich fibrils, somewhat similar to those,
caused by Alzheimers disease
• PrPSc is itself capable to catalytically convert PrPc to
another PrPSc molecule
• Knockout mouse lacking PrPc show normal development,
indicating that presence of PrPSc fibrils and not absence of
PrPc is fatal
• PrPSc form of protein is extermely stable – it can survive
temperatures of over 100oC
Mechanism of
Sc
PrP
fibril formation
PrPSc
Normal
PrPc
function ?
PrPc
PrPc
PrPc
PrPc
External PrPSc
Spontaneous
structural
rearrangement
PrPSc
PrPSc induced structural
rearrangement
PrPSc
PrPSc
PrPSc
PrPSc
PrPSc
polymerization
PrPSc
PrPSc fibril
PrPSc
PrPSc
PrPSc
Both Alzheimer's and prion diseases are characterized by the deposition of
pathological proteins in the brain, often in the form of plaques. The brown color is
indicative of immunostained deposits of the Aß peptide and of the PrPSc protein in
brains of patients suffering from Alzheimer's disease (A) and Creutzfeldt-Jakob
disease (B), respectively.
PrPc and PrPSc monomers
PrPc (crystal structure)
PrPSc (model – not a real structure!)
Different models of fibrous form of prions
Is BSE transmittable to humans?
• As we know from newspapers, there is a clear link
from BSE to human CJD
• CJD occurs worldwide with frequency ~1 per
million people per year. This makes about 60 cases
per year in UK
• Since 1996 in UK there have been identified
additional ~20 cases per year of CJD with somewhat
different symptoms, called vCJD
• There is no direct evidence that BSE can cause
vCJD
BSE and vCJD statistics
vCJD
BSE
26
19
10
3
10
15