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Subviral Entities and Viral
Evolution
What are they and where did they
all come from?
Subviral entities
 Viroids
 They are small single stranded infectious RNAs
with a circular genome that is self-complementary
 Their RNA genomes of 246-375 nucleotides long
are much smaller than the smallest RNA virus
known
 They are capable, however, of autonomous
replication
 They appear to encode no proteins and are not
classified under the Baltimore viral classification
scheme
 Their genomes all contain 5 regions called
domains.
Subviral entities
 A central conserved domain (C)
 A P domain containing a run of purines which
appears to be involved in the pathogenic
effects of the viroid.
 A V domain of variable sequence
 Left (T1) and right (T2) terminal domains
Viroid structure
Subviral entities
 Viroids are transmitted through vegetative
propagation of the host, by seeds, by
aphids, or through mechanical damage.
Therefore there is no need for a receptor
on the host that the viroid must bind to as
a first step in its replication.
 If viroids don’t encode any proteins (i. e., a
replicase), how then do they replicate?
Subviral entities
 They use the host cell RNA polymerase II. It appears as
if the extensive double stranded helical arrangement of
the RNA competes effectively with normal DNA for the
enzyme!
 The host cell RNA polymerase I may also play a role in
the viroid replication
 They appear to use a rolling circle mode of replication
 The genomic strand (+) serves as a template for the
synthesis of a concatameric, linear antigenomic strand of
RNA using the host cell RNA polymerase II.
Subviral entities
 The antigenomic concatameric strand is a template
for synthesis of a concatameric genomic strand using
the host RNA polymerase I.
 The concatamers are cleaved to genomic length.
 The DNA is ligated to form the circular genome.
 Details on how the last two steps occur are lacking.
Model of viroid replication
Subviral entities
 Viroids cause plant diseases – how do they cause
disease?
 Their P domains are complementary to 7S RNA, a
molecule that is involved in protein translocation after
synthesis.
 The formation of viroid-7S RNA hybrids might prevent
the 7S RNA from functioning properly in the translocation
of newly synthesized proteins.
 This could lead to the alteration in plasma membrane
derived structures that is seen in viroid infections.
Subviral entities
 Other RNA containing subviral entities
 Include satellite viruses, satellite RNAs, virisoids,
and the hepatitis delta virus
 All of these differ from viroids in that they are not
autonomous. To replicate, they require that the
host cell be co-infected with a helper virus that
provides essential functions in their replication and
transmission cycles
 Satellite viruses, virisoids, and satellite RNAs infect plants
 Hepatitis delta virus infects animals
A comparison of viroids and other
infectious RNAs
Subviral entities
 Hepatitis delta virus particles are enveloped with a
membrane containing three envelope proteins of hepatitis
B virus (the helper virus).
 Within the envelope is the nucleocapsid containing the
covalently closed circular, single-stranded negative sense
RNA genome complexed with multiple copies of the major
gene product of this RNA, the delta antigen.
 The delta antigen contains two RNA binding domains,
a nuclear localization signal, and a multimerization
domain characteristic of members of proteins in the
leucine zipper family. Many of these proteins are
known to play a role in transcriptional regulation.
Subviral entities
 After entry and uncoating, the genome and associated
delta antigen are transported to the nucleus where the
genome is transcribed and replicated by the host cell RNA
polymerase II!
 How this occurs is unknown since these enzymes
normally cannot use RNA as a template to make a
complementary copy of RNA!
 RNA is transcribed to the antigenomic + RNA
 Transcription also generates a subgenomic mRNA that
is capped, polyadenylated, and translated into the
delta antigen. Generation of this subgenomic RNA
may be via interrupted replication or by ribozyme
activity of the RNA itself.
Hepatitis delta virus replication and
transcription
Subviral entities
 The mRNA may be edited by cellular enzymes to
alter the first translational terminator resulting in
a delta antigen protein that is 19 amino acids
longer than that expressed from the unedited
mRNA.
 The short form (unedited) of the delta antigen is
required for genome replication (inhibits mRNA
synthesis)
 The long form (edited) suppresses replication
and promotes assembly. It has a lipid attached
to it that permits it to interact with the
cytoplasmic membrane in the location where
hepatitis B surface protein is located.
Hepatitis delta antigen
Subviral entities
 HDV is spread by blood contamination and causes a
pathology similar to that caused by other hepatitis
viruses.
 The severity of the disease results from co-infection
with HBV or superinfection of an HBV-positive
individual with HDV. Fatality rates can be as high as
20%.
 An interesting note is that the antigenomic RNA has
sequences complementary to mammalian 7S RNA
suggesting that HDV may interrupt normal protein
translocation by forming HDV-7S RNA hybrids
Subviral entities
 Prions
 Cause spongiform encephalopathies in man and
other mammals
 The diseases that they cause in man are Kuru and
Creutzfeldt-Jakob disease (and recently, mad cow disease
also called variant Creutzfeldt-Jakob disease )
 Do not appear to contain any nucleic acid!
 They are infectious proteins!
 The name prion comes from proteinaceous
infectious agent plus “on” a suffix originally used
to denote particles in physics!
Subviral entities
 Prion proteins (PrP) are 27-30 kd in size
 In electron micrographs PrP appears as
large macromolecular fibrils similar to but
distinct from the amyloid fibrils seen in
Alzheimer’s disease victims
Prion fibrils
Subviral entities
 How do prions replicate?
 Studies have shown that PrP is encoded by a
chromosomal gene that is expressed at the
same level in the brains of both infected and
non-infected animals.
 The normal gene product PrPc (c for cellular) is
a glycoprotein of 33-35 kd. It is attached to
the plasma membrane by a
glycosylphospphatidylinositol (GPI) anchor
where it may act as a cell surface receptor
involved in signal transduction in neurites.
Subviral entities
 The conversion of PrPc into fibrils is a multistep process:
 PrPc has four alpha helical regions in its native
conformation.
 The triggering event is the conversion of two of the alpha
helices into an anti-parallel beta pleated sheet
conformation. This molecule is termed PrPsc and this is the
infectious form of the molecule that catalyzes the
conversion of native PrPc molecules to the PrPsc
conformation.
 Proteolytic removel of 67 amino acids from the N-terminus
of PrPsc produces a molecule that aggregates into the
amyloid fibrils seen in the disease.
 Some types of prion disease (Creutzfeldt-Jakob disease)
appear to arise spontaneously (as described above) rather
than via infection, while others are clearly via infection
with a PrP (Kuru, mad cow disease)
Prion structure
Viral evolution
 What is the origin of subcellular entities
(includes viruses)?
 There are three different theories:
 One theory, called the regressive theory, asserts that
viruses are the degenerative progeny of other obligate
intracellular parasites
 According to this theory, viruses are entities that have
regressed to the point that they have dispensed with all
but a few genes and they rely entirely upon their host for
their metabolic needs, especially protein synthesis
 The problem is that this does not explain where RNA
viruses came from
 There is also a huge difference between Chlamydia
and viruses (see chart on next slide). An intermediate
form, that would be predicted by the theory, has
never been found.
Regression of bacteria to
viruses (regressive theory)
Viral evolution
 The cellular constituent theory also proposes that viruses
developed after their hosts. According to this theory,
viruses are thought to have descended from normal
cellular DNAs or RNAs that developed the ability to
replicate themselves autonomously
 This mechanism requires that free DNA molecules acquire
an origin of replication and gene or genes encoding a viral
capsid
 RNA molecules would also have to acquire a gene
encoding a replicase
 Transposons and retrotransposons that can move around
in cellular DNA may have contributed to this process
Viral evolution
 Retrotransposons move by a three step process:
the retrotransposon is first transcribed into an
RNA molecule which is then reverse transcribed
back into a cDNA molecule which then reinserts
into a new location.
 The prebiotic RNA model asserts that the RNA
viruses are the descendents of self-replicating
prebiotic RNA molecules that became parasites
within true cells when they in turn evolved.
 This theory is based on current ideas that suggest
that the first genetic material to develop was RNA.
 The theory does not consider how DNA viruses arose
Theories of viral origin
Viral evolution
 What factors affect viral evolution?
 Mutation – the polymerases of RNA viruses and
the small DNA viruses do not have proofreading
capabilities, so mutations are quite common and
can lead to rapid evolution (antigenic drift with
influenza virus)
 Recombination – the creation of new molecules by
combining or substituting pieces of nucleic acid
particularly when host cell genes are recombined
into a viral genome (transduction)
Viral evolution
 Reassortment with viruses having
segmented genomes – when a host cell is
coinfected with viruses of two different
strains, new viruses may contain various
combinations of genetic segments from
both viruses (antigenic shift with influenza
virus)
Emerging viruses
 What is meant by the word “emerge”?
 This may refer to a virus that has been present in
the human population for a long time, but some
change in the virus or in the host (susceptible
population) results in the disease that the virus
produces emerging into an epidemic form:
 Polio is a disease of civilization. Children used to get the
disease early in life through contaminated water.
However, with the development of sanitation and water
treatment, individuals often did not get the virus until
later in life. The risk of developing paralytic poliomyelitis
rises markedly in individuals over the age of 5.
Emerging viruses
 Changes in population density may allow a
virus that requires a sizable population to
maintain itself to cause continuing disease
when the population density increases –
measles is an example of this
 New techniques may allow us to identify
previously unidentified viruses – hepatitis C and
human herpesvirus 8 which causes Kaposi’s
sarcoma are examples of this
Emerging viruses
 Zoonotic viruses can cross the species barrier
to cause human diseases – the modern ease of
movement and the encroachment of humans
into previously unpopulated areas may
contribute to this
 Some zoonotic viruses have humans as a dead end
host (i.e., no human to human transmission occurs)
(Sin Nombre hantavirus and West Nile virus)
 Some zoonotic viruses can cause human diseases in
which human to human transmission may occur
(Ebola virus, SARS virus,Lassa fever virus)
 Some zoonotic viruses may mutate to become
human viruses (HIV)
Emergence of new viruses
HIV-SIV genetic relationships