The Structure & Complexity of Virus Genomes

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• The Structure Complexity of Virus Genomes
• more varied than any of those seen in the entire
  bacterial, plant or animal kingdoms

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• The Structure Complexity of Virus Genomes
• more varied than any of those seen in the entire
  bacterial, plant or animal kingdoms
• may be single-stranded or double-stranded,
  linear, circular or segmented

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• The Structure Complexity of Virus Genomes
• more varied than any of those seen in the entire
  bacterial, plant or animal kingdoms
• may be single-stranded or double-stranded,
  linear, circular or segmented
• Single-stranded virus genomes may be
• positive ()sense, i.e. of the same polarity
  (nucleotide sequence) as mRNA
• negative (-)sense
• ambisense - a mixture of the two.

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• The Structure Complexity of Virus Genomes
• more varied than any of those seen in the entire
  bacterial, plant or animal kingdoms
• may be single-stranded or double-stranded,
  linear, circular or segmented
• Single-stranded virus genomes may be
• positive ()sense, i.e. of the same polarity
  (nucleotide sequence) as mRNA
• negative (-)sense
• ambisense - a mixture of the two.
• Virus genomes range in size from approximately
  3,200 nucleotides (nt) (e.g. Hepadnaviruses) to
  approximately 800 kilobase pairs (kbp,
  Mimivirus)

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• Virus genomes may contain in either DNA or RNA.
• Viruses are obligate intracellular parasites
• genome must contain information which can be
  recognized decoded its host cell
• The viral genetic code must match or at least be
  recognized by the host organism.
• Control signals which direct the expression of
  virus genes must be appropriate to the host.

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• Molecular Genetics
• Questions about any virus genome will usually
  include the following
• Composition - DNA or RNA, single-stranded or
  double-stranded, linear or circular.
• Size number of segments.
• Terminal structures.
• Nucleotide sequence.
• Coding capacity - open reading frames.
• Regulatory signals - transcription enhancers,
  promoters terminators.
• Mechanisms for evading host defense systems

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Direct analysis by electron microscopy, if
calibrated with known standards, can be used to
estimate the size of nucleic acid molecules. The
most important single technique has been gel
electrophoresis. It is most common to use agarose
gels to separate large nucleic acid molecules
(several megabases or kilobases) polyacrylamide
gel electrophoresis (PAGE) to separate smaller
pieces (a few hundred bp down to a few
nucleotides).
The relative simplicity of virus genomes
(compared with even the simplest cell) offers a
major advantage - the ability to 'rescue'
infectious virus from purified or cloned nucleic
acids. Infection of cells caused by nucleic acid
alone is referred to as transfection
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Virus genomes which consist of ()sense RNA (i.e.
the same polarity as mRNA) are infectious when
the purified vRNA is applied to cells in the
absence of any virus proteins. This is because
()sense vRNA is essentially mRNA the first
event in a normally-infected cell is to translate
the vRNA to make the virus proteins responsible
for genome replication. In this case, direct
introduction of RNA into cells merely circumvents
the earliest stages of the replicative cycle. In
most cases, virus genomes which are composed of
double-stranded DNA are also infectious. The
events which occur here are a little more
complex, since the virus genome must first be
transcribed by host polymerases to produce mRNA.
Using these techniques, virus can be rescued from
cloned genomes, including those which have been
manipulated in vitro.
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Types of Viral Genomes

• RNA viruses

ds
sense ss
- sense ss
retroviruses

• DNA viruses

ds
Gapped circle
ss
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RNA Virus Genomes Positive-Strand RNA
Viruses The ultimate size of single-stranded RNA
genomes is limited by the fragility of RNA the
tendency of long strands to break. In addition,
RNA genomes tend to have higher mutation rates
than those composed of DNA because they are
copied less accurately, which also tends to drive
RNA viruses towards smaller genomes.
Single-stranded RNA genomes vary in size from
those of Coronaviruses (the largest RNA
viruses--cause respiratory infections in humans)
at approximately 30kb long to those of
bacteriophages such as MS2 Q? at about 3.5kb.
http//chagall.scripps.edu/viper/2ms2.html (MS2)
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• Purified ()sense vRNA is directly infectious
  when applied to susceptible host cells in the
  absence of any virus proteins (although it is
  about one million times less infectious than
  virus particles).
• There is an untranslated region (UTR) at the 5'
  end of the genome which does not encode any
  proteins a shorter UTR at the 3' end. These
  regions are functionally important in virus
  replication are thus conserved in spite of the
  pressure to reduce genome size.
• Both ends of ()stranded eukaryotic virus genomes
  are often modified, the 5' end by a small,
  covalently attached protein or a methylated
  nucleotide 'cap' structure the 3' end by
  polyadenylation. These signals allow vRNA to be
  recognised by host cells to function as mRNA.

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e.g. Norwalk?
New, uncharacterized
Polio, Rhino
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Negative-Strand RNA Viruses Viruses with
negative-sense RNA genomes are a little more
diverse than positive-stranded viruses. Possibly
because of the difficulties of expression, they
tend to have larger genomes encoding more genetic
information. Because of this, segmentation is a
common though not universal feature of such
viruses.
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Negative-sense RNA genomes are not infectious as
purified RNA. Virus particles all contain a
virus-specific polymerase. The first event when
the virus genome enters the cell is that the
(-)sense genome is copied by the polymerase,
forming either ()sense transcripts which are
used directly as mRNA, or a double-stranded
molecule known either as the replicative
intermediate (RI) or replicative form (RF), which
serves as a template for further rounds of mRNA
synthesis.
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Ambisense Genome Organization Some RNA viruses
are not strictly 'negative-sense' but ambisense,
since they are part (-)sense part ()sense
Hanta La Crosse
Lymphocyte Choriomenengitis Virus
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DNA Virus Genomes 'Small' DNA Genomes Bacteriopha
ges have been extensively studied as examples of
DNA virus genomes. Although they vary
considerably in size, in general terms they tend
to be relatively small.
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• The structure of the filamentous bacteriophage
  M13 genome has been studied in great detail
  modified extensively for use as a vector for DNA
  sequencing and cloning. The genome of this virus
  is
• circular
• single-stranded DNA
• approximately 7,200 nucleotides long
• Unlike other virion structures, the filamentous
  M13 capsid can be lengthened by the addition of
  further protein subunits. The genome size of this
  virus can also be increased by the addition of
  extra sequences in the non-essential intergenic
  region without the penalty of becoming incapable
  of being packaged into the capsid. This is very
  unusual. In other viruses, the packaging
  constraints are much more rigid, e.g. in phage
  lambda, only DNA of between approximately 95 -
  110 (approximately 46kbp - 54kbp) of the normal
  genome size (49kbp) can be packaged into the
  virus particle.

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As further examples of small DNA genomes,
consider those of two families of animal viruses,
the parvoviruses polyomaviruses

• Parvovirus genomes are
• linear
• non-segmented
• ()sense
• single-stranded DNA
• about 5kb long

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• These are very small genomes, even the
  replication-competent parvoviruses contain only
  two genes
• rep, which encodes proteins involved in
  transcription
• cap, which encodes the coat proteins.
• The ends of the genome have palindromic sequences
  of about 115 nt, which form 'hairpins'. These
  structures are essential for the initiation of
  genome replication.

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The genomes of polyomaviruses consist of
double-stranded, circular DNA molecules,
approximately 5kbp in size
Harmful to immunocompromized people.
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The entire nucleotide sequence of all the viruses
in the family is known the architecture of the
polyomavirus genome (i.e. number arrangement of
genes function of the regulatory signals
systems) has been studied in great detail at a
molecular level. Within the particles, the virus
DNA is associated with four cellular histones.
The genomic organization of these viruses has
evolved to pack maximal information (6 genes)
into minimal space (5kbp). This has been achieved
by the use of both strands of the genome DNA
overlapping genes.
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'Large' DNA Genomes There are a number of virus
groups which have double-stranded DNA genomes of
considerable size complexity. In many respects,
these viruses are genetically very similar to the
host cells which they infect. Two examples of
such viruses are the adenovirus herpesvirus
families
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Herpesvirus genomes The herpesviruses are a
large family containing more than 100 different
members, at least one for most animal species
which have been examined to date, including seven
human herpesviruses (including simplex, varicella
and cytomegalovirus. Herpesviruses have very
large genomes composed of up to 230kbp linear,
double-stranded DNA. The different members of the
family are widely separated in terms of genomic
sequence proteins, but all are similar in terms
of structure genome organization. Some
herpesvirus genomes consist of two covalently
joined sections, a unique long (UL) a unique
short (US) region, each bounded by inverted
repeats.
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Adenovirus genomes The genomes of adenoviruses
consist of linear, double-stranded DNA of
30-38kbp. These viruses contain 30-40 genes. The
terminal sequences of each DNA strand are
inverted repeats of 100-140bp therefore, the
denatured single strands can form 'panhandle'
structures. These structures are important in DNA
replication.
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Adenovirus infections are very common, most are
asymptomatic. Most people have been infected with
at least 1 type at age 15. Virus can be isolated
from the majority of tonsils/adenoids surgically
removed, indicating latent infections. It is not
known how long the virus can persist in the body,
or whether it is capable of reactivation after
long periods, causing disease (it is hard to
isolate this occult virus as it may be present in
only a few cells). It is known that virus is
reactivated during immunosuppression, e.g. in
AIDS patients.
Adenoviruses have been the workhorse of
molbio 1st identified oncogenic DNA virus 1st
demonstration of RNA splicing 1st soluble DNA
replication in vitro 1st mapping of ORFs 1st
experiment showing that MHC expression is under
viral control
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• Segmented Multipartite Virus Genomes
• Segmented virus genomes are those which are
  divided into two or more physically separate
  molecules of nucleic acid, all of which are then
  packaged into a single virus particle.
• Multipartite genomes are those which are
  segmented where each genome segment is packaged
  into a separate virus particle. These discrete
  particles are structurally similar may contain
  the same component proteins, but often differ in
  size depending on the length of the genome
  segment packaged.

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• There are many examples of segmented virus
  genomes, including many human, animal plant
  pathogens such as orthomyxoviruses (Flu),
  reoviruses (respiratory enteric orphan viruses
  rotaviruses cause infantile diarrhea)
  bunyaviruses (Hanta). There are rather fewer
  examples of multipartite viruses, all of which
  infect plants. These include
• bipartite viruses (which have two genome
  segments/virus particles)
• tripartite viruses (three genome segments/virus
  particles)

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Separating the genome segments into different
particles removes the requirement for accurate
sorting, but introduces a new problem in that all
of the discrete virus particles must be taken up
by a single host cell to establish a productive
infection. This is perhaps the reason why
multipartite viruses are only found in plants.
Many of the sources of infection by plant
viruses, such as inoculation by sap-sucking
insects or after physical damage to tissues,
results in a large input of infectious virus
particles, providing the opportunity for
infection of an initial cell by more than one
particle.
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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.