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VIRAL GENOMES
Molecular Virology
• Dr. Sobia Manzoor
Viral Genomes, Dr. Sobia Manzoor
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VIRUS GENOMES
• A virion contains the genome of a virus in the form of
one or more molecules of nucleic acid.
• For any one virus the genome is composed of either
RNA or DNA.
• If a new virus is isolated, one way to determine
whether it is an RNA virus or a DNA virus is to test
its susceptibility to Ribonuclease (e.g., RNAse A, H,
T) or deoxyribonuclease (e.g., DNAse 1, or S1
Nuclease).
• The virus nucleic acid will be susceptible to
degradation by only one of these enzymes.
Viral Genomes, Dr. Sobia Manzoor
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• In order to optimize the cell for virus replication, Viruses
also encode enzymes and proteins involved in modifying
the cell in which the virus replicates.
• DNA Viruses utilize the infected cell’s nucleus as the site
of genome replication share many common patterns of
gene expression and genome replication along with similar
processes occurring in the host cell.
• RNA Viruses have devised some way to replicate such
since the cell does not have machinery for RNA-directed
RNA replication. The replication of RNA viruses requires
expression of specific enzymes that are not present in the
uninfected host cell.
Viral Genomes, Dr. Sobia Manzoor
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VIRUS GENOMES
Examples
DNA genomes
ss, linear
Parvoviruses
ds, linear
Poxviruses
ss, circular
Phage φX174
ds, circular
SV40, Baculoviruses
ss, linear
Tobacco mosaic virus
RNA genomes
ds, linear
ss, circular
Viral Genomes, Dr. Sobia Manzoor
Reoviruses
Hepatitis delta virus
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GENOME SIZE
• Porcine circovirus (ssDNA) and hepatitis delta virus (ssRNA)
each have a genome of about 1.7 kilobases (Kb).
• While at the other end of the scale there are viruses with
dsDNA genomes comprised of over 1000 kilobase pairs
(Kbp).
• The maximum size of the virus genome is subject to
constraint are less severe for dsDNA all of the large virus
genomes are composed of dsDNA.
• The largest RNA genomes known are those of some
coronaviruses, which are 33kb of ssRNA.
• The largest virus genomes, such as that of the mimivirus, are
larger than the smallest genomes of cellular organisms, such
as some mycoplasmas.
• Virus genomes span aVirallarge
range of sizes.
Genomes, Dr. Sobia Manzoor
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Mimivirus
(1,181,404 bp)
GENOME MANIPULATION
EsV-1
(335,593 bp)
Human
Cytomegalovirus
(229,354 bp)
Lambda
(48,502 bp)
φX174
(5375 b)
Lambda
(12 bp)
Year
1971
MS2
(3569 b)
1975
1977
1982
1990
2001
2004
The first genome sequenced
The first DNA sequenced
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SECONDARY AND TERTIARY STRUCTURE

The virus genome carries information, such as signals for the control of gene expression as well as encoding
the virus protein (and in some cases untranslated RNAs) to be synthesized in the infected cell.

Some of this information is contained within the nucleotide sequences, while for the single-stranded genomes some of it is
contained within structures formed by intramolecular base pairing.
Viral Genomes, Dr. Sobia Manzoor
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SECONDARY AND TERTIARY STRUCTURE
• In ssDNA complementary sequences may base pair through G-C and A-T
hydrogen bonding; in ssRNA weaker G-U bonds may form in addition to
G-C and A-U base pairing.
• Intramolecular base pairing results in regions of secondary structure with
stem loops and bulges.
• In some ssRNAs intramolecular base pairing results in structures known as
pseudoknots
• Regions of secondary structures in single-stranded nucleic acids are folded
into tertiary structures with specific shapes, many of which are important in
molecular interactions during virus replication.
• The 5 end of poliovirus, HCV RNA, forms such structure called internal
ribosome entry site (IRES) to which cell proteins bind to initiate
translation.
• Some pseudoknots have enzyme activity, while others play a role in
ribosomal frameshifting.
Viral Genomes, Dr. Sobia Manzoor
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NON COVALENT PROTEIN DNA INTERACTIONS
• Proteins bound to viral nucleic acids are noncovalently attached.
• These proteins have regions that are rich in
basic amino acids lysine and arginine which
are positively charged and able to bind
strongly to the negatively charged nucleic
acids.
• DNA viruses such as Papillomaviruses and
polyomaviruses have cell histones bound to
the virus genome.
• Most proteins associated with virus genomes,
however, are virus coded.
• Nucleic-acid-binding proteins may have
other characteristics, such as zinc fingers the
HIV-1 nucleocapsid protein has two zinc
fingers.
• In some viruses such as tobacco mosaic virus
the protein coating the genome constitutes
the capsid of the virion.
Viral Genomes, Dr. Sobia Manzoor
A zinc finger in a protein
molecule
A zinc finger has recurring
cysteine and/or histidine
residues at regular intervals. In
this example there are two
cysteines and two histidines.
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SECONDARY STRUCTURES RESULTING FROM INTRAMOLECULAR
BASE-PAIRING IN SINGLE-STRANDED NUCLEIC ACIDS.
(a) Stem loops and bulges in ssRNA and ssDNA. (b) Formation of a pseodoknot in ssRNA. A pseudoknot is formed when a
sequence in a loop (L1) base-pairs with a complementary
sequence
outside the loop. This forms a second loop (L2). 10
Viral Genomes,
Dr. Sobia Manzoor
MODIFICATIONS AT THE ENDS OF VIRUS GENOMES
Virus Genomes
Examples
ssRNA
protein
5'
protein
5'
3
An '
Poliovirus Cowpea mosaic virus
3'
Barley yellow dwarf virus
5'
SARS coronavirus
A3n'
5'
3'
5'
Black beetle virus
3'
Cucumber mosaic virus
tRNA-like structure
5'
Rotaviruses virus
3'
dsRNA
3'
5'
protein 5'
3'
3'
5'
Infectious pancreatic necrosis virus
protein
Viral Genomes, Dr. Sobia Manzoor
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TERMINAL REPEATS IN VIRUS GENOMES
Type of repeat
Nucleic acid
XY
dsDNA
XY
XY
XY
Examples
DTR
Some herpes viruses, T phages
ITR
Adenoviruses Tectiviruses
(phages)
ITR
Some Parvoviruses
DTR
Retroviruses
ITR
Influenza viruses, Bunyaviruses
XY
YX
dsDNA
YX
XY
XY
ssDNA
XY
ssRNA(+)
XY
ssRNA(-)
YX
YX
XY
yx
yx
•
•
•
•
•
•
•
1 DTR: direct terminal repeats
ITR: inverted terminal repeats
X and X represent complementary sequences.
Y and Y represent complementary sequences.
ssRNA (+) has the same sequence as the virus mRNA.
ssRNA (-)has the sequence complementary to the virus mRNA.
The RNAs of single-stranded RNA viruses with ITRs can circularize; a “panhandle” is
Viral by
Genomes,
Dr. Sobia
Manzoor
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formed
base pairing
between
the complementary sequences at the termini.
STRATEGIES OF VIRAL m RNA SYNTHESIS FOR NUCLEUSAND CYTOPLASM-BASED VIRUSES
Site of mRNA
synthesis
Viral Genome (in
Virion)
Template for
mRNA
Synthesis
Enzyme
Responsible
Examples
Cytoplasm
RNA
RNA
Viral RdRP
Picornaviruses(ss
+),Reoviruses(ds),
Rhabdoviruses
(ss-)
DNA
DNA
Viral RNA
polymerase
Poxviruses (ds)
DNA
DNA
Host pol ll
Polyomaviruses
(ds),Parvoviruses(
ss)
RNA
DNA
Host pol ll
Retroviruses(ss+)
RNA
RNA
Viral RdRp
Orthomyxoviruse
s(ss-)
RNA
RNA
Host pol ll
Hepatitis delta
virus (ss-)
Nucleus
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RNA MODIFICATIONS
Capping
Reovirus mRNA
Methylated mRNA cap structure
Splicing
Ad2 mRNA
Exons and introns
Polyadenylation
Poxvirus and SV40 mRNA
Polyadenylation and signals for
Polyadenylation
RNA transport
E1B55k,HVI-1Rev
mRNA transport to cytoplasm
Protein transport
SV40 T antigen
Nuclear localization signal
(NLS)
Viral Genomes, Dr. Sobia Manzoor
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Signal transduction
V-rsc(RSV)
Tyrosine kinases
Protein modification
Polyoma T antigen
Tyrosine phosphorylation
Malignant
transformation
Oncogenes (RSV), retroviral Proto-oncogenes, insertional
genome
mutagenesis
Tumor suppressor
genes
SV40 T antigen,adenovirus Tumor suppressor genes
E1A Papilloma virus E6/E7 (Rb, p53)
Apoptosis
Baculovirus IAP p35
Inhibitor of Apoptosis
Proteins (IAP)
Interferon
Inactivated and live
influenza virus
Anti-viral state, viral
interferon antagonists
Adaptive immne
response
Lymphocytic
choriomeningitis virus
infection
Antigen persentation and
MHC restriction
Immune defenses
Viral Genomes, Dr. Sobia Manzoor
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CELLULAR TARGETS OF THE DNA TUMOR VIRUS ONCOPROTEINS
Virus
Gene Product
Cellular Target
Adenovirus
E1A
Rb
E1B
p53
SV40
Large T antigen
Rb,p53
Polyomavirus
Large T antigen
Rb
Middle T antigen
Src,Pl 3-k
E7
Rb
E6
p53
E5
PDGF receptor
Papillomavirus
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