1. Viral Genomes, Dr. Sobia Manzoor
Molecular Virology
Dr. Sobia Manzoor
Viral Genomes, Dr. Sobia Manzoor

2. Viral Genomes, Dr. Sobia Manzoor
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

3. Viral Genomes, Dr. Sobia Manzoor
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

4. Viral Genomes, Dr. Sobia Manzoor
VIRUS GENOMES
DNA genomes
Examples
ss, linear
Parvoviruses
ds, linear
Poxviruses
ss, circular
Phage φX174
ds, circular
SV40, Baculoviruses
RNA genomes
ss, linear
Tobacco mosaic virus
ds, linear
Reoviruses
ss, circular
Hepatitis delta virus
Viral Genomes, Dr. Sobia Manzoor

5. Viral Genomes, Dr. Sobia Manzoor
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 a large range of sizes.
Viral Genomes, Dr. Sobia Manzoor

6. GENOME MANIPULATION Mimivirus (1,181,404 bp) EsV-1 (335,593 bp) Human
Cytomegalovirus
(229,354 bp)
Lambda
(48,502 bp)
φX174
(5375 b)
MS2
(3569 b)
Lambda
(12 bp)
Year
1971
1975
1977
1982
1990
2001
2004
The first genome sequenced
The first DNA sequenced
Viral Genomes, Dr. Sobia Manzoor

7. 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

8. 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

9. A zinc finger in a protein molecule
NON COVALENT PROTEIN DNA INTERACTIONS
Proteins bound to viral nucleic acids are non-covalently 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.
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.
Viral Genomes, Dr. Sobia Manzoor

10. Viral Genomes, Dr. Sobia Manzoor
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).
Viral Genomes, Dr. Sobia Manzoor

11. MODIFICATIONS AT THE ENDS OF VIRUS GENOMES
Examples
ssRNA
protein 5' 3'
Poliovirus Cowpea mosaic virus An
protein 5' 3'
Barley yellow dwarf virus 5'
SARS coronavirus An 3' 5' 3'
Black beetle virus 5' 3'
Cucumber mosaic virus
tRNA-like structure 5'
Rotaviruses virus 3'
dsRNA 3' 5'
protein 5' 3'
Infectious pancreatic necrosis virus 3' 5'
protein
Viral Genomes, Dr. Sobia Manzoor

12. TERMINAL REPEATS IN VIRUS GENOMES
Nucleic acid
Type of repeat
Examples XY
dsDNA XY
DTR
Some herpes viruses, T phages XY XY XY
dsDNA YX
ITR
Adenoviruses Tectiviruses (phages) YX XY XY
ssDNA YX
ITR
Some Parvoviruses XY
ssRNA(+) XY
DTR
Retroviruses
ssRNA(-) YX
ITR
Influenza viruses, Bunyaviruses XY
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 formed by base pairing between the complementary sequences at the termini. yx yx
Viral Genomes, Dr. Sobia Manzoor

13. STRATEGIES OF VIRAL m RNA SYNTHESIS FOR NUCLEUS-AND CYTOPLASM-BASED VIRUSES
Site of mRNA synthesis
Viral Genome (in Virion)
Template for mRNA Synthesis
Enzyme Responsible
Examples
Cytoplasm
RNA
Viral RdRP
Picornaviruses(ss+),Reoviruses(ds), Rhabdoviruses (ss-)
DNA
Viral RNA polymerase
Poxviruses (ds)
Nucleus
Host pol ll
Polyomaviruses (ds),Parvoviruses(ss)
Retroviruses(ss+)
Viral RdRp
Orthomyxoviruses(ss-)
Hepatitis delta virus (ss-)
Viral Genomes, Dr. Sobia Manzoor

14. Viral Genomes, Dr. Sobia Manzoor
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

15. Viral Genomes, Dr. Sobia Manzoor
Signal transduction
V-rsc(RSV)
Tyrosine kinases
Protein modification
Polyoma T antigen
Tyrosine phosphorylation
Malignant transformation
Oncogenes (RSV), retroviral genome
Proto-oncogenes, insertional mutagenesis
Tumor suppressor genes
SV40 T antigen,adenovirus E1A Papilloma virus E6/E7
Tumor suppressor genes (Rb, p53)
Apoptosis
Baculovirus IAP p35
Inhibitor of Apoptosis Proteins (IAP)
Immune defenses
Interferon
Inactivated and live influenza virus
Anti-viral state, viral interferon antagonists
Adaptive immne response
Lymphocytic choriomeningitis virus infection
Antigen persentation and MHC restriction
Viral Genomes, Dr. Sobia Manzoor

16. Viral Genomes, Dr. Sobia Manzoor
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
Middle T antigen
Src,Pl 3-k
Papillomavirus E7 E6 E5
PDGF receptor
Viral Genomes, Dr. Sobia Manzoor