Section R Viruses R1 Introduction to Viruses R2 Bacteriophages R3 DNA Viruses R4 RNA Viruses

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Section R Viruses R1
Introduction to Viruses R2
Bacteriophages R3 DNA Viruses
R4 RNA Viruses
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R1 Introduction to Viruses

• Viruses
• Virus genomes
• Replication strategies
• Virus Virulence

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Viruses-I

• Definition Viruses are extremely small (20-300
  nm) parasites, Incapable of replication,
  transcription or translation outside of a host
  cell. Viruses of bacteria are called
  bacteriophages.

Nucleic acid genome
Nucleocapsid
Protein coat / capsid
Virus particles
Nonstructural proteins
For transcription or replication soon after
infection
Outer envelope
Bi-layer lipoprotein, derived from host cell
membrane
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Capsids of Some Viruses
(A) Tomato bushy stunt virus (B) poliovirus
(C) simian virus 40 (SV40) (D) satellite
tobacco necrosis virus.
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The Coats of Viruses
(A) Phage T4, (B) Potato virus X (C)
Adenovirus (D) Influenza virus
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Virus genomes
Genome features and classifications
Types of nucleic acid
RNA or DNA
Double-stranded or Single-stranded
Strand construction
Defined relative to the mRNA sequence
Positive, negative or ambi-sense
Virus genomes
Small (1kb ) Large (300kb)
Size
Replication enzyme source
Viral enzymes and Cellular enzymes.
Shapes
Linear or Circular
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Schematic drawings of several types of viral
genomes
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Replication strategies

• Viral replication strategies depend largely on
  the type of nucleic acid and size of genome
• Large DNA viruses e.g. herpesvirus, often encode
  their own polymerases
• Small DNA viruses e.g. SV40, may use the host
  cellular DNA polymerases
• RNA viruses require virus-encoded RNA-dependent
  polymerases for their replication
• RNA retroviruses use an RNA-dependent DNA
  polymerase (reverse transcriptase) to replicate
  via a DNA intermediate.

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Virus virulence

• Virulence is the capacity to cause disease. The
  Virulence mechanisms of viruses fall into six
  categories
• 1. Damage to cellular metabolism (e.g.
  competition for enzymes and nucleotides, or
  growth factors essential for virus replication).
• 2. Damage to the cell membrane during
  transmission between cells (e.g. lysis by many
  bacteriophages or cell fusion by herpes viruses).
  
• 3. Disease signs helps the transmission between
  hosts (e.g. sneezing caused by common cold
  viruses).
• 4. Immune evasion of the hosts immune system,
  for example by rapid mutation.
• 5. Harmful immune responses directed at viral
  antigens (e.g. hepatitis B virus) or
  cross-reactive responses leading to autoimmune
  disease.
• 6. Transformation of cells and tumor formation
  (e.g. SV40).

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R2 Bacteriophages

• General properties
• Lytic and lysogenic inferction
• Bacteriophage M13
• Bacteriophage l
• Transposable phage

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General properties

• Features Phages are viruses which infect
  bacteria.
• Their genomes can be of RNA or DNA
• Their size is from around 2.5 to 150 kb
• They can have simple lytic life cycles or more
  complex life cycles involving integration in the
  host genome.
• Functions
• Bacteriophages have played an important role in
  the research history of both virology and
  molecular biology
• They have been studied intensively as model
  viruses.

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Lytic and lysogenic infection

• Lytic infection (e.g. phage M13 infection)
• In lytic infection, the phages are released from
  the cell by lysis, but some phages (e.g. M13)
  release without lysis of the host cell.
• Their DNA replication in the cytosol
  independently
• They replicate very quickly infection,
  replication, assembly and release by lysis of the
  host cell may all occur within 20 minutes

• Lysogenic infection (e.g. phage Mu infection)
• In lysogenic infection, phages integrate their
  genomes into that of the host DNA, and may be
  stably inherited through several generations
  before returning to lytic infection.
• Another group of phages replicate while
  integrated into the host DNA via a combination.
  of replication and transposition

• Alternative infection (e.g. bacteriophage l).
• Other phages alternate between a lylic phase of
  infection, and a lysogenic phase.

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Bacteriophage M13

• Genome features Size is small (6.4 kb)
  Single-stranded Circular genome DNA
  Positive-sense. The genome has 10 tightly packed
  genes and two terminators.

Infection M13 particles attach specifically to
E.coli sex pili (encoded by a plasmid called F
factor), through a minor coat protein (g3p).
Binding of g3p induces a structural change in the
major capsid (??) protein. This causes the whole
particle to shorten, injecting the viral DNA into
the host cell.
g3p
g6p
g8p
Host enzymes
g9p
g7p
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Bacteriophage M13

• Replication Host enzymes convert the viral ssDNA
  into dsDNA replicative form (RF). Normal dsDNA
  replication produce multiple copies of the RF.
• ssDNA making If RF replication involves
  elongation of the 3'-OH group of a nick made in
  the () strand by a viral endo-nuclease (the
  product of gene 2), rather than RNA priming, the
  () ssDNAs are made by continuous replication of
  each RF.
• Assembly and release
• The packaging precursors are transported to the
  cell membrane and there, the DNA binds to the
  major capsid protein.
• At the same time, new virions are extruded from
  the cell's surface without lysis.
• M13-infected cells continue to grow and divide
  (even if at a low rate), giving rise to
  generations of cells, each of which is also
  infected and continually releasing M13 phage.

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Bacteriophage M13

• Why phage M13 is an ideal cloning vector?
• RF likes plasmid The double-stranded, circular
  RF can be handled in the laboratory just like a
  plasmid
• No strict limit for insert The lack of any
  strict limit on genome and particle size means
  that the genome will tolerate the insertion of
  relatively large fragments of foreign DNA
• ssDNA The genome is single-stranded makes viral
  DNA an ideal template for DNA sequencing
• Non-lytic nature of the cell makes it very easy
  to isolate large amounts of pure viral DNA.

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Bacteriophage l
An head
Is icosahedral , containing the 48.5 kb linear
dsDNA genome
Construction of the virion
A tail
Long and flexible
Infection

• The phage binds to membrane of E. coli, and the
  viral dsDNA is injected by the tail into the
  cell.
• In the cell, the linear dsDNA rapidly bind their
  cos ends producing a nicked circular genome, then
  which is repaired by cellular DNA ligase.

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Bacteriophage l

• Within the infected cell, the l phage may either
  undergo lytic or lysogenic life cycles. In the
  lysogenic life cycle, the phage DNA becomes
  integrated as a prophage in the host cell's
  genome.

Lytic life
Lysogenic life
UV
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Bacteriophage l

• Phage l has 61 genes which are expressed at
  different times after infection, and they can be
  divided into three classes.
• 1. Immediate-early genes N?pL and pR?Cro
• 2. Delayed-early genes
• att, int, gam, cIII, red, N?pL and pR?cro,
  cII, O, P, Q
• cI ?pcI makes phage l into lysogenic life cycle
• 3. Late genes produces the structural proteins
  necessary for the
• assembly of new virus particles and lysis
  of the cell.

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Bacteriophage l
3
3
3
5
Cycling amplification
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Bacteriophage mu
Definition Phage mu is one of the transposable
phages that have lytic and lysogenic life cycles.
The name Mu stands for mutation , because it
may cause insert mutation in host genome.
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R3 DNA Viruses

• DNA genomes
• replication and transcription
• Small DNA viruses (SV40)
• Large DNA viruses (Herpesviruses)
• Herpes simplex virus-1

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DNA genomes replication and transcription

• DNA virus genomes
• Can be double-stranded or single-stranded.
• Replication and transcription
• Almost all eukaryotic DNA viruses replicate in
  the host cell's nucleus and make use of host
  cellular replication and transcription as well as
  translation.
• Life cycles
• Large dsDNA viruses often have more complex life
  cycles, including temporal (??) control of
  transcription, translation and replication of
  both the virus and the cell.
• Small DNA viruses their genomes may be much more
  dependent on the host cell for replication.

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Life cycle of DNA virus
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Small DNA viruses (SV40)

• SV40 is one of the smallest viruses. It is
  belong to papovavirus , and well studied, because
  it is a tumorigenic virus.
• Genome SV40 has a 5 kb, double-stranded circular
  genome, which is supercoiled and packaged with
  cell-derived histones within a 45 nm,
  icosahedral virus particle.
• Overlap genes In order to pack five genes into
  so small a genome, the genes are found on both
  strands and overlap each other.

T(t) tumor
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R4 RNA Viruses

• RNA genomes general features
• Classification of animal virus
• SARS coronaviruses
• Retroviruses
• Life cycle of retroviruses
• Oncogenic retroviruses
• Retroviral genome structure and expression

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General features

• Viral RNA genomes may be
• single-stranded or double-stranded,
• positive sense or negative sense,
• replications have a wide variety of mechanisms.
• All, however, rely on virus-encoded RNA-dependent
  pol, the inaccuracy of which in terms of making
  complementary RNA is much higher than that of
  DNA-dependent pol.
• Evolution This feature affects the evolution of
  RNA viruses by increasing their ability to adapt,
  but limits their size.
• Guasi-species Some RNA viruses mutate so rapidly
  that they exist as guasi-species, that is to say
  as populations of different genomes (often
  replicating through complementa-tion), within any
  individual host, and can only be molecularly
  defined in terms of a majority or average
  sequence.

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Classification of animal virus
or
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Life cycle of SARS virus

• 1. () ssRNA invades cell and translates its RNA
  polymerase
• 2. With the RNA pol the ()ssRNA transcribes its
  (-) ssRNA, which is the template
• 3. (-)ssRNA transcribe several mRNA, which then
  are expressed as proteins
• 4. (-)ssRNA replicates ()ssRNAs with RNA
  dependant RNA pol
• 5. The virus particles are assembled, and release
  from the cells.
• 6. All of the processes of the life cycle of SARS
  virus are taken place in the cytoplasm.

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Retroviruses

• 1. Retroviruses have a ssRNA genome.
• 2. Two copies of the sense ssRNA genome are
  within the viral particle.
• 3. When they infect a cell, the ssRNA is
  converted into a dsDNA copy by the RT (class VI).
  
• 4. Replication and transcription occur from this
  dsDNA intermediate, i.e. the pro-virus.
• 5. which is integrated into the host cell genome
  by a viral integrase enzyme.
• 6. Retroviruses vary in complexity. At one
  extreme there are HIVs.

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Oncogenic retroviruses
LTR
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Retroviral genome expression
LTR

• gag proteins of the icosahedral capsid
• pol RT, RNase H, integrase and protease
• env the envelope proteins.
• v-onc protein of regulation of cell division.

U3 Strong promoter R RT binding site U5
RNA binding Site
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HIV Genome
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• Thats all for Section R