Section R Viruses
R1 Introduction to Viruses
R2 Bacteriophages
R3 DNA Viruses
R4 RNA Viruses
Section R: Bacteriophages and Viruses
Yang Xu, College of Life Sciences
R1 Introduction to Viruses
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Viruses
Virus genomes
Replication strategies
Virus Virulence
Section R: Bacteriophages and Viruses
Yang Xu, College of Life Sciences
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
Virus
particles
Protein coat
/ capsid
Nucleocapsid
Nonstructural
proteins
For transcription or replication
soon after infection
Outer
envelope
Bi-layer lipoprotein, derived
from host cell membrane
Section R: Bacteriophages and Viruses
Yang Xu, College of Life Sciences
Capsids of Some Viruses
(A) Tomato bushy stunt virus; (B) poliovirus;
(C) simian virus 40 (SV40); (D) satellite tobacco necrosis virus.
Section R: Bacteriophages and Viruses
Yang Xu, College of Life Sciences
The Coats of Viruses
A
C
(A) Phage T4,
(B) Potato virus X
(C) Adenovirus
(D) Influenza virus
B
Section R: Bacteriophages and Viruses
D
Yang Xu, College of Life Sciences
Virus genomes
Genome features and classifications:
Types of nucleic acid
Virus
genomes
Strand construction
RNA or DNA
Double-stranded
or Single-stranded
Defined relative to
the mRNA sequence
Positive, negative
or ambi-sense
Size
Small (1kb ~)
Large (~300kb)
Replication enzyme
source
Viral enzymes and
Cellular enzymes.
Shapes
Linear or Circular
Section R: Bacteriophages and Viruses
Yang Xu, College of Life Sciences
Schematic drawings of several
types of viral genomes
Section R: Bacteriophages and Viruses
Yang Xu, College of Life Sciences
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.
Section R: Bacteriophages and Viruses
Yang Xu, College of Life Sciences
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 host‘s 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).
Section R: Bacteriophages and Viruses
Yang Xu, College of Life Sciences
R2 Bacteriophages
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General properties
Lytic and lysogenic inferction
Bacteriophage M13
Bacteriophage l
Transposable phage
Section R: Bacteriophages and Viruses
Yang Xu, College of Life Sciences
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.
Section R: Bacteriophages and Viruses
Yang Xu, College of Life Sciences
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.
Section R: Bacteriophages and Viruses
Yang Xu, College of Life Sciences
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 (衣
壳) protein. This causes the whole particle to shorten, injecting the
viral DNA into the host cell.
g3p
g6p
T
g8p
RF
Host
enzymes
O
g9p
g7p
Section R: Bacteriophages and Viruses
Yang Xu, College of Life Sciences
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 endonuclease (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.
Section R: Bacteriophages and Viruses
Yang Xu, College of Life Sciences
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.
Section R: Bacteriophages and Viruses
Yang Xu, College of Life Sciences
Bacteriophage l
Construction
of the virion
An head Is icosahedral ,
containing the 48.5 kb
linear dsDNA genome
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.
Section R: Bacteriophages and Viruses
Yang Xu, College of Life Sciences
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
Section R: Bacteriophages and Viruses
Lysogenic
life
Yang Xu, College of Life Sciences
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.
pL pR
A W B C D E F Z UV G H M L K I J b2 att int xis gam red cIII N cI cro cII O P Q S R
Section R: Bacteriophages and Viruses
Yang Xu, College of Life Sciences
Bacteriophage l
3‘ 3‘
5’
3’
5‘
Cycling amplification
Section R: Bacteriophages and Viruses
Yang Xu, College of Life Sciences
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.
Mu
Host
DNA
transpoase
New copy
Section R: Bacteriophages and Viruses
Yang Xu, College of Life Sciences
R3 DNA Viruses
• DNA genomes:
replication and transcription
• Small DNA viruses (SV40)
• Large DNA viruses (Herpesviruses)
• Herpes simplex virus-1
Section R: Bacteriophages and Viruses
Yang Xu, College of Life Sciences
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 (时序) 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.
Section R: Bacteriophages and Viruses
Yang Xu, College of Life Sciences
Life cycle of DNA virus
病毒
Section R: Bacteriophages and Viruses
Yang Xu, College of Life Sciences
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.
Ori
5’ BglI
3’
Ori
VP1
VP3
VP2
t
T
EcoRI
3’
5’
T(t) = tumor
Section R: Bacteriophages and Viruses
Yang Xu, College of Life Sciences
R4 RNA Viruses
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RNA genomes: general features
Classification of animal virus
SARS coronaviruses
Retroviruses
Life cycle of retroviruses
Oncogenic retroviruses
Retroviral genome structure and expression
Section R: Bacteriophages and Viruses
Yang Xu, College of Life Sciences
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.
Section R: Bacteriophages and Viruses
Yang Xu, College of Life Sciences
Classification of animal virus
RNA viruses
DNA viruses
I
Class
_
Genome +
II
III
+ or +
_
_
IV
+
_
V
VI
+
_
+
_
_
+
_
+
mRNA
Section R: Bacteriophages and Viruses
Yang Xu, College of Life Sciences
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.
Section R: Bacteriophages and Viruses
Yang Xu, College of Life Sciences
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.
Section R: Bacteriophages and Viruses
Yang Xu, College of Life Sciences
Oncogenic retroviruses
+RNA
- DNA
5’
3’
gag
gag
pol
pol
env
env
v-onc
v-onc
3’
5’
RT
Host DNA pol
+DNA
- DNA
5’
3’
gag
gag
pol
pol
env
env
v-onc
v-onc
3’
5’
Virus Integase
Host 5’
DNA 3’
gag
gag
LTR
pol
pol
env
env
v-onc
v-onc
3’Host
5’DNA
Host RNA pol. II
U3 R U5
Section R: Bacteriophages and Viruses
Yang Xu, College of Life Sciences
Retroviral genome expression
5’
3’
gag
gag
pol
pol
env
env
v-onc
v-onc
3’
5’
LTR
U3 R U5
gag: proteins of the icosahedral capsid;
U3: Strong promoter; pol: RT, RNase H, integrase and protease;
env: the envelope proteins.
R: RT binding site;
U5: RNA binding Site v-onc: protein of regulation of cell division.
Section R: Bacteriophages and Viruses
Yang Xu, College of Life Sciences
HIV Genome
Section R: Bacteriophages and Viruses
Yang Xu, College of Life Sciences
That’s all for Section R
Section R: Bacteriophages and Viruses
Yang Xu, College of Life Sciences