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Struktur dan Keragaman Virus
Department of Biology FMIPA-IPB
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Viruses have one major characteristic in common: they
are obligate intracellular parasites.
Virology; the study of viruses
Viruses are UNABLE to grow and reproduce outside
of a living cell. No virus is able to produce its own
energy (ATP) to drive macromolecular synthesis.
However, in many other respects, they are a
highly diverse group.
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Definition of a Virus
Viruses are segments of nucleic acid enclosed in a protein coat (virion / virus particle : extracellular state)
Poliovirus
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Viruses are genetic elements that can replicate independently of a cell’s chromosomes but not independently of cells themselves (intracellular state)
Definition of a Virus
a host (a place for initiating the intracellular state)
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Properties of Viruses
Small size>range>0.02 - 0.3 micrometers
Picornavirus (“little RNA virus”) is
one of the smallest viruses, about
20 nanometers in diameter
Smallpox virus, one of the largest
viruses, about 300 nanometers, near
the resolution of the light microscope
• Size alone does not differentiate viruses & bacteria!
• smallest bacteria (e.g. Mycoplasma, Ralstonia pickettii)
are only 200-300 nm long.
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Properties of Viruses
Various morphologiespolyhedralhelicalsphericalfilamentouscomplex
Ebola virus Rabies virus
Poliovirus Herpes virus Coronavirus Lassa virus
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Properties of Viruses
Obligate intracellular parasites
Bacteriophage T4, a virus that
Infects E. coli
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Properties of Viruses
Lack membranes and a means to generate energy
HIV
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Properties of Viruses
Lack metabolic and biosynthetic enzymes
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Properties of Viruses
Lack ribosomes
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Properties of Viruses
Do not grow in size
Viruses grow by independent synthesis and assembly of their components inside of a host cell
Human adenoviruses growing in the
nucleus of their host cell
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Virion Structure
Nucleic Acid
Spike
Projections
Protein
Capsid
Lipid Envelope
Virion
Associated
Polymerase
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Structure of Viruses
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Virion Components
Protein Structural proteins
Membrane proteins
Receptor recognition
Enzymes
Genomic nucleic Acid DNA
RNA
Lipid envelope Plasma membrane – Paramyxoviruses
Nuclear membrane – Herpes viruses
Golgi membrane - Bunyaviruses
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Structure of Viruses
The viral genome is DNA or RNA
Most bacterial viruses contain double-stranded DNA
Many animal viruses contain ds DNA or ssRNA
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Structure of Viruses
Most common morphologies are polyhedral (icosahedral) and helical
Polyhedral virusHelical virus
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Structure of Viruses
Some viruses have additional structures: animal viruses may have envelopes and “spikes”
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Structure of Viruses
bacterial viruses may have tails and related structures
T4
virus
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Classification of VirusesCriteria:
Type of nucleic acid
Size and morphology
Additional structures such as envelopes and tails
Host range > refers to the range of cells that can be infected by the virus, most often expressed as bacteria, plant and animal hosts
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Classification of Viruses
Comparative size and shape of various groups of viruses representing diversity of form and host range
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Some Families of Bacteriophage
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Some Families of Animal Viruses
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Some Families of Animal Viruses (continued)
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11
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DNA
viruses
RNA
viruses
ds DNA ss RNA ss RNAss DNA
RNA DNA
viruses
ss RNA(Retroviruses)
ds DNA(hepadnaviruses)
Viral genomes
• genome can function as mRNA
• genome is template for mRNA
• genome is template for DNA synthesis
("retrovirus")
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Baltimore Classification of Viruses
2 ssDNA ParvovirusdsDNA mRNAssDNA
4 +ve ssRNA dsRNA +ve ssRNA [Acts as mRNA] Enterovirus
5 -ve ssRNA Influenza Avirus
dsRNA -ve ssRNA mRNA
6 ssRNA mRNAdsDNAssRNA Retrovirus(e.g. HIV)
7 Nicked dsDNA Hepatitis Bvirus
nicked dsDNA intact dsDNA mRNA
RNA
Group Genome Replication Example
1 dsDNA dsDNA mRNA Herpes simplexvirus
3 dsRNA ReovirusdsRNA mRNA
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Virus Groups
Some members possess large DNA genomes encoding a range of enzymes involved in nucleic acid synthesis.
Depending on virus group viruses show temporal regulation of protein synthesis.
Small DNA genomes with limited coding capacity.
Some members of this group are dependant upon other viruses for their replication.
1 dsDNA dsDNA mRNA Herpes simplexvirus
2 ssDNA ParvovirusdsDNA mRNAssDNA
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Virus Groups
Viruses possessing RNA genomes all encode an RNA-dependant RNA polymerase.
RNA viruses show a higher mutation rate compared to DNA viruses.
Segmented genomes.
Transcribes mRNA from the dsRNA genome without prior protein synthesis using a virion associated RNA-polymerase
Early phase of mRNA synthesis is monocistronic mRNA molecules.
3 dsRNA dsRNA mRNA Reovirus
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Virus Groups
“Positive” RNA viruses - Genome RNA is of the same sense as mRNA and can be infectious.
First stage in replication is the translation of the genome RNA with the production of the virus polymerase.
“Negative” RNA viruses – Genome RNA is complementary to mRNA.
Virion-associated RNA-polymerase and first stage in replication is mRNA transcription.
4 +ve ssRNA dsRNA +ve ssRNA [Acts as mRNA] Enterovirus
5 -ve ssRNA Influenza Avirus
dsRNA -ve ssRNA mRNA
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Virus Groups
Unique among RNA viruses in that they induce tumours.
Characteristic feature is their ability to produce a DNA copy of the genome RNA using a virion associated Reverse Transcriptase.
DNA copy integrates into the cellular genome.
Circular DNA genome - double stranded with a nick in one strand.
The nick is repaired at an early stage in the virus replication cycle.
The virus encodes RNA polymerase with a reverse transcriptase activity which produces a RNA intermediate from which the genome DNA can be copied.
6 ssRNA mRNAdsDNAssRNA Retrovirus(e.g. HIV)
7 Nicked dsDNA Hepatitis Bvirus
nicked dsDNA intact dsDNA mRNA
RNA
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UNINFECTED CELLS
INFECTED
CELLS
Ra
te o
f P
rote
in S
ynth
esis
2 4Hours after Infection
7MeG
p220
IRES
AUGU5’
A. Cellular mRNA
B. Picornavirus mRNA
Poliovirus protein synthesis
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The (dsDNA) Virus Life
Cycle
1. Virus enters host cell (method is variable, involves host receptor molecule on cell surface)
2. Viral DNA replicated using the host's DNA polymerase, nucleotides, etc.
3. DNA transcribed into mRNA using host's RNA polymerase, nucleotides
4. mRNA translated using host's ribosomes, tRNAs, amino acids, GTP, etc.
DNAProtein
capsid
1
32
mRNA
DNA
capsid
proteins
4
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The dsDNA Virus Life Cycle
5. New DNA and capsid proteins assemble into new virus particles, exit the cell (in various ways)
DNAProtein
capsid
1
32
mRNA
DNA
capsid
proteins
4
5
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The ssRNA (type V) Virus Life
Cycle
1. Virus enters host cell
2. Capsid removed, RNA released
3. complementary RNA made from genomic RNA by enzyme encoded in viral genome
4. new genomic RNA made from complementary strand
5. complementary strand is mRNA, transcribed into viral proteins
6. Virus assembled, exits cell (by various means)
1
2
5
4
3
6
RNA
cRNA
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The Retrovirus Life
Cycle
1. Virus enters host cell
2. Reverse transcriptase (encoded in viral genome) catalyzes synthesis of DNA complementary to the viral RNA (cDNA)
3. RTase catalyzes synthesis of 2nd strand of DNA complementary to the first
4. dsDNA incorporated into host genome ("provirus")
provirus may remain unexpressed for a period of latency
1
4
3
2
5
6
Host's DNA
RNA
cDNA
RTase
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The Retrovirus Life
Cycle
5. Proviral genes are transcribed by host's transcriptional machinery into RNA
• RNA serves as mRNA for translation into viral proteins andas genomic RNA
6. New viruses are assembled containing genomic RNA and Reverse Transcriptase
7. Virus exits cell
1
4
3
2
5
6
Host's DNA
RNA
cDNA
RTase
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Bacteriophages
Viruses that infect bacterial cells
Two types of infections:
1. Lytic infection: phage replicates its DNA and lyses the host cell
2. Lysogenic infection: phage DNA is maintained by the host cell, which is only rarely lysed
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Virulent phages only
undergo a lytic cycle
Temperate phages can
follow both cycles
Prophage can
exist in a dormant
state for a long
time
It will undergo
the lytic cycle
Bacteriophage
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Lytic phages
Clockwise: Pseudomonas aeruginosa phage; Aeromonas
phage; Shigella K II phage; Listeria phage
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Life Cycle of a Lytic Phage
Step 1 Adsorption: virus attaches to the cell wall surface
Step 2 Penetration: entry of the viral DNA
Phage T4 adsorption to the cell wall of E. coli
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Life Cycle of a Lytic Phage
Step 3 Synthesis of early viral proteins
Step 4 Replication of viral DNA
Phage T2 attacks E. coli
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Life Cycle of a Lytic Phage
Step 5 Synthesis of late viral proteins
Step 6 Assembly
Step 7 Lysis and release of mature viruses
Lysis of E. coli cell by Phage T4
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Life Cycle of a Lytic Phage
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Temperate phages can
follow both cycles
Prophage can
exist in a dormant
state for a long
time
It will undergo
the lytic cycle
Bacteriophage
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Lysogeny
Lysogenic phages are also called temperate phages
Lysogenic infection begins like a lytic infection with adsorption of the virus and penetration of the viral DNA
Lambda phage, adsorbed to the surface of E. coli,
injecting Lambda DNA
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Lysogeny
After penetration, phage DNA interates into the bacterial chromosomal DNA
Integrated phage DNA is called prophage
Prophage genes for DNA replication and coat proteins are repressed
Phage lambda, a lysogenic phage of E. coli
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Lysogeny
Bacterial cell containing prophage DNA is lysogenized
Lysogenized bacteria replicate the prophage DNA
Lysogenized bacteria divide normally and appear normal
Phage mu,another lysogenic phage of E. coli
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Lysogeny
Occasionally (1/10,000 in lambda) prophage deintegrates (excises) from the bacterial chromosome
This is called derepression and leads to a lytic cycle that reproduces more phage particles
A lambda particle reeling in a headfull of
DNA during an occasional lytic cycle in
E. coli
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Viruses are usually very host-specific:
one virus infects only one strain,
maybe not even other members of the
same species
Why?
Viruses enter cells via specific proteins in
the membrane
Phage’s host specificity
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Lipid bilayer
(same in all
cells) cannot
be penetrated
Proteins differ,
even within a
species
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Consequences of viruses attacking
specific proteins
1. A cell cannot be totally immune to all
viruses because it needs the membrane
proteins to communicate with outside
environment
Best example: lambda phage attacks
E.coli via the maltose transporter. No
transporter, no phage problem—but no
maltose (a sugar) also.
So, viruses can affect uptake, etc.
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Bacteriophages: Quantification
There are three methods :
Electron Microscopy
Epifluorescence microscopy
Plaque Assay
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Electron microscopy:
Difficult, expensive
More definitive—you’re sure it’s a virus
More information from morphology
Epifluorescence microscopy
Easy, less expensive
Less definitive: “viral-like particles”
More quantitative
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VV
BB
A drop of seawater viewed with an electron microscope
(from Eric Wommack)
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Phage
One of many
phages
27
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Virus counts with epifluorescence are higher
than with electron microscopy (TEM). Why?
1.Epifluorescence counts things that are
viruses.
2.TEM misses things that are viruses
3.Loss of viruses during preparation of
samples for TEM.
24
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Quantification of bacteriophages by plaque assay:
host bacterial cells plaques
“lawn” of host bacteria
Ph2
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l forms plaques on a lawn of bacteria
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Uses for Bacteriophages
Phages as vectors in genetic engineering and biotechnology designs
Phage lytic enzymes to control infections
Phage therapy in animals and other uses of phage in agriculture
Bacteriophage therapy
Phages for detection of pathogenic bacteria
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TERIMA KASIH