Struktur dan Keragaman Virus

Department of Biology FMIPA-IPB

Virology; the study of viruses

Viruses have one major characteristic in common: they are obligate intracellular parasites.

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.

Definition of a Virus
Viruses are segments of nucleic acid enclosed

in a protein coat (virion / virus particle : extracellular state)

Poliovirus

Definition of a Virus
Viruses are genetic elements that can

replicate independently of a cells chromosomes but not independently of cells themselves (intracellular state)

a host (a place for initiating the intracellular state)

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

Size alone does not differentiate viruses & bacteria! smallest bacteria (e.g. Mycoplasma, Ralstonia pickettii) are only 200-300 nm long.

Smallpox virus, one of the largest viruses, about 300 nanometers, near the resolution of the light microscope

Properties of Viruses
Various morphologies

polyhedral helical spherical filamentous complex

Ebola virus

Rabies virus

Poliovirus

Herpes virus

Coronavirus

Lassa virus

Properties of Viruses
Obligate intracellular parasites

Bacteriophage T4, a virus that Infects E. coli

Properties of Viruses
Lack membranes and a means to generate energy

HIV

Properties of Viruses
Lack metabolic and biosynthetic enzymes

Properties of Viruses
Lack ribosomes

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

Virion Structure
Lipid Envelope Nucleic Acid

Protein Capsid Virion Associated Polymerase

Spike Projections

Structure of Viruses

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

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

Structure of Viruses
Most common morphologies are polyhedral

(icosahedral) and helical

Helical virus

Polyhedral virus

Structure of Viruses
Some viruses have additional structures:

animal viruses may have envelopes and spikes

Structure of Viruses
bacterial viruses may have tails and related

structures

T4 virus

Classification of Viruses
Criteria:

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

Classification of Viruses

Comparative size and shape of various groups of viruses representing diversity of form and host range

Some Families of Bacteriophage

Some Families of Animal Viruses

Some Families of Animal Viruses (continued)

11

Viral genomes
DNA viruses RNA viruses RNA DNA viruses

ss DNA

ds DNA

ss RNA

ss RNA

ss RNA
(Retroviruses)

ds DNA
(hepadnaviruses)

genome can function as mRNA genome is template for mRNA genome is template for DNA synthesis ("retrovirus")

Baltimore Classification of Viruses

Group
1
2

Genome
dsDNA
ssDNA ssDNA

Replication
dsDNA
dsDNA

Example
mRNA
mRNA

Herpes simplex virus

Parvovirus

3 4
5

dsRNA +ve ssRNA

-ve ssRNA dsRNA dsRNA ssRNA

dsRNA

mRNA +ve ssRNA [Acts as mRNA]

-ve ssRNA mRNA

Reovirus Enterovirus
Influenza A virus

6 7

ssRNA Nicked dsDNA

dsDNA intact dsDNA

RNA

mRNA
mRNA

Retrovirus (e.g. HIV) Hepatitis B virus

nicked dsDNA

Virus Groups
1 dsDNA dsDNA mRNA Herpes simplex virus

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.
2 ssDNA ssDNA dsDNA mRNA Parvovirus

Small DNA genomes with limited coding capacity. Some members of this group are dependant upon other viruses for their

replication.

Virus Groups
Viruses possessing RNA genomes all encode an RNA-

dependant RNA polymerase. RNA viruses show a higher mutation rate compared to DNA viruses.
3 dsRNA dsRNA mRNA Reovirus

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.

Virus Groups
4 +ve ssRNA dsRNA +ve ssRNA [Acts as mRNA] Enterovirus

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.

5 -ve ssRNA dsRNA -ve ssRNA mRNA Influenza A virus

Negative RNA viruses Genome RNA is complementary to mRNA. Virion-associated RNA-polymerase and first stage in replication is

mRNA transcription.

Virus Groups
6 ssRNA ssRNA dsDNA mRNA Retrovirus (e.g. HIV)

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.
7 Nicked dsDNA nicked dsDNA RNA intact dsDNA mRNA Hepatitis B virus

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.

Poliovirus protein synthesis

Rate of Protein Synthesis

A. Cellular mRNA UNINFECTED CELLS

p220 7MeG

INFECTED CELLS

B. Picornavirus mRNA

5 U
Hours after Infection

AUG
IRES

The (dsDNA) Virus Life Cycle

1.

Protein capsid

DNA

Virus enters host cell (method is variable, involves host receptor molecule on cell surface) Viral DNA replicated using the host's DNA polymerase, nucleotides, etc. DNA transcribed into mRNA using host's RNA polymerase, nucleotides mRNA translated using host's ribosomes, tRNAs, amino acids, GTP, etc.

2 3
DNA mRNA

2.

3.

capsid proteins

4.

The dsDNA Virus Life Cycle

Protein capsid

DNA

1
5.

New DNA and capsid proteins assemble into new virus particles, exit the cell (in various ways)

2 3
DNA
mRNA

5
capsid proteins

The ssRNA (type V) Virus Life Cycle

1
1. 2. 3.

Virus enters host cell Capsid removed, RNA released complementary RNA made from genomic RNA by enzyme encoded in viral genome new genomic RNA made from complementary strand complementary strand is mRNA, transcribed into viral proteins Virus assembled, exits cell (by various means) 6 4

2
RNA

3
cRNA

4. 5. 6.

The Retrovirus Life Cycle

1. 2.

Virus enters host cell Reverse transcriptase (encoded in viral genome) catalyzes synthesis of DNA complementary to the viral RNA (cDNA) RTase catalyzes synthesis of 2nd strand of DNA complementary to the first dsDNA incorporated into host genome ("provirus")

RTase RNA

cDNA

3
Host's DNA

3.

4.

provirus may remain unexpressed for a period of latency

5 6

The Retrovirus Life Cycle

5.

Proviral genes are transcribed by host's transcriptional machinery into RNA

RTase RNA

RNA serves as mRNA for translation into viral proteins and as genomic RNA

cDNA

3
Host's DNA

6.

New viruses are assembled containing genomic RNA and Reverse Transcriptase

5 6

7.

Virus exits cell

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

Bacteriophage

It will undergo the lytic cycle

Prophage can exist in a dormant state for a long time

Virulent phages only undergo a lytic cycle

Temperate phages can follow both cycles

Lytic phages

Clockwise: Pseudomonas aeruginosa phage; Aeromonas phage; Shigella K II phage; Listeria phage

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

Life Cycle of a Lytic Phage Step 3 Synthesis of early viral proteins Step 4 Replication of viral DNA

Phage T2 attacks E. coli

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

Life Cycle of a Lytic Phage

Bacteriophage

It will undergo the lytic cycle

Prophage can exist in a dormant state for a long time

Temperate phages can follow both cycles

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

Lysogeny
After penetration, phage DNA

interates into the bacterial chromosomal DNA prophage

Integrated phage DNA is called Prophage genes for DNA

replication and coat proteins are repressed

Phage lambda, a lysogenic phage of E. coli

Lysogeny
Bacterial cell containing

prophage DNA is lysogenized the prophage DNA

Lysogenized bacteria replicate Lysogenized bacteria divide

normally and appear normal

Phage mu,another lysogenic phage of E. coli

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

Phages host specificity

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

Proteins differ, even within a species

Lipid bilayer (same in all cells) cannot be penetrated

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 problembut no maltose (a sugar) also. So, viruses can affect uptake, etc.

Bacteriophages: Quantification
There are three methods :
Electron Microscopy

Epifluorescence microscopy
Plaque Assay

Electron microscopy:
Difficult, expensive More definitiveyoure sure its a virus More information from morphology Epifluorescence microscopy Easy, less expensive Less definitive: viral-like particles

More quantitative

V V

B B

A drop of seawater viewed with an electron microscope (from Eric Wommack)

Phage

27
One of many phages

24

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.

Quantification of bacteriophages by plaque assay:

Ph2

host bacterial cells

plaques

lawn of host bacteria

l forms plaques on a lawn of bacteria

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

TERIMA KASIH