Struktur dan Keragaman Virus

Department of Biology FMIPA-IPB

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.

Definition of a Virus

Viruses are segments of nucleic acid enclosed in a protein coat (virion / virus particle : extracellular state)

Poliovirus

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)

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.

Properties of Viruses

Various morphologiespolyhedralhelicalsphericalfilamentouscomplex

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

Nucleic Acid

Spike

Projections

Protein

Capsid

Lipid Envelope

Virion

Associated

Polymerase

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

Polyhedral virusHelical 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 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

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

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")

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Temperate phages can

follow both cycles

Prophage can

exist in a dormant

state for a long

time

It will undergo

the lytic cycle

Bacteriophage

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

Integrated phage DNA is called prophage

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

Lysogenized bacteria replicate the prophage DNA

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

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

Lipid bilayer

(same in all

cells) cannot

be penetrated

Proteins differ,

even within a

species

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.

Bacteriophages: Quantification

There are three methods :

Electron Microscopy

Epifluorescence microscopy

Plaque Assay

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

VV

BB

A drop of seawater viewed with an electron microscope

(from Eric Wommack)

Phage

One of many

phages

27

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

Quantification of bacteriophages by plaque assay:

host bacterial cells plaques

“lawn” of host bacteria

Ph2

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