Virus

INTRODUCTION

• Viruses are simple, acellular entities

• Small in size: range between 10-400 nm in diameter

• Obligate intracellular parasites: completely dependent upon the internal

environment of the cell to create new infectious virus particles, or virions.

• The genetic material of viruses can be composed of DNA or RNA

Cont.
Viruses exist in two different states/phases:

1. Extracellular phase: virus is called a virion and isn't capable to reproduce.

2. Intracellular phase: viruses exist primarily as replicating nucleic acids that

induce host metabolism to synthesize virion components; eventually

complete virus particles or virions are released

 Structure of virus

Virus particle consist of nucleocapsid core which is composed of a nucleic

acid, usually either DNA or RNA, held within a protein coat called the capsid,
which protects viral genetic material and aids in its transfer between host
cells.

Cont.
• Capsids are large macromolecular structures that self-assemble from
many copies of one or a few types of proteins.
• The proteins used to build the capsid are called protomers.

• The virus capsid functions to protect the nucleic acid from the
environment, and some viruses surround their capsid with a membrane
envelope.
contain carbohydrates,
lipids, and proteins

Cont.
• Capsid of the virion is composed of one or only a few proteins that repeat

over and over again to form the structure.

• These viruses often have proteins, called matrix proteins, that function to

connect the envelope to the capsid inside.

• Each virus also possesses

a virus attachment

protein embedded in its

outer-most layer.
Cont.
• The virus attachment protein is the viral protein that facilitates the docking of
the virus to the plasma membrane of the host cell, the first step in gaining
entry into a cell.
Types of capsid symmetry

1. Helical

2. Icosahedral

3. Complex.
 Helical capsid structure

• Shaped like hollow tubes with protein walls

• Viral nucleic acid coils into a helical shape and
the capsid proteins wind around the inside or
outside of the nucleic acid, forming a long tube
or rod-like structure
• The protein that winds around the nucleic acid
is often called the nucleocapsid protein
• Only one type of capsid protein is required which is repeated over and over

again to form the capsid.

• Helical viruses can be enveloped or naked.

• Mostly all helical plant viruses are naked. e.g. TMV

• In contrast, all helical animal viruses are enveloped. These include well-

known viruses such as influenza virus, measles virus, mumps virus, rabies

virus, and Ebola virus

• Tobacco mosaic virus provides a well-studied example of helical capsid
structure
• Self-assembly of protomers in a helical or spiral arrangement produces a long,
rigid tube, 15 to 18 nm in diameter by 300 nm long.
• The influenza virus genome is enclosed in thin, flexible helical capsids that are
folded within an envelope

Helical structure of tobacco mosaic virus

 Icosahedral Capsid Structure

• More prevalent than the helical architecture.

• Genomes of icosahedral viruses are packaged completely within an icosahedral
capsid that acts as a protein shell.
• The icosahedron is a regular polyhedron with 20 equilateral triangular faces and
12 vertices.

Adenovirus Polyomavirus
Picornavirus
• The capsids are constructed from ring- or knob-shaped units called
capsomers, each usually made of five or six protomers.
• Pentamers (pentons) have five subunits; hexamers (hexons) possess six.

• Pentamers are usually at the vertices of the Pentons

Hexons
icosahedron, whereas, hexamers generally
form its edges and triangular faces
 Viral Envelopes and Enzymes

• Enveloped viruses predominantly infect animal cells although a few are

known to infect plants and bacteria.
• Animal virus envelopes usually arise from host cell nuclear or plasma
membranes; their lipids and carbohydrates are normal host constituents.
• In contrast, envelope proteins are coded for by virus genes and may even
project from the envelope surface as spikes, which are also called
peplomers.
• In many cases, these spikes are involved in virus attachment to the host cell
surface. Because they differ among viruses.
• The envelope is a flexible, membranous structure, so enveloped viruses
frequently have a somewhat variable shape and are called pleomorphic.
 Influenza virus
• Spikes project about 10 nm from the surface at 7 to 8 nm intervals.
• Some spikes possess the enzyme neuraminidase, which functions in the
release of mature virions from the host cell.

• Other spikes have hemagglutinin proteins,

so named because they can bind the
virions to red blood cell membranes and
cause the red blood cells to clump
together (agglutinate). This is called
hemagglutination.
• Hemagglutinins participate in virion Influenza virus
attachment to host cells.
• Spike proteins that are exposed on the outer envelope surface, are generally

glycoproteins—that is, the proteins have carbohydrate attached to them.

• A nonglycosylated protein, the M or matrix protein, is found on the inner

surface of the envelope and helps stabilize it.

 Complex Viral Structures
• Few viruses have a complex architecture that does not strictly conform to
a simple helical or icosahedral shape.
• They have exceptionally complex internal structure with an ovoid- to brick
shaped exterior.
• e.g. Poxviruses and many bacteriophages
• The poxviruses are the largest of the animal viruses (about 400X240X200
nm in size)
• Poxviruses are brick or oval-shaped viruses with large double-stranded
DNA genomes.
• Some large bacteriophages are even more elaborate than the poxviruses.
• The T2, T4, and T6 phages (T-even phages) that infect Escherichia coli are
said to have binal symmetry
• They have a head that resembles an icosahedron and a tail that is helical.
• The icosahedral head is elongated by one or two rows of hexamers in the
middle and contains the DNA genome
• The tail is composed of a
collar joining it to the head, a
central hollow tube, a sheath
surrounding the tube, and a
complex baseplate.
 Bacteriophages
• Bacteriophages are viruses that can infect and kill bacteria without any negative
effect on human or animal cells.
• For this reason, it is supposed that they can be used, alone or in combination with
antibiotics, to treat bacterial infections.
• Bacteriophages also can carry a variety of virulence factors that convert their
bacterial hosts into potent pathogens.
• These bacterial viruses have genetic material in the form of either DNA or RNA,
encapsidated by a protein coat
• The capsid is attached to a tail which has fibers, used for attachments to receptors
on bacterial cell surface.
• Bacteriophages exhibit a wide degree of diversity in terms of genome

structure.

• Although most possess double-stranded DNA (dsDNA) genomes, phages

with single-stranded DNA (ssDNA), single-stranded RNA (ssRNA), and

double-stranded RNA(dsRNA) genomes have been identified and studied

Life cycle of bacteriophage

1. Adsorption and Penetration

2. Synthesis of Phage Nucleic Acids and Proteins

3. Assembly of Phage Particles
4. Release of Phage Particles
 Adsorption and Penetration
• Like all viruses, bacteriophages do not randomly attach to the surface of a host cell; rather,
they fasten to specific surface structures called receptors.
• Nature of these receptors varies with the phage; cell wall lipopolysaccharides and proteins,
teichoic acids, flagella, and pili can serve as receptors.
• The T-even phages of E. coli use cell wall lipopolysaccharides or proteins as receptors.

T4 Phage Adsorption
and DNA Injection.

• As more tail fibers make contact, the baseplate settles down on the surface.
• Binding is probably due to electrostatic interactions and is influenced by pH and the presence
of ions such as Mg2+ and Ca2+.
• After the baseplate is seated firmly on the cell surface, conformational

changes occur in the baseplate and sheath, and the tail sheath reorganizes

so that it shortens from a cylinder 24 rings long to one of 12 rings.

• That is, the sheath becomes shorter and wider, and the central tube or core

is pushed through the bacterial wall.

• The baseplate contains the protein gp5, which has lysozyme activity which

aids in the penetration of the tube through the peptidoglycan layer. Finally,

the linear DNA is extruded from the head, through the tail tube, and into the

host cell
 Synthesis of Phage Nucleic Acids and Proteins

• All double-stranded DNA viruses follow a similar route for synthesis of viral

nucleic acids and proteins except Hepadnaviridae

• The DNA genome serves as the template for mRNA synthesis

• The mRNA molecules made are translated to yield viral proteins.

• Sometime after the onset of mRNA synthesis, DNA replication ensues and

more viral genomes are made.

• After injection of T4 DNA into a host E. coli
• cell, the E. coli RNA polymerase starts synthesizing
T4 mRNA.
• Early mRNA directs the synthesis of protein factors
and enzymes required to take over the host cell
and force it to manufacture additional viral
constituents The Life Cycle of Bacteriophage T4

• Some early virus-specific enzymes degrade host DNA to nucleotides, thereby simultaneously halting
host gene expression and providing raw material for viral DNA synthesis.
• Within 5 minutes, viral DNA synthesis commences.
• DNA replication is initiated from several origins of replication and it proceeds bidirectionally
• from each.
• Viral DNA replication is followed by the synthesis of late mRNAs, which are important in later stages
of the infection
 Assembly of Phage Particles

• The assembly of T4 phage is an exceptionally complex self-

assembly process that involves special virus proteins and some host
cell factors.
• Late mRNA directs the synthesis of three kinds of proteins:
1. Phage structural proteins,
2. Proteins that help with phage assembly without becoming part
of the virion structure,
3. Proteins involved in cell lysis and phage release.
 Release of Phage Particles

• The lysis of E. coli by T4 takes places after about 150 virus particles have
accumulated in the host cell
• Two proteins are involved.
1. One directs the synthesis of an enzyme that attacks peptidoglycan in
the host’s cell wall. It is sometimes called T4 lysozyme.
2. Another T4 protein called holin creates holes in the E. coli plasma
membrane, enabling T4 lysozyme to move from the cytoplasm to the
peptidoglycan.
• Phages infect bacteria and can propagate in two possible ways; lytic life cycle
and lysogenic life cycle.
• A phage life cycle that culminates with the host cell bursting and releasing
virions is called a lytic cycle, and viruses that reproduce solely in this way are
called virulent viruses.
• On the other hand some phages known as temperate phages can grow
vegetatively and can integrate their genome into host chromosome replicating
with the host for many generations.
• If induction to some harsh conditions occurs then the prophage will escape via
lysis of bacteria
Lytic vs Lysogenic cycle
 Application of bacteriophage in genetic engineering
• Bacteriophages can be modified to identify nonbacterial targets including eukaryotic
proteins and tissues by altering the tail fibers or capsid proteins to include
eukaryotic targeting motifs using phage display
• vaccines can be designed using phages that either display a protein antigen from a
human pathogen or a cancer cell on their surface or carry the genetic information to
encode the antigen
• Engineered phages to directly deliver drugs to specific cancer cells has the
potential to minimize the side effects and off target toxicity of more traditional
cancer therapies
• Increase phage killing efficacy or to introduce other desirable properties, such as
expanded host range, increased biofilm degradation, elimination of lysogeny