Virology: Virion Structure and Components

• Viruses are subcellular particles replicating specifically inside a living host cell.
• They are obligate intracellular parasites, stealing energy and macromolecules from the host, and are found in organisms across all three domains of life.
• Viruses exist in two states: extracellular as a virion (infectious) and intracellular as a replicating genome (non-infectious).

Virions

• Virions range greatly in size, from Poliovirus (28 nm, about the size of a ribosome) to Pandoravirus (1200 nm, larger than most bacterial cocci).
• Most virions have symmetrical structures such as helical, icosahedral, or complex (non-symmetrical).

Virion Structural Components

• All viruses have a capsid, a protein "coat" that surrounds the genomic material, with subunits known as capsomeres.
• Some viruses possess an envelope, a phospholipid bilayer often containing glycoprotein "spikes," while non-enveloped viruses are "naked."
• Some virions contain viral enzymes required for infection.

Viral Genomes

• Viral genomes consist of either DNA or RNA, which can be single-stranded or double-stranded, and linear or circular.
• Virions vary widely in genome size; Circovirus has a genome of 1.75kb coding for 3 genes, while Pandoravirus has a genome of 2.5Mb coding for 2500 genes.

Bacteriophage

• Bacteriophages are viruses infecting bacteria and archaea and are complex virions.
• They attach to host cells using tail fibers and inject their genome into the host cytosol, leaving the capsid on the cell surface.

Culturing Phage – Plaque Assays

• Culturing phage involves preparing a bacterial lawn on an agar plate and then spreading a viral solution on top.
• Plaques (clear areas) form where the bacteria have been killed, and counting plaque-forming units (PFU) provides estimates of titer.

Phage Receptors

• Host cell phage receptors perform normal functions for the host cell, and viral evolution has targeted these cell components for attachment.

The Lytic Infection

• The lytic infection is an infection cycle of virulent phage that results in replication of the virus and the death of the host cell.
• For example, bacteriophage T4 (linear dsDNA) and its E. coli host, the tail fibers adsorb (attach) to LPS carbohydrates on the host outer membrane.

T4 Penetration

• T4 tail fibers retract, bringing tail pins into contact with the lipid bilayer.
• The tail sheath contracts, pushing a tail tube through the outer membrane
• T4 lysozyme forms a pore through the cell wall
• T4 dsDNA moves into the cytosol.

T4 Synthesis

• During "early" T4 protein synthesis, the host RNA polymerase transcribes a series of viral genes that are only expressed at the start of infection.
• Anti-sigma factor proteins that inhibit host sigma factors are included, stopping host Tc/Tl, and a phage-specific replisome is included.
• During "middle" and "late" T4 protein synthesis, capsomere, tail, and tail fiber proteins are included, as are enzymes to facilitate assembly and release.

T4 Assembly and Release

• "Late" T4 genes encode a packaging motor complex, which fills viral capsids with copies of the viral dsDNA, and the remaining virion components assemble.
• "Late" T4 genes encode enzymes that compromise the host cell membrane and cell wall.
• The host cell lyses and progeny virions are released.

Circular Permutation

• During replication, the linear copies of T4 dsDNA are joined to generate a long concatemer.
• During assembly, the phage DNA is moved into each capsid until it is full and then cut from the rest of the molecule, establishing a "headful" packaging mechanism.
• Because more than a genome-length of DNA fits into each capsid, the DNA is cut at different sites, and each progeny virion has a different gene order.
• The T4 genome is terminally redundant, with genes at one end of the molecule repeated at the other end.

The Lysogenic Infection

• The lysogenic infection is an infection cycle of temperate phage, resulting in a latent infection where the viral genome is replicated as the host continues to grow and divide.
• For example, bacteriophage λ (linear dsDNA) and its E. coli host, the viral DNA becomes integrated into the host genome during lysogeny.
• Integrated viral DNA is called a prophage, and a host with integrated viral DNA is called a lysogen.

λ Adsorption/Penetration

• The λ tail attaches to a host maltose transport protein, with penetration occurring like T4.
• The 5' ends of the λ DNA contain short, single-stranded, complementary, "cohesive ends".
• Following entry into the host cytosol, λ DNA circularizes, forming a cos site.

To Lysogeny or not to Lysogeny

• Most infections result in lytic infection.
• If the λ repressor (cI) gene is expressed upon penetration, cI accumulates, and most λ genes are repressed, leading to λ DNA becoming a prophage.
• If the cro repressor (cro) gene is expressed upon penetration, cro accumulates, and the cI gene is repressed with λ entering the lytic cycle.
• A few λ genes are expressed during lysogeny to "monitor" host stress levels and induce a switch to the lytic cycle if conditions deteriorate.

λ DNA Integration/Excision

• Both λ and host DNA contain att sequences.
• λ integrase nicks the DNA at the att sites: the viral DNA enters the host chromosome.
• If a switch to the lytic cycle is made, a λ excision enzyme cuts the prophage out of the host chromosome.

λ Synthesis

• If expressed, "early" through "late" λ protein synthesis occurs like in a T4 infection.
• The circular λ DNA is copied by rolling circle replication.
• The λ DNA is copied continuously, generating long concatemers with the individual λ genomes being cut from the concatemer at each cos site.
• Genomes are then packaged into assembling phage capsids.