the art of reconstruction. in order to survive, viruses must be able to do the following: ◦ 1....
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Virus Life Cycles in 3D
The Art of Reconstruction
In order to survive, viruses must be able to do the following:◦ 1. Find a host cell it can replicate in◦ 2. Bind to that cell◦ 3. Enter the cell◦ 4. Release its genome in order to replicate◦ 5. Replicate its genome◦ 6. Transcribe and translate its viral proteins◦ 7. Package its genome and proteins◦ 8. Escape from the cell
Virus Life Cycle
Virus Life Cycle
All these processes can be visualized by cryo
These visualizations allows for a better understanding of viruses and may lead to vaccination development
For each virus, there is a unique life cycle but all viruses accomplish the same steps in order to survive
Virus Life Cycle
Semliki Forest Virus is an enveloped Alphavirus
It has 2 transmembrane proteins (E1 and E2) in its envelope
The virus binds to the cellular receptor, endocytosed, and fuses with the endosome membrane to release its nucleocapsid for replication
Enveloped Virus
SFV as an example
Poliovirus is a non enveloped virus in the Picornavirus family
It differs from SFV in that when it binds to its cellular receptor, it goes through a conformational change.
This conformational change may facilitate the release of genome into the cell for replication
Also releases from the cell by lysis instead of budding
Non enveloped Viruses
Non enveloped virus
The first step in viral replication is to be able to bind to the correct host cell.
Virus recognize host cells by certain receptors.
Bind to these receptors through specific interactions.
Binding sites on viruses are typically conserved to ensure survival
Cell Attachment
Picornaviruses shield their receptor binding site in a region called the canyon in order to protect it from antibodies.
Must be conserved so that the virus can bind to the correct cell in order to replicate.
HRV16 + ICAM-1 interaction was one of the first to be studied through cryo
Was believed that the binding site for ICAM-1 was located in the canyon region of HRV16
The Receptor binding region of HRV14
The Receptor binding region of HRV14
HRV16 complexed with the 2 N terminal domains of ICAM-1
The footprint of ICAM-1 was centered over the canyon as predicted showing that the canyon was in fact the binding site of the receptor
HRV16 complexed with ICAM-1
HRV16 complexed with ICAM-1
VP4 of rotavirus is important to the viral life cycle
It is a determinant of virulence, has hemagglutination activity and is also a neutralization site
The reconstruction showed that VP4 extends from the surface of the virus, which may then be able to bind to the cellular receptor more easily
Simian Rotavirus
Simian Rotavirus
Viruses must be stable enough to survive the extracellular environment but must also be unstable enough to release their genome when they reach susceptible cells.
Certain conformational changes must occur in the virus when it reaches the proper environment in order to release its genome in the correct place and at the correct time.
Activation
SFV has a spike protruding from its envelope comprised of E1, E2, and E3
Reconstruction showed that the spike has a hole in its center
From previous studies, E3 was determined to be on the outside of the spike
Preferential extraction and reconstruction comparison determined that E1made up the outside of the spike while E2 extended from the center
SFV Spikes
SFV with envelope and capsid
SFV spike structure
SFV spike structure
In order to determine the conformational changes needed for activation, the particles were treated with low pH and vitrified within milliseconds
Comparison between treated and untreated particle reconstructions showed that E1 and E2 move around each other
E2 is the receptor binding portion while E1 is the membrane fusion protein
E2 moves outward while E1 moves inward to form a trimmer and trigger fusion
SFV spike conformational changes
SFV spike conformational changes
SFV process of fusion
Adenovirus is made up of hexons and two proteins at the five fold vertice: penton base and fiber
It binds two receptors: CAR and an integrin CAR binds to the fiber while the penton
base binds the integrin and causes activation
Adenovirus
Adenovirus 2 and hexons
Adenovirus uses 2 receptors
CAR Integrins
The conformational changes needed for activation were determined by comparing particles which had the fiber attached and which did not
A small region which was determined to contain the RGD sequence by MAb binding changed orientation
Structural changes in penton
Structural changes in penton
The genome of the virus is released in order to make viral proteins and reproduce the genome.
Viruses can employ several strategies to do this: injection, release into the cytoplasm, release into the nucleus
Exception: Reoviruses
Genome Release
FHV is comprised of 180 copies of a single protein which undergoes a post assembly cleavage
The cleavage produces γ peptides which lie in different orientations according to the subunit it is located on
γa lies in pentamers under the five fold γb interacts with the bulk RNA and γc γc also interactes with the ordered RNA
Flock House Virus
Flock House Virus
FHV γ helices
This data suggested a method of FHV entry and release of genome
The virus binds and contacts the membrane at the five fold vertex
The contact releases a pocket factor which then allows the γa pentamer to insert into the membrane
The RNA is then dragged into the cell by its contacts by the other γ peptide contacts
FHV entry into cell
FHV entry into cell
CCMV releases its genome by expansion At low metal ion concentration and high pH,
the particle swells The particle does not fall apart due to
interactions between subunits and RNA However, the three fold vertices open up
which allow for flow of molecules
CCMV particle expansion
CCMV particle expansion
In order to multiply, the virus must be able to produce viral proteins and replicate its genome.
Process is intrinsically asymmetric which leads to difficulties in icosahedral reconstructions.
Reovirus have provided many clues to the process due to its unusual replication.
Transcription and Translation
Acridine orange was used to visualize RNA in the reconstruction
Channels throughout the rotavirus capsid in which allow the newly synthesized RNA to be exported
Transcribing DLP of Rotavirus
Transcribing DLP of Rotavirus
L-A virus is a fungal virus which contains 2 RNA dependent RNA polymerases on the inside of two of its capsid proteins
The RNA moves past the polymerases as it is synthesized and is exported through pores in the capsid
The capsid protects the RNA from degradation while allowing for the import of important metabolites
L-A Virus
L-A virus transcription
The End!
Swine FluSwine Flu
HIV
SmallpoxAvian Flu