Assembly, exit and maturation Flashcards
What are viral factories?
What is their function?
Viral factories are also known as viroplasms or viral inclusion bodies. It is an intense are of replication and assembly.
Their functions:
1) Location for efficient viral RNA synthesis (has all machinery)
2) Protect nucleic acids from nucleases
3) Prevent viral RNAs from activating host intrinsic immune defences
4) Possibility to coordinate different steps in the viral life cycle (protein synthesis, genome replication and exit)
(T/F) Each sub factory of viral factories have a speciality. Ratio of them changes as viral life cycle progresses!
True!
Some are needed more than the others depending on the stage of the viral life cycle.
(T/F) Viral factories are not present in normal cells! It is part of the cytopathic effects.
True!
Briefly describe the assembly of protein shells/capsids.
The first steps are the formation of the various components of virus particles from their parts.
These intermediates must then associate in ordered fashion.
These reactions need to proceed with reasonable efficiency, and the overall pathway need to be IRREVERSIBLE.
*it is kind of like putting furniture together
*viral factories help co-ordinate these steps
Why does the overall pathway for assembly of protein shells need to be irreversible?
To drive it to the final product.
Or it needs to be highly concentrated.
What are the three ways of formation of structural units? Briefly describe each.
1) Assembly from individual protein molecules: they assemble individually and have complementary surfaces where they bind to. the structures are generally stable but can disassemble (intermolecular).
2) Assembly from a poly-protein precursor: all structural units are encoded in one transcript that is covalently linked with no stop codons in between. when it gets translated, it is one big polypeptide. after folding, a viral protease cleaved linker region and now the process is IRREVERSIBLE! (intramolecular)
3) Chaperone-assisted assembly: proteins have a chaperone with them that catalyze their formation, making no mistakes.
What are the advantages and disadvantages of assembly from individual protein molecules?
Advantages: no energy required, subunits simply interlock
Disadvantages: proteins need to be produced in excess and concentrated (it must be saturated because two molecules have to come together and interact with each other).
What are the advantages and disadvantages of assembly from poly-protein precursor?
Advantages: the intramolecular interaction avoids the need for high concentration of protein. the process is irreversible after protease cleavage.
Disadvantage: need to encode protease
What are the advantages and disadvantages of chaperone-assisted assembly?
Advantages: highly specific
Disadvantages: need to encode chaperone
(T/F) Vaccines use assembly from individual protein molecules to make protein shells.
True!
First, capsid proteins are in excess and then they self-assemble and are purified and are used in vaccines!
Assisted assembly reactions (for assembly of protein shells) need:
1) participation of viral genome (helical nucleocapsid symmetry require protein-protein interaction and protein-genome (mostly RNA) interactions)
2) cellular or viral chaperone assisted assembly
What are viral scaffolding proteins?
These participate in the reactions by which the capsid/nucleocapsid is constructed (assembly of protein shells) but are then removed (usually degraded by proteases)
They are especially prevalent in complicated and larger protein coats.
For the herpes virus:
Pre-VP22a, a viral _________ protein, self-associates and stimulates binding to VP5, which regulates the ______ ______ of nucleocapsid proteins for self-assembly.
Other proteins such as _________ ______ is incorporated. Via interactions with pre-vp22a, a _______ is created. Then Pre-VP22a is ______ by the protease to accommodate the viral ________.
Scaffolding; intrinsic capacity
Protease Vp24; portal; degraded; genome
*all occurs in the nucleus
What are the two mechanisms of selective packaging of the viral genome in virus particles?
1) Concerted: the structural units of the protective protein shell assemble productively ONLY IN ASSOCIATION WITH GENOMIC NUCLEIC ACID.
2) Sequential: The genome is inserted into a preformed protein shell.
Which kinds of viruses use the concerted packaging?
All (-) ssRNA viruses, retroviruses, and other RNA viruses.
(viruses with a helical nucleocapsid requires protein-protein and protein-RNA interactions with the genome)
(formation of protein coat and genome interaction occur at the same time)
Which kinds of viruses use the sequential packaging?
Most DNA viruses and dsRNA viruses use the sequential packaging mechanism.
For example, ADENOVIRUS (a DNA virus) capsid assembly is followed by genome packaging. The capsid proteins need to go into the nucleus via the nuclear pore complex!
What are packaging signals?
What kinds are there?
Packaging signals are specific recognition of sequences or structures UNIQUE to the viral genome.
The nucleic acid packaging signals: DNA signals and RNA signals.
*unique = not found in cellular RNA or DNA!
Match the terms to their definitions:
1) DNA packaging signals
2) RNA packaging signals
3) Packaging of segmented genomes
A) Secondary STRUCTURES
B) To be infectious, each segment (whether DNA or RNA) of a virus has to be encapsulated. RNA SEQUENCES and INTERMOLECULAR INTERACTIONS among RNA segments allow this to happen.
C) Repeats of short SEQUENCES positioned close to Origin of Replication. They are recognized directly or indirectly by viral proteins (allowing the packaging of the genome; mostly sequential).
DNA packaging signals: Repeats of short SEQUENCES positioned close to Origin of Replication. They are recognized directly or indirectly by viral proteins (allowing the packaging of the genome; mostly sequential).
RNA packaging signals: Secondary STRUCTURES
Packaging of segmented RNA genomes: To be infectious, each segment (whether DNA or RNA) of a virus has to be encapsulated. RNA SEQUENCES and INTERMOLECULAR INTERACTIONS among RNA segments allow this to happen.
How do the different segments of the a segmented virus (i.e, influenza, an enveloped -RNA virus that undergoes concerted packaging) come together in the cytoplasm?
Each segment of a segmented virus has to be ACTIVELY transported from the nucleus to the plasma membrane through the membranes of vesicles (endosomes mostly) on the microtubules (not directly).
As they move close to the cytoplasm, they interact with each other, through FUSION EVENTS of the endosomes, until they make a stable structure. The most stable structure occurs when one copy of each segment is bound!
In many cases, the production of infectious particles requires essential viral enzymes.
1) What do (-)ssRNA and dsRNA need?
2) What do retroviruses need?
3) What does influenza need?
1) RdRp
2) RT, Integrase, protease, cellular tRNA primer
3) Because it is a (-) RNA segmented virus, it need RdRp.
Enveloped viruses can bud from the plasma membrane and release the viral particle from the host cell. However, they can also bud from the __________ membrane which requires _________ to release from the host cell.
Budding in general is ___________ and allows the infected cells to ____________ and continuously _________ viral particles.
Intracellular; exocytosis
Nondestructive; survive; release
*sometimes apoptosis can occur.
*nondestructive also means no pores being formed
Non-enveloped viruses undergo host ____ ____ that releases the viral particles from the host cell causing the cell to die.
cell lysis
(T/F) All non-enveloped viruses undergo host cell lysis.
False! A few non-enveloped viruses use other mechanisms.
(T/F) Large quantities of assembled viruses may accumulate within infected cells for hours and days before viral release through host cell lysis. It is timed!
True!
Lysis occurs at the peak of production to maximize the amount of viral particles released as after lysis the cell dies.
