15. Viral structure( genome, envelope, enzymes) and viral life cycle Flashcards
Where do animal cell envelopes usually arise from
From the plasma or organelle membranes of the host cell
Where are envelope lipids and carbohydrates acquired from
The host cell
Who codes viral proteins
Viral genes and often project from the envelope surface as spikes also called peplomers
Where are spikes involved in
Virion attachment to the host cell surface and sometimes viral proteins have enough enzymatic activity for entry into or exit from the host cell
Can spikes be used for identification of viruses
Yes because they differ among viruses
Where can virion enzymes be located
They can be associated with envelope or capsid but they can also be inside a capsid
What do enzymes inside a capsid do
They are usually involved in nucleic acid replication
What do enzymes with RNA genome carry
Enzyme that synthesizes RNA using an RNA template
Can virion enzymes be essential for something
Yes, for completion of their life cycle
What king of nucleic acid do cellular genomes have
Always double-stranded( ds) DNA
What kind of nucleic acids can virions have
dsDNA, single-stranded( ss)DNA, ssRNA, dsRNA
What kind of nucleic acid do animal, plant, bacterial and archaeal viruses have
All 4 types are in animal viruses. Plant viruses have ssRNA genome and most microbial and archaeal viruses have dsDNA
How ca viruses change their genome size
They can save space by overlapping genes or have really big genomes(ex: pandoraviruses, which infect protists) that can exceed some bacteria and archaea in coding capacity
What do most DNA viruses have
dsDNA
If DNA virus has ssDNA, which kind can it be
The genomes may be either linear or circular
What is some ssDNA virus
Parvovirus
What are characteristic of linear ssDNA genome
It can be covalently closed, attached to a protein or otherwise masked
What is more rare in RNA viruses, ss or ds
dsRNA genomes
What are some examples of ssRNA virus
Coronavirus, tobacco mosaic, rabies and human immunodeficiency virus(HIV)
What is characteristic structure of RNA genome
It can be segmented where each segment codes for one protein and there may be 10-12 segments. Usually all segments are enclosed in the same capsid
What is example of segmented viruses
Influenza
What is a general scheme of main phases of virus life( replication) cycle
- Attachment( receptor-antireceptor)
2.Penetration( entrance)
3.Uncoating
4.Macromolecular synthesis( viral genome replication, viral gene expression)
5.Assembly - Release of virions ( mature and infectious viruses)
Do viruses have different replication strategies or the same one
Different
What is viral attachment protein
Viral attachment protein(VAP) is ‘‘key’’ that unlocks the cell by interacting with the ‘‘lock’‘(cell receptor) on the host cell surface
Where can viral proteins bind to
These are some different partners: host glycans, receptor proteins, adhesion proteins or peptidases.
What are common cell receptors
-Sialylated glycans such as sialic acid
-CAM(cell adhesion molecules)s
-Phosphatidylserine receptors
What are differences in penetration of enveloped and non enveloped viruses
Enveloped viruses:
-Fusion between virus membrane and host membrane
-Cell-to-cell transmission(ex: syncytia)
-Endocytosis ( and subsequent pH-dependent membrane fusion)
Viruses without envelopes
-Endocytosis( and subsequent membrane crossing or destruction of the endosome)
-Direct penetration( viropexy or translocation, many phages, papillomaviruses…)
What enveloped virus goes through fusion between virus membrane and host cell membrane
HIV-1
What are some examples of enveloped viruses going through cell-to-cell transmission
Vaccinia virus, HIV
What are some enveloped viruses going through endocytosis
Rabies and Influenza
What is some example of a virus without an envelope going through endocytosis
Poliovirus capsid undergoes pH-dependent conformational changes resulting in the release of the genome into the cytoplasm
How does direct penetration of viruses without envelope go in poliovirus
Translocation of poliovirus RNA across the cell membrane: after receptor binding there is a release of a pocket factor( lipid that stabilizes the virus particle). VP1 N-terminus anchors the virion to the endosomal membrane and myristoyl-VP4 forms hexameric membrane pores, Viral RNA is transported through these pores into the cytoplasm, aided by the host protein PLA2G16 via an unknown mechanism
What is uncoating
Uncoating is defined as the process by which the viral nucleic acid is( partially in some cases) freed from the protein component that surrounds it and transported to the appropriate location so that it is accessible to the cellular biosynthesis apparatus which can mediate its expression and replicatiom
Can uncoating occur with penetration
It can on not; uncoating can also be complete or now
Why can uncoating be complete or not
Because the transcription can start inside a capsid
What’s step by step process of ejection in phages to Gram - bacteria
1.Attachment to the host cell outer membrane(OM) receptor
2.Tail sheath contraction. Ejection of the internal rigid tube through the OM using the puncturing device
3. Virion associated exolysin(if present) hydrolyzes the peptidoglycan layer
4. Complete interaction and ejection of the internal rigid tube. Fusion with the inner membrane
5. Viral DNA translocation
What’s step by step process of ejection in phages to Gram + bacteria
1.Attachment to a host wall cell wall receptor
2.Tail sheath contraction. Virion-associated exolysin(if present) hydrolyzes the peptidoglycan layer. Ejection of the internal rigid tube through the cell wall
3. Complete contraction and ejection of the internal rigid tube. Possible ejection of the tape-measure protein and opening of the proximal plug. Fusion with the plasma membrane
4. Viral DNA translocation into host cytoplasm
What is specific about interaction between pili and viruses
Each bacterial virus binds specifically to a precise type of pili. Some absorb the tip of F-pili and enter the cell at the pili basal pore. Other target different kinds of pili and some may be absorbed onto the sides of a pili (icosahedral viruses)
What are some core differences between DNA and RNA viruses when it comes to replication
DNA viruses
nuclear replication
RNA viruses
cytoplasmic replication
What happens when mRNA synthesis happens in nucleus and in cytoplasm
In the nucleus:
-Viruses exploit cellular enzymes(RNA polymerase); mRNAs have CAP and poly-A. There is possible removal of introns
In the cytoplasm:
Viruses provide necessary enzymes(RNA polymerase); CAP and poly-A depend on the virus
How can we divide into categories viral proteins
-Structural- part of the virions
-Non structural- not part of the virions
Who mediates duplication of viral genome in numerous copies
Some viral proteins( virus-specific DNA polymerase), together with certain number of cellular proteins( host factors) regulate it. This process is heterogeneous and can occur either in the nucleus or cytoplasm
What are the exception of the location of mRNA synthesis with viruses
-DNA: Poxviridae->cytoplasm
-RNA: Orthomyxoviridae-> nucleus
What is the final stage of maturation in viruses before release
Assembling
Is assembling an error-prone process
Yes, because many defective capsids are formed
What happens to some viral proteins when they are assembled
They must undergo proteolytic cleavage mediated by viral enzymes
What do enveloped viruses require during assembly before release
Envelope
Are components of the viruses self-assembled
Yes, it’s process that happens in stages and in orderly manner.
What is done as a preparation of the final process
Protomers are pre-formed
Where does genome assembly start
It begins at a particular genomic locus called packing site(psi)
How does assembly of segmented genome go
One copy of each segment must be packed. And in this case, errors(defective viruses) can occur
How are viruses released based on if they have envelope or not
Enveloped viruses:
-plasma membrane budding(HIV)
-Release via endocytic vesicles(Herpesviruses)
Viruses without envelopes
-Cell death(lysis)
How are archaeal viruses assembled and released
The virions are assembled in the cytoplasm, and seven-sided pyramid structure forms near the cell envelope- Virus-associated pyramids puncture the envelope and open up the cell. They get out and leave empty cell behind
What is cell-to-cell spread and what kinds do we have
When virion isn’t released in the environment but from one host cell to the other
We have:
1. Formation of actin tails
2.Syncytia formation
3.By filopodia
4.Formation of intercellular membrane pored
Explain the process of cell-to-cell transfer with formation of acting tails
Example of a virus: VACV-vaccina virus
1. Enveloped particles are transported to budding site where outer membrane fuses with a plasma membrane. Many cellular factors are recruited to the site through cascade pf events initiated by phosphorylation of the A36R protein cytosolic tail
2. Polymerization of F-actin occurs through activation of pathways N-WASP/Arp2/3 and FHOD1/Rac1, leading to elongation of acting tails
3. Viral particles can then reach adjacent cells for rapid cell-to-cell spread
Explain the process of syncytia formation in cell-to-cell spread
Infected cells show a lot of viral proteins on their cell surfaces. When uninfected cell comes to the proximity of infected one, following things happen:
1.Fusion proteins are first in an inactive fusion state
2.When binding to the receptor of the other cell, fusion protein experiences conformational changes that bring 2 membranes of 2 cell in close proximity, followed by partial fusion(hemifusion)
3. Full merge results in opening of a fusion pore
4. That pore becomes bigger, allowing mixing of cytoplasmic material and spreading of viral components between the cells
5.Repetition of the fusion results in formation of large multinucleated syncytia
Explain the process of cell-to-cell spreading by filopodia
Filopodial bridges-mechanism for direct cell-to-cell transmission by different viruses.
ACell infected by retroviruses can establish filopodial bridges with viral particles surfing along the surface of filopodia towards the cell body to initiate infection
BSingle particles budding from filopodial extension (on the end) facilitate cell-to cell spread
CSame as B but multiple particles
DFilamentous pneumovirus, including human metapneumovirus(HMPV), bud from filopodia reaching surface of adjacent cell for direct cell-to-cell spread. Viral proteins and genome have been detected in filopodia induced by pneumoviruses
Explain the process of formation of intercellular membrane in cell-to-cell spread
Infection of epithelial cells by measles virus results in the opening of the membrane pores between adjacent cells. Those pores are stabilized by the interaction of the viral glycoprotein H and cellular receptor Nectin 4 which is anchored to the cell cytoskeleton through Afadin protein. There are physical constrains because of the presence of F-acting which prevents those pores to become bigger but they are still big enough for spreading ribonucleoprotein complexes that can initiate infection
What are advantages of cell-to-cell spread
AViral particles aren’t accessible to the neutralizing bodies( at cell-junction specialized membrane contacts)
BMultiple viral particles can saturate restriction factors and proceed with an infection
CViral genomes can be transmitted through intercellular pores which bypasses the uncoating step and inhibition by restriction factors, proceeding more efficiently with replication
D Several viral genomes will be more efficient in replication leading to rapid infection
What are characteristic of fungal viruses
Fungal viruses lack an extracellular phase in their replicative cycles. They are transmitted by cell division, spore formation or during mating
What are characteristics of plant viruses
Genomes or nucleocapsids move directly from cell to cell through small connections called plasmodesmata that link the cells together. This spread typically involves virus-encoded movement proteins
What is susceptibility and what does it depend on
Susceptibility is a state of being influenced or harmed by particular thing. It indicates the susceptibility of the cell to allow the virus to enter. Susceptibility of viruses depends on adsorption, entrance and uncoating
What is permissivity and what does it depend on
Permissivity indicates the ability of the virus to replicate within the cell. Cell must allow expression of all the viral genes for the completion of replication cycle with the production of viral progeny. It depends on: genome replication expression, viral particle assembly, virion release
What are possible outcomes of viral infection
-
Productive infection- susceptible and permissive cells
2.Abortive or latent infection-susceptible but non-permissive cell
3.Restrictive infection-susceptible and permissive cells only in certain physiological conditions(ex:phase S)
4.Result is cellular transformation- abortive or restrictive infection that results in virus shedding or persists within the cell
What happens when cell isn’t susceptible
There is no infection
What is productive infection
When cell is both susceptible and permissive, it involves the production and release of virions outside the infected cell
What is abortive infection
Abortive infection- virus doesn’t replicate but only expresses proteins without being able to give rise to the new virions, and after a certain period it’s eliminated. In some cases it persist and can cause cellular transformation
What’s latent infection
Latent infection-virus doesn’t replicate at high levels, but it’s not removed in the cell. Viral genome is kept in the cell for a long time, and following various stimuli it can be capable of initiating a productive infection
