Chapter 3 -V Flashcards
key steps in replication cycle of viruses
The replication cycle of all viruses have 5 key steps
- adsorption and attachment o susceptible host cell - occurs by chance
- Genome enters the cell
- vaires:
- synthesis or mRNA, proteins or replication of viral genome - Assembly of virus particle from parts
- viral components have affinity for each other . Parts are assembled into pre-virion structures
- at some point, the virus genome must be inserted - Release from the host cell - egress
- Naked virus : cell lyses, dies , all progeny egress at once
Enveloped: virus buds out, continued virus production
Virus assembly
Capsid is made of many copies of identical subunits
The identical subunits can spontaneously assemble to form capsid structure
The protein molecules themselve are asymmetrical
Interactions between capsomeres (polypeptides:
- Folding, secondary and tertiary structures
- H bonding
- Proline residues
di -sulfide bonds
- Hydrophobic interactions etc
The association of capsids with genome structures is complex process
- They must be stable enough to persist outside of host cell
- But also unstable enough to release genome
Most common structure is helical or icosahedral symmetry
Why are capsids made using subunit construction?
- Genetic economy
- All viruses contain protein and nucleic acid, at least 50% -90% of mass of virus particle is protein
- A single copy of a large protein cannot cover the genome
- Less genetic material is required if the protein unit is used as a repeated unit
- Protein Economy
- Misfolding of protein molecules is quite common
- there is no repair mechanism for misfolded protein
- therefore if a protein subunit is folded, only a small part of the capsid is affected - Stability/instability
- the virus capsid must be irreversible in the cell where the virus particle is replicating, but reversible in the cell being infected with the virus particle
- must be a switch that can trigger to initiate change in stability of capsid structure
- trigger might be binding of receptor and change in pH
(hold itself but also allow the release of genome etc)
General Feature of Viral Replication cycle
All virus particles completes a common set of assembly
- formation of individual structural units of the protein shell from one or several viral proteins
- assembly of protein shell by appropriate and variable interactions among structural units
- selective packaging of nucleic acid genome and other essential virion components
- some get an envelope
- egress
- some maturation
Maturation involves change in viral protein
- cleavage pf polypeptide
- conformational change
- some changes to protein as it leaves host cell
Helical Capsid assembly:
The capsids of many ssRNA viruses have helical symmetry
For these viruses, assembly and packaging of the genome are linked
The RNA is coiled in the form of an alpha helix and many copies of the same proteins are arranged around the RNA forming the ribonucleocapsid
For many viruses, the RNA is within the coil, but for some it is outside the coil - but also usually has an envelope layer or additional protein layers
In a capsid with helical symmetry, proteins are aligned in a helix around the nucleic acid
These are elongated to have a rod like appearance
The capsid can be rigid or flexible depending on the properties of the capsid protein
The viruses uses as many proteins as needed to make capsid
Icosahedral Capsid Assembly
For virus particles with icosahedral symmetry, the process starts by the construction of a protein shell known as procapsid
The procapsid is filled with virus genome during or after construction
Some capsids are roughly icosahedral in shape
Icosahedron = 20 sides
WHY?:
Many virus takes this shape because having this shapes limit contact with the genome than a helical capsid
- Proteins forming icosahedral symmetry require less amount of energy compared to other structures
- The smallest of icosahedral capsids are built using 60 identical polypeptides
- 3 polypeptide in each triangle
- they are usually build in multiple of 60
Viral Genome packaging
How are virus genomes selected from all the nucleic acids that might be present in an infected cell? (eg only virus and not host cell nucleic acid)
- specific nucleic acid protein interation
- e: spliceosomes removing introns from RNA, sites where DNA pol bind to replicate chromosomes, RNA pol binding to promoters
Most don’t but some viruses do package cellular nucleic acid - these may play a role in initiation of genome replication when the next host cell is infected
(RDRP)
Specific packaging of virus genome is achieved through the recognition
- By virus protein of a specific nucleic acid sequence (ss or ds genome)or
- presence of secondary structures of the genome (ss genomes)
For viruses with ss genomes, the virus has to identify the correct strand to package
- either + or - sense
If an RNA was supposed to package + strand but packaged - strand
- It would not have RDPD packaged with it and not able to transcribe, thus translate then unable to replicate
It would not have RDPD packaged with it and not able to transcribe, thus translate then unable to replicate
Polyamines, cations with genome
- binds DNA/RNA
Small basic proteins encoded by virus
- basic proteins have positive charges at neutral pH
Use cell histones
Viral Assembly:
Many animal viruses have an external lipid bilayer = envelope that surrounds capsid
The viruses acquire their envelopes by budding through a cellular membrane
- Usually cell membrane but some use membrane of golgi or nuclear membrane
Associated with the envelope are integral proteins that were encoded by the virus’ genome but made by host cell
Viral Assembly:
Most of enveloped proteins have
- relatively large glycosylated external domain
- hydrophobic transmembrane domain anchor of abotu 20 aa
- short cytoplasmic tails
Glycosylation of external domain ensures that external surface of the virus particle is hydrated - can interact with the hydrophilic environment
Purpose of external domains
- involvement in attachment of virus to host cell or fusion of envelope and membrane
Purpose of short cytoplasmic tail
- Connects the envelope to the internal virus structures (matric protein or capsid)
- Attract virus parts to assemble so they can egress
Viral Envelope
Envelopes can adopt a variety of shapes as determined by the shape of capsid.nucleocapsid
Specific packaging signals direct the incorporation of viral genomes into virus particles
Formation of viral envelopes by budding is driven by interactions between viral proteins
Viral Matrix Proteins
Some enveloped viruses will have a protein layer between the envelope and the nucleocapsids
The matrix proteins are not usually glycosylated
Matrix proteins link the nucleocapsids to the envelope by transmembrane anchor domains
Can also be anchor point for stuff like spike proteins
Where are glycosylated and non glycosylated proteins synthesized?
- glycosylated: membrane bound proteins - ER associated ribosomes: has to pass through golgi before exit the cell
- Non glycosylated: non membrane bound protein - cytoplasmic ribosomes
Viral Genomes:
Many viruses encode within their genomes for non-structural proteins
these include:
- RDRP
- RT
- proteases
- ion channel proteins
- proteins that interfere with host immune response
Some viruses will package these proteins with the genomes in the capsid structure
- This depends on the virus’ genomes
- And when the proteins are needed during replication
Viral release:
Cell lysis is a common outcome of viral replication
It consists of a distribution of cellular membranes leading to cell death and release of cytoplasmic compounds into the extracellular space
Some viruses income viroporins in their genomes to actively induce lysis by disturbing the cell membrane
- viruses do this because cells rarely trigger lysis on its own
Most non-enveloped and a few enveloped virus require cell lysis in order to release new virus particle from infected cell
Cell lysis is associated with neurosis
- Triggers inflammatory response (released of cell contents called DAMPs - recognized by TLRs)
- Some virus infections result in inflammation which causes a lot of pathogenesis
Virus Budding
Some virus egress by budding from the plasma membrane
Enveloped icosahedral virus that assemble in the cytoplasm approach the plasma membrane and in to the cytoplasmic tails of the viral envelope protein
Progressive formation of contacts between the surface of capsid and cytoplasmic tails of the viral glycoproteins drives pinching off of the bilayer by fusion (in way in, virus “budded in “ so has its spike proteins on the host surface)
Many enveloped viruses with helical nucleocapsids have an internal matrix protein that mediates the association between viral glycoproteins inserted into plasma membrane and nucleocapsids in the cytoplasm
-Helps drive budding process
