*** Virology Chapter 2-3: General Features of Virus Replication Cycle Flashcards
What are the 5 key steps of the replication cycles of ALL viruses?
- virus adsorption and attachment to susceptible host cell - chance
- genome (and any needed proteins) enters the cell
- one of the following:
- synthesis of viral mRNA
- synthesis of viral proteins
- replication of viral genome - assembly of virus from parts
- release from host cell
What are all virus genomes surrounded by?
proteins
Why is the virus particle a gene delivery system?
moves the virus’ genome from one host cell to another host cell (within or to different organisms)
How is the virus genome packaged?
in a protein structure known as a capsid
For some viruses, what does the virion consist of?
only the genome and the capsid (nucleocapsid = capsid with enclosed genome)
For some viruses, the virion consists of only the genome and the capsid. What additional layers may other viruses have?
- lipid bilayer envelope at the surface.
- layer of protein between the capsid and the envelope,
- internal lipid layers,
- protein occlusion bodies
What are capsid proteins?
structural proteins
What are the 2 functions of the proteins that make up the capsid?
- protection of the chemically labile virus genome:
- from nucleases in the environment
- from agents that might damage the base of a nucleotide
- shearing of the viral genome from mechanical forces - delivery of the virus’ genome to the location within cell where genome can be replicated
If the virus is a naked particle, what binds to the host cell?
capsid has the structure to bind
If the virus is an enveloped particle, what binds to the host cell?
envelope has the structure to bind
capsid does NOT have the appropriate structure
Virus Replication Step 1: virus-host cell interaction
adsorption and attachment to a susceptible host:
- virus and host cell must have complementary structures to be able to interact – chance event (recognition, specificity)
Virus Replication Step 1: virus-host cell interaction
What structure does the host cell have?
virus receptor – normal cell structure that the virus exploits as a binding site
cell structure can be: protein, carbohydrate attached to protein
Virus Replication Step 1: virus-host cell interaction
What structure does the virus have?
anti-receptor – virus structure that binds to host cell
Virus Replication Step 1: virus-host cell interaction
When is a host cell susceptible?
if it has the proper virus receptor
Why might a cell have a structure that is not complementary to the virus’ anti-receptor?
could be the wrong shape or the chemistry of the side groups of the amino acids
Virus Replication Step 2: entry
virus’ genome (and replicative enzymes) needs to enter the cell
Virus Replication Step 2: entry
Do all viruses use the same strategy for entry?
different strategies for different viruses, but a given species of virus always uses same method
Virus Replication Step 2: entry
How does a virus enter the cell after binding to the cell’s virus receptor?
for some viruses:
- only the genome enters the cell
- virus enters the cell in an endosome, genome is released to cytoplasm/nucleus
- virus envelope fuses to cell membrane, releasing genome into the cytoplasm/nucleus
What is the virus particle designed to do?
interact with host cell receptors to initiate the process of infection
For virus particles, what is the capsid stable enough to do? Unstable enough to do?
stable enough to: persist in the environment
unstable enough to: allow for the release of the genome into the cell’s cytoplasm
What types of interactions exists between the protein subunits in the capsid?
-
What might cause the capsid to change from a stable structure to an unstable structure?
- interactions with other proteins
- changes in pH
- cleavage of proteins
- unfolding of proteins
What does the release of the genome require?
some triggering event and a succession of interactions
ie. reversible adsorption, strong irreversible attachment, conformational change in virus’ anti-receptor, internalization, change in pH, unfolding of virus proteins, dissociation of capsid proteins
What is adsorption?
random weak collisions that lead to the attachment of the virus particle to the virus receptor
What is attachment?
multiple molecular interactions that lead to a firm binding so that the virus’ genome can enter the cell
What must happen for a virus to be successful in nature?
virus must encounter a host cell that is both susceptible to viral infection, and permissive to viral replication
Is a host cell susceptible to viral infection?
-
Does the host cell have a structure, the “virus receptor”, that the specific virus
can attach to for delivering the virus and/or its genome into the host cell?
-
Does the virus have an “anti-receptor” structure that recognizes the virus receptor on the cell?
-
For viruses to be successful in nature, they need to infect susceptible and
permissive host cells.
What must viruses do?
- reproduce and package entire viral genome
- package functional enzymes involved in the replication of its genome (if necessary)
- be able to remain intact and capable of infecting a new host cell when it is in the environment (ie. exposure to the environment must not damage the virus in such a way that it can no longer infect a host cell)
- virus must have multiple structures to interact with the surface of the host cell – this ensures that in the event that some are damaged (by enzymes, oxidation), the virus can still infect a new cell
Why must a virus have multiple structures to interact with the surface of the host?
ensures that in the event that some are damaged (by enzymes, oxidation), the virus can still infect a new cell
What do susceptibility and permissiveness describe?
describe different attributes of a host cell relative to virus infection and replication
- attributes can be demonstrated experimentally
- viruses that persist in nature have been successful at encountering host cells that are both susceptible and permissive
What is susceptibility?
ability of virus to get its genome into the host cell (cell surface structure)
What is permissiveness?
ability of the virus to replicate its genome in the host cell (presence of enzyme, expression is linked to the cell cycle)
Virus Replication Step 3: gene expression
a lot of variation – sometimes virus must express its genes to make the enzymes necessary for its replication
can be any combination of the following:
- synthesis of viral mRNA
- synthesis of viral proteins
- replication of viral genome
How do polymerases work?
they work the same way – applies to both DNA and RNA polymerases
- read template in 3’ to 5’ direction
- synthesize complementary (and anti-parallel) strand in 5’ to 3’ direction
For viruses, how can the process that polymerase does be different?
- template (DNA or RNA)
- how it starts the process
- how it finishes the process
- where in the cell it does the process
For cells, what is the template that polymerases work on?
always DNA
For cells, where in the cell does the polymerase work?
always in the nucleus
How do ribosomes work?
all ribosomes work the same way
- read mRNA template in 5’ to 3’ direction
- synthesize polypeptide in N to C direction
With viruses, what be different with the process that ribosomes do?
how it starts the process
- cap-dependent
- cap-independent
Why do some viruses package their own replicative enzymes in their capsids?
- some species of viruses replicate their genomes in the cytoplasm of the cell – can’t use the cellular DNA or RNA polymerases that are in the nucleus (these viruses also have to encode the genes for their polymerases)
- for RNA viruses, the cell’s RNA polymerase does not read an RNA template
(it reads a DNA template)
What do all RNA viruses must have in their genome?
gene that encodes a polymerase that can read RNA as a template and synthesize RNA or DNA, and some even have a functional copy of the enzyme inside the particle
For DNA viruses, where does polymerase for replicating/expressing genome in the nucleus come from?
- use cell’s DNA polymerase
- use cell’s RNA polymerase
For DNA viruses, where does polymerase for replicating/expressing genome in the cytoplasm come from?
- genome encodes a DNA polymerase
- genome encodes an RNA polymerase
- capsid contains pre-made RNA polymerase
- capsid might contain pre-made DNA polymerase
For RNA viruses (excluding retroviruses), where does polymerase for replicating/expressing genome in the nucleus come from?
- genome encodes an RNA polymerase
- capsid may contain pre-made RNA polymerase
For RNA viruses (excluding retroviruses), where does polymerase for replicating/expressing genome in the cytoplasm come from?
- genome encodes an RNA polymerase (RNA-dependent RNA polymerase = viral RDRP)
- capsid may contain pre-made RNA polymerase depending on whether the RNA is (+) or (–) sense
What is the difference between (+) sense and (-) sense RNA viruses?
(+) sense: can synthesize pre-made RNA polymerase
(-) sense: must have some packaged within their capsid
What does (+) or (-) sense mean?
molecular biologists have developed a convention for discussing nucleic acids
- basis of this is that mRNA is defined as being positive sense [(+) sense], therefore, everything is discussed relative to this
What are retroviruses?
RNA → ssDNA → dsDNA → integrate into host cell DNA → RNA
- viruses that use an alternative approach in which they transcribe ssRNA to dsDNA first
- dsDNA is transcribed to make more of the ssRNA viral genome
What enzyme do retroviruses need?
reverse transcriptase (RT): reads RNA and synthesizes DNA
In retroviruses, what virus enzymes are needed to go from dsDNA to integrating into host cell DNA?
reverse transcriptase (RT) and integrase
What are the 3 distinct enzyme activities of reverse transcriptase (RT)?
- RNA-dependent DNA polymerase – results in DNA-RNA hybrid molecule
- Rnase H – enzyme that removes RNA in DNA-RNA hybrids
- DNA-dependent DNA polymerase to make the complementary DNA strand so that the ssDNA becomes a dsDNA molecule
Where do all viruses translate their mRNAs (or (+) sense)?
on cell’s ribosomes
What do eukaryotic ribosomes like?
mRNA with 5’ cap start codon single ORF stop codon polyA tail at 3’ end
For some viruses, why is translation of mRNAs a challenge?
- sometimes assembly of the mRNA on the ribosome is a big challenge
- eukaryotic ribosomes are designed to translate eukaryotic mRNA
- some types of viruses have mRNA have mRNA with a 5’ cap and polyA tail
- some types of viruses have mRNA that does not have a 5’ cap, and instead they use a secondary structure – not as efficient as a 5’ cap, but is adequate
What does monocistronic mean?
one gene
+/- cap may or may not be present
What does polycistronic mean
more than one gene
+/- cap may or may not be present
Viral mRNAs can be…
monocistronic or polycistronic
For polycistronic mRNA, eukaryotic ribosomes are not good at translating mRNAs like what?
start codon ORF stop codon start codon ORF stop codon start codon ORF stop codon polyA tail at 3’ end
- only gene 1 (between first start and stop codons) would be translated
- ribosome would dissociate at first stop and not reassemble on downstream start codons (AUGs)
- not a good strategy for a virus that needs to make several proteins
- prokaryotic ribosomes might be able to reassemble on a mRNA, but eukaryotic ribosomes cannot – the cap is essential in ribosome assembly on the mRNA
- in cap independent translation, a secondary RNA structure takes the place of the
cap
What is the simple strategy that viruses have evolved for translation?
translating the entire mRNA into a polyprotein, then cutting up the polyprotein into the individual proteins (ie. capsid, RDRP and protease)
- fold (2o or 3o structure)
- one of the genes encodes a protease that becomes active when the protein folds
- self-proteolytic cleavage into separate proteins
What do coronaviruses have as their genome?
one piece of single stranded (+) sense RNA
Where do coronaviruses replicate and express their genome?
in the cytoplasm of the infected cell
Can the coronavirus use the host cell’s RNA polymerase to replicate/transcribe their genome?
-
Would you expect to find some RNA-dependent RNA polymerase packaged with the genome of a coronavirus?
no
Can a coronavirus synthesize its own RNA polymerase after it has infected a cell?
yes
At least how many genes must be present in the genome of a coronavirus?
4 (there are quite a few more)
Virus Replication Step 4: virus assembly
- viral components have ‘affinity’ for each other
- parts are assembled into pre-virion structures
- at some point, viral genome must be inserted
Virus Replication Step 4: virus assembly
What is the capsid made of?
many copies of identical, asymmetric subunits – they can spontaneously assemble to form the capsid structure
Virus Replication Step 4: virus assembly
What type of interactions do you expect to see in the polypeptide?
- folding
- secondary and tertiary structures
- H-bonding
- proline residues
- disulfide bonds
- hydrophobic interactions
Virus Replication Step 4: virus assembly
Describe the association of capsids with genomes.
complex process, but must result in a structure that is stable enough to persist outside of a host cell
most common structures have helical or icosahedral symmetry
Why are capsids made using subunit construction?
genetic economy
economy
stability/instability of structure
Why are capsids made using subunit construction?
economy
misfolding of a protein molecule is quite common, and there is no repair mechanism
Why are capsids made using subunit construction?
genetic economy
single copy large protein (presumably encoded by virus) cannot cover the genome – less genetic material is required if protein unit is used as a repeated unit
Why are capsids made using subunit construction?
stability/instability of structure
- virus capsid has to be constructed in way that is stable to survive in the environment (when it is “between host cells”), but unstable to release the
genome into the host cell so that it can be expressed/replicated - must be a “built-in switch” that can be triggered to initiate the change in the stability of the capsid’s structure
- trigger that activates the switch might be: binding to a receptor, change in [H+]*, or a combination of both
- for the change in pH, the virus exploits the cell’s normal response to an endocytotic event
What is the common set of assembly reactions that all virus particles complete?
- formation of individual structural units of the protein shell from one or several viral proteins
- assembly of the protein shell by appropriate, and sometimes variable, interactions among structural units
- selective packaging of the nucleic acid genome and other essential virion components
- (some viruses only): acquisition of an envelope
4. release from host cell - (some viruses only): virion maturation
What does virus maturation involve?
changes in proteins
- cleavage of polypeptide
- conformational changes
When does virus maturation occur?
- for some virus species, this happens while virus is still inside
- for others, this happens while virus is leaving the cell or after it has left the cell
Capsids of what viruses have helical symmetry
ssRNA viruses
Describe helical capsid assembly in ssRNA viruses.
- assembly and packaging of the genome are linked
- RNA is coiled in the form of a helix, and many copies of the same protein are arranged around the RNA forming the ribonucleocapsid
- process of the assembly of a helical capsid appears to be similar for all helical capsids
Describe the appearance/structure of helical capsids.
- elongated, rod-like appearance
- can be rigid or flexible depending on properties of capsid proteins
- viruses use as many proteins as needed to make the capsid
Describe the process of capsid assembly.
