Control Of Virus Replication - RNA Viruses Flashcards
What two strategies are used by RNA viruses that need to copy their genome in a host cell that only copies DNA molecules?
- Conversion into DNA, followed by host RNA transcription
- Specific viral replication machinery utilising a viral RNA-dependent RNA polymerase
What must all RNA viruses have in their life cycle to enable protein synthesis?
An mRNA equivalent
In the case of dsRNA, what has to happen for translation to occur?
Genome cannot function as mRNA so requires synthesis of (+)RNA before translation can occur
What happens with translation in the case of (+)ssRNA?
Virus genome acts as mRNA directly
Translation can occur immediately
What happens with transcription/translation in the case of (-)ssRNA?
Transcription required before translation
Transcription either in cytoplasm or nucleus
What happens with ambisense ssRNA?
Z mRNAs produce backwards 5’ to 3’
L ORF is produced in opposite direction
Common hair pin structure in middle of RNA molecule
This acts as a break
Can have genes made in two directions, so one piece of RNA is encoding two proteins in different directions
How do retroviruses undergo transcription?
Use reverse transcriptase to make dsDNA then use cellular polymerase to make mRNA
What do dsRNA viruses use for transcription?
Use a polymerase carried with the virus inside of the virion when it infects
Do RNA or DNA viruses have a higher evolution and mutation rate?
RNA viruses have much higher rate
What is quasi-species a fancy name for?
A population
Why are proteins that RNA viruses make multifunctional?
Because they can’t encode multiple proteins, the genomes are too small
Where do RNA viruses undergo translation and transcription?
In the cytoplasm unlike DNA viruses
What RNA virus needs to go into the nucleus?
Influenza because it needs to initiate translation by snatching mRNAs being made in nucleus and transcribed
What is the advantage of influenza being segmented?
Can make proteins in each areas
What is the consequence of segmented genomes to the host?
If you get infected with two viruses, they can be very different and may pick up one segment from each parent resulting in antigenic shift
What type of genome do paramyxoviruses have?
Negative strand RNA virus
What do + strand copies of a negative genome terminate in different places?
Capsid proteins and viral glycoproteins encoded by genes at one end
Polymerase and helicases encoded by genes at other end
Need less coding potential to make enzymes, whereas to make virus particle, need tens of thousands of capsid proteins
Will there be more structural or non structural proteins in replication cycle?
More structural
What type of genome does hepatitis C virus have?
Linear, ss, (+) RNA genome
What are the 4 receptors used for hepC binding?
CD81, SR-B1, claudin1, occludin
What happens when hepC goes into endosome?
There is a pH change, fuses membrane
What happens when RNA then goes to ER?
Goes to ribosome, get translation and get polyprotein. This is manufactured as a single protein that passes through the ER membrane many times
What are the two models for HCV?
First is virus particle with glycoproteins on the outside, viral RNA in the middle. Attached to LDL and HDL (2 particle model)
Second is hybrid-particle model. Blob of fats with some apo lipo proteins on the outside, then a few copies of glycoproteins sticking out to allow it to dock
What is the HCV entry process?
- HCV lipo-viral particles assocaited with glycoaminoglycans and LDL receptor
- The E2 glycoprotein interacts with cell-surface receptors SR-B1 and CD81
- Interaction with the tight junction proteins claudin 1 and occludin
- Entry into the cytoplasm occurs by pH-dependent fusion of the viral envelope with the endosomal membrane, releasing the viral RNA
What is HCV protein synthesis process?
Ribosome binds directly to IRES
What is miR122 specific to?
Hepatocytes
What does miR-122 do?
Binds to the end of the 2 seed sites
Stabilises the structure , this supports translation
Without it you will not get translation
How does polyprotein processing in HCV work?
Starts at one end and each boundary is cleaved e.g. core then E1, E2 etc.
Later on NS2 protein cleaves NS2 and 3 junction
Then NS3 major role is to cleave boundaries between NS3, 4A then 4B etc.
What is NS3 major role?
Cleave boundaries between NS3, 4A, 4B etc.
Why are host cell proteases used initially in polyprotein processing then viral proteases?
NS3 is not active until it becomes the most N terminal part of the block
How does NS3 become active?
When NS2 is removed by auto catalytic cleavage and NS2 then floats off, NS3 then folds up and it is tagged by C terminal tale that connects it to NS4A
What are the bubbles of invagination of the membrane?
Stops inflammation and interferon response as RIGI recognises dsRNA
But the pore is only big enough for nucleotide to get in not RIGI so have lots of dsRNA being made inside the bubble
What is the structure of HCV polymerases?
Right hand molecules
How do polymerases of HCV work?
RNA flies through and allows synthesis of dsRNA
Polymerase in this state can’t make RNA because it is too close to membrane
Has a flexible linker that stretches away from membrane away from ER membrane in the VMV and allows access for a new piece of template, then starts incorporating nucleotides into this newly made dsRNA molecules
What are the two conformations for HCV genome replication?
Replication conformation and translation conformation
When they are coming together and interacting, you get the polymerase go round and round
As dynamics change and it stretches out, the IRES becomes available and now you get translation
