Control Of Virus Replication - RNA Viruses

Question 1

What two strategies are used by RNA viruses that need to copy their genome in a host cell that only copies DNA molecules?

Answer 1

1. Conversion into DNA, followed by host RNA transcription
2. Specific viral replication machinery utilising a viral RNA-dependent RNA polymerase

Question 2

What must all RNA viruses have in their life cycle to enable protein synthesis?

Answer 2

An mRNA equivalent

Question 3

In the case of dsRNA, what has to happen for translation to occur?

Answer 3

Genome cannot function as mRNA so requires synthesis of (+)RNA before translation can occur

Question 4

What happens with translation in the case of (+)ssRNA?

Answer 4

Virus genome acts as mRNA directly
Translation can occur immediately

Question 5

What happens with transcription/translation in the case of (-)ssRNA?

Answer 5

Transcription required before translation
Transcription either in cytoplasm or nucleus

Question 6

What happens with ambisense ssRNA?

Answer 6

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

Question 7

How do retroviruses undergo transcription?

Answer 7

Use reverse transcriptase to make dsDNA then use cellular polymerase to make mRNA

Question 8

What do dsRNA viruses use for transcription?

Answer 8

Use a polymerase carried with the virus inside of the virion when it infects

Question 9

Do RNA or DNA viruses have a higher evolution and mutation rate?

Answer 9

RNA viruses have much higher rate

Question 10

What is quasi-species a fancy name for?

Answer 10

A population

Question 11

Why are proteins that RNA viruses make multifunctional?

Answer 11

Because they can’t encode multiple proteins, the genomes are too small

Question 12

Where do RNA viruses undergo translation and transcription?

Answer 12

In the cytoplasm unlike DNA viruses

Question 13

What RNA virus needs to go into the nucleus?

Answer 13

Influenza because it needs to initiate translation by snatching mRNAs being made in nucleus and transcribed

Question 14

What is the advantage of influenza being segmented?

Answer 14

Can make proteins in each areas

Question 15

What is the consequence of segmented genomes to the host?

Answer 15

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

Question 16

What type of genome do paramyxoviruses have?

Answer 16

Negative strand RNA virus

Question 17

What do + strand copies of a negative genome terminate in different places?

Answer 17

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

Question 18

Will there be more structural or non structural proteins in replication cycle?

Answer 18

More structural

Question 19

What type of genome does hepatitis C virus have?

Answer 19

Linear, ss, (+) RNA genome

Question 20

What are the 4 receptors used for hepC binding?

Answer 20

CD81, SR-B1, claudin1, occludin

Question 21

What happens when hepC goes into endosome?

Answer 21

There is a pH change, fuses membrane

Question 22

What happens when RNA then goes to ER?

Answer 22

Goes to ribosome, get translation and get polyprotein. This is manufactured as a single protein that passes through the ER membrane many times

Question 23

What are the two models for HCV?

Answer 23

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

Question 24

What is the HCV entry process?

Answer 24

1. HCV lipo-viral particles assocaited with glycoaminoglycans and LDL receptor
2. The E2 glycoprotein interacts with cell-surface receptors SR-B1 and CD81
3. Interaction with the tight junction proteins claudin 1 and occludin
4. Entry into the cytoplasm occurs by pH-dependent fusion of the viral envelope with the endosomal membrane, releasing the viral RNA

Question 25

What is HCV protein synthesis process?

Answer 25

Ribosome binds directly to IRES

Question 26

What is miR122 specific to?

Answer 26

Hepatocytes

Question 27

What does miR-122 do?

Answer 27

Binds to the end of the 2 seed sites
Stabilises the structure , this supports translation
Without it you will not get translation

Question 28

How does polyprotein processing in HCV work?

Answer 28

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.

Question 29

What is NS3 major role?

Answer 29

Cleave boundaries between NS3, 4A, 4B etc.

Question 30

Why are host cell proteases used initially in polyprotein processing then viral proteases?

Answer 30

NS3 is not active until it becomes the most N terminal part of the block

Question 31

How does NS3 become active?

Answer 31

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

Question 32

What are the bubbles of invagination of the membrane?

Answer 32

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

Question 33

What is the structure of HCV polymerases?

Answer 33

Right hand molecules

Question 34

How do polymerases of HCV work?

Answer 34

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

Question 35

What are the two conformations for HCV genome replication?

Answer 35

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