Synthesis of RNA from RNA templates

Question 1

RNA genomes share a common requirement:

1. they must be efficiently copied within the infected cell to provide both
   genomes for assembly into progeny virus particles
2. creation of messenger RNAs (mRNAs) for the synthesis of viral proteins

Why do RNA viruses have to provide their own viral enzymes?

Answer 1

The synthesis of these RNA molecules is a unique process that has no parallel in the cell. The genomes of all RNA viruses except retroviruses encode an RNA-dependent RNA polymerase to catalyze the synthesis of new genomes
and mRNAs.

Viruses that are (-) strand, or double-stranded RNA must use RNA polymerase, because incoming viral RNA can not be translated or copied by cellular machinery.

Question 2

HDV is a unique incomplete virus with RNA genome

What is special about how the RNA is copied?

Answer 2

The single-stranded RNA genome of hepatitis delta virus is copied by host cell DNA-dependent RNA polymerase.

synthesis of RNAs occurs in nucleus

Question 3

What is the benefit of RNA-dependent RNA polymerase having low fidelity?

Answer 3

It is error prone, so can lead to mutations

This in combination with reassortment and recombination yields diversity in viruses

RNA virus populations exist as quasispecies, as each virus has small differences in genomic sequences

Question 4

What does the term transcription mean?

Answer 4

Transcription - refers to copying information in DNA to RNA strictly

Synthesis of mRNA from RNA is termed mRNA synthesis

Question 5

(+)strand RNA viruses

What actions can happen to the nuclear material once enters cell?

Answer 5

mRNA synthesis
(+)strand used directly as mRNA

Replication
(+)strand used to make a complementary (-)strand, which is used as a template to create more (+)strands

Question 6

(-)strand RNA viruses

What actions can happen to the nuclear material once enters cell?

Answer 6

mRNA synthesis
(-)strand used as template to create (+)sense mRNA

Replication
(-) strand used to make complementary (+)strand, which is used as a template to create more (-)strands

Question 7

In what direction to polymerases synthesis nucleic acid?

Answer 7

5’ to 3’ direction

RNA polymerase synthesizes an RNA transcript complementary to the DNA template strand in the 5’ to 3’ direction. It moves forward along the template strand in the 3’ to 5’ direction, opening the DNA double helix as it goes.

The two ends of a strand of DNA or RNA strand are different from each other. That is, a DNA or RNA strand has directionality.

At the 5’ end of the chain, the phosphate group of the first nucleotide in the chain sticks out. The phosphate group is attached to the 5’ carbon of the sugar ring, which is why this is called the 5’ end.

At the other end, called the 3’ end, the hydroxyl of the last nucleotide added to the chain is exposed. The hydroxyl group is attached to the 3’ carbon of the sugar ring, which is why this is called the 3’ end.

Question 8

Do RNA or DNA polymerases require primers to initiate RNA synthesis?

Answer 8

DNA polymerases - primer dependent

DNA depdendent RNA polymerase - initiate RNA synthesis de novo starting at 3’ end

RNA depdendent RNA polymerase - initiate RNA synthesis de novo starting at 3’ end, or requires primer depending on virus

Question 9

Viral RNA-dependent RNA polymerases must select viral templates for replication, from a vast excess of cellular mRNAs

What are ways in which viral RNA-dependent RNA polymerases have specificity?

Answer 9

Initiation specificity - some viral polymerases have a high affinity for specific nucleotides in viral genome, rather than host genome

Concentration - as replication occurs, viral RNAs increase in infected cell, increasing chance of further binding between enzymes and nuclear material

Question 10

dsRNA viruses

What additional enzymes are required for replication, apart from RNA dependent RNA polymerase?

Answer 10

Helicase - unwind dsRNA, and prevent the separate RNA strands from re-binding

Question 11

What is unique about ambisense RNA virus?

Answer 11

Consists of both (+) and (-) strands - mRNA produced from both

Arenavirus have ambisense genomes. Synthesis of mRNA comes from both strands. After initial infection synthesis of mRNA is translated to produce nucelocapsid and RNA polymerase protein. Later in infection, the full length of both strands is used to make mRNA and replicate

Question 12

Why does DNA polymerase have high fidelity?

Answer 12

Has proofreading capabilities - exonucleases can correct mistakes

RNA could have 1 error per every 1,000,000 nucelotides polymerised, whereas DNA replication is about 10,000 lower

Question 13

What is the mechanism of action of ribavirin?

Answer 13

Mutagen as it can be substituted for any of the four nucleotides in newly synthesised RNA molecules