Richard Kingston Topic 3

Question 1

What are the general features of genome replication for positive sense single stranded RNA viruses?

Answer 1

These viruses have genomes that can act as mRNAs and be directly translated by host ribosomes
Genome alone is able to initiate infection as long as it is delivered into the cytoplasm
Genome replication requires the formation of a negative sense intermediate to act as a template strand

Question 2

What are the general features of genome replication for negative sense single stranded RNA viruses?

Answer 2

These genomes cannot be directly translated by the ribosome and therefore the virion must contain a RNA polymerase to make mRNA in order to be infectious
Genome replication involves a positive sense intermediate

Question 3

What are the general features of genome replication for double stranded RNA viruses?

Answer 3

Despite containing a positive sense RNA strand, the strands must be separated to be translated therefore the virion must package an RNA polymerase

Question 4

What are the general features of genome replication for single stranded DNA viruses?

Answer 4

Cells can only make mRNA from double stranded DNA therefore DNA synthesis precedes mRNA production however no enzymes need to be packaged in the virion

Question 5

What are the general features of genome replication for double stranded DNA viruses?

Answer 5

These follow the host cell mechanism of nucleic acid replication

Question 6

What are the general features of genome replication for retroviruses?

Answer 6

These contain a positive sense RNA single stranded genome and can be translated by the cell causing reverse transcriptase to be expressed resulting in a DNA intermediate in genome replication

Question 7

What is the difference in the structure of the nucleic acid genome in positive and negative sense RNA genomes?

Answer 7

Positive sense RNA viruses inject a naked RNA genome into the host while negative sense viruses inject a protein-nucleic acid complex allowing for protection and organization of the genome. The protein must be resent for the RNA to be replicated

Question 8

What are internal ribosome entry sites?

Answer 8

While host mRNA uses a 5’ cap to recruit the ribosome, many viruses use a cap independent mechanism and bind to the ribosome using a specific 3D structure, found in the internal ribosome entry sites

Question 9

How are DNA viruses generally transcribed?

Answer 9

mRNA synthesis occurs in the nucleus via RNA polymerase II, many viruses also encode transcriptional regulators for orderly and regulated gene expression

Question 10

How are the genomes of DNA viruses generally replicated?

Answer 10

The genomes of DNA viruses may be replicated by cellular machinery however larger DNA viruses encode DNA polymerases of their own to perform this function

Question 11

What are the differences between viral and cellular primers used for DNA replication?

Answer 11

In some cases viruses do use the cellular RNA primers, however they can also use things such as proteins and unique structures in the genome which allow self-priming

Question 12

How are viral genomes compressed?

Answer 12

Production of multiple transcripts through RNA editing
Leaky ribosomal scanning 
Ribosomal frame shifting
Ribosomal read through
Messenger RNA splicing

Question 13

How does leaky ribosomal scanning compact the viral genome?

Answer 13

The RNA sequence or structure surrounding the first AUG codon of the mRNA disturbs recognition by the ribosome allowing two overlapping open reading frames to be translated on the same mRNA

Question 14

How does ribosomal frameshifting compact the viral genome?

Answer 14

The secondary structure in the RNA impedes the ribosome causing slippage and changing the reading frame

Question 15

How does ribosomal read through compact the viral genome?

Answer 15

The ribosome fails to recognise stop codons causing the virus to express two types of a protein, one where it has terminated normally (major product) and one where it has not terminated

Question 16

What are the features of the paramyxoviridae virion?

Answer 16

It is enveloped, pleiomorphic (but basically spherical in shape), it has no fixed size and a helical nucleocapsid housing the viral genome in the interior

Question 17

What diseases are caused by paramyxoviruses?

Answer 17

The family has members responsible for measles, mumps as well as nipah and hendra which can cause potentially fatal encephalitis

Question 18

What are the features of the genome of paramyxoviruses?

Answer 18

Linear, negative sense single stranded RNA, it is non-segmented and 15-18 Kb in size and always encapsidated by its nucleocapsid

Question 19

What are the genes of paramyxoviridae and how are they expressed?

Answer 19

There is 5-9 genes transcribed in series from the 3’ end of the genome. There are conserved regulatory sequences between genes signalling for the end of transcription and initiation of the next transcript
Transcription results in monocistronic mRNA encoding a single protein
RNA editing, leaky scanning result in at least one gene encoding multiple proteins

Question 20

How does transcription of the paramyxoviridae genome occur?

Answer 20

It must precede replication and can only be initiated at the 3’ end of the genome via attachment to a leader sequence. This results in sequential synthesis of mRNAs, as the polymerase may dissociate at gene boundaries this produces a transcriptional gradient used by the virus to control gene expression with proteins needed in a large amount close the 3’ end and those less necessary closer to the 5’ end
The virus also puts on a conventional 5’ cap to its mRNA but uses a different mechanism to host cells to achieve this

Question 21

What are the features of genome replication of paramyxoviridae?

Answer 21

There is a switch in the virus from transcription mode to replication mode how this switch occurs is not well understood but it is believed to be a response to a buildup of viral proteins
In the replicative mode the polumerase can attach to the 3’ end of the genome or antigenome as the promoters are similar in sequence due to reverse complementarity
Intergenic termination sequences are ignored resulting a full length copy of the genome or antigenome being produced
The genome is packaged as it is synthesized

Question 22

What are the disease caused by parvoviridae?

Answer 22

Can be asymptomatic or cause rash and fever (typically mild) or serious disease in canines

Question 23

What are the general features of the parvoviridae genome?

Answer 23

Linear single stranded DNA which may be either sense, it is replicated in the nucleus by host mechanisms and can therefore only replicate in cells going through S phase
Makes use of self-complimentary hairpin structures for priming DNA synthesis during genome replication

Question 24

What are the genes on the parvoviridae genome?

Answer 24

There are 103 transcriptional promoters on the same DNA strand transcribed by cellular RNA polymerase II
Two open reading frames with multiple initiation codons and alternative splicing allowing up to 7 mRNAs to be generated
Left half of the genome contains the regulatory proteins while the right half contains the structural proteins

Question 25

How does parvoviral genome replication occur?

Answer 25

The ends of the viral genome both have inverted terminal repeats which form a T shape critical for replication as this shape froms a small section of ds DNA used to prime DNA synthesis by cellular proteins
In order to complete the viral the Rep 78/68 protein nicks and attaches to the genome becoming covalently attached to the 5’ end via a phosphor-tyrosine linkage and exposing the genome for replication

Question 26

What diseases are caused by picornaviridae?

Answer 26

Acute liver disease (Hepatitis A), Myocarditis (Coxsackie virus) the common cold (rhinovirus), poliomyelitis (poliovirus), foot and mouth disease of livestock (foot and mouth disease virus)

Question 27

How is the genome of picornaviridae organized?

Answer 27

Linear positive sense RNA genome with a viral VPg protein covalently bound to the 5’ end
A long 5’ non-coding region making up 10% of the genome containing the initiation of translation and additional RNA structures that are important for genome replication
One massive open reading frame coding for a polyprotein. Genome encoded polyA tail. 3’ NCR containing additional RNA structures important for genome replication

Question 28

How is the viral polyprotein of picornavirus processed?

Answer 28

Undergoes autoproteolysis during translation during translation due to several protease domains are embedded within the polyprotein yielding several non structural proteins which play a role in polyprotein processing, RNA replication, Host translation shutoff, cellular membrane remodelling as well as structural proteins which form the icosahedral capsule

Question 29

How do picornaviruses shut off host translation?

Answer 29

The viral proteins 2A and L proteases cleave a component of the EIF-4F initiation factor complex preventing host RNA from recruiting ribosomes as it no longer recognizes the 5’ cap on mRNAs. This leaves more ribosomes free to translate picornavirus RNA as they recruit ribosomes via a different mechanism

Question 30

How does picornavirus replicate its genome?

Answer 30

Process uses both host and viral proteins which are recruited by structures in the 5’ and 3’ non-coding regions. Synthesis is primed by viral Vpg protein which is covalently bound to two uridine residues. Replication requires a negative sense intermediate, synthesis of this initiates at the 3’ end of the genome