ICL 1.2: DNA Viruses

Question 1

what’s the difference between how a virus with a small genome vs. large genome replicates?

Answer 1

small genomes usually use host machinery

viruses with larger genomes usually just make their own machinery

Question 2

which families of DNA viruses are naked?

Answer 2

1. parvoviridae
2. polyomaviridae
3. papillomaviridae
4. adenoviridae

Question 3

which families of DNA viruses are enveloped?

Answer 3

1. herpesviridae
2. poxviridae
3. hepadnaviridae

Question 4

how long do DNA viruses last?

Answer 4

DNA viruses often result in life-long persistent infections

they’re really good at sticking around by becoming latent or replicating in hidden areas

they manipulate the host cell so that is keeps replicating which could lead to tumor production…

Question 5

are DNA or RNA virus genomes larger?

Answer 5

most DNA viruses have more genes than RNA viruses and allow DNA viruses to have more complicated life styles

DNA viruses appear better suited than RNA viruses to regulate and modulate expression of their and the host’s genes

Question 6

what are non-essential genes?

Answer 6

genes for host immune response interaction

these are the ones we can mutate with drugs and it won’t effect the virus at all!

all these genes do is make it easier for the virus to replicate or stick around longer in the cell but they aren’t involved at all in the replication or structure of the virion

we can use this though to engineer viruses by deleting the non-essential proteins and putting in other struff – this is hard to do in viruses that have a small genome though

Question 7

how does RNA synthesis work?

Answer 7

RNA synthesis aka transcription!!

it is primer independent and requires RNA polymerase and ribonucleotide triphosphates (rATP, UTP, etc)

Question 8

what are the 3 RNA polymerases?

Answer 8

polymerase I: rRNA - Class I genes are transcribed by RNA polymerase I

polymerase II: mRNA - Class II genes are transcribed by RNA polymerase II that is inhibited by low doses of alpha-amanitin

polymerase II: tRNA - Class III genes are transcribed by RNA polymerase III

Question 9

which cells have transcriptional machinery?

Answer 9

all cells except RBCs have nuclear transcriptional machinery

Question 10

which viruses use host polymerase II to synthesize mRNA?

Answer 10

all DNA viruses (except poxviruses) use the host polymerase II to synthesize mRNA in the nucleus of infected cells

viral DNA goes to the nucleus after uncoating

the viral DNA has promoters that direct polymerase II to make viral mRNA

Question 11

which DNA virus doesn’t replicate in the nucleus of host cells?

Answer 11

poxvirus

it’s the only DNA virus that doesn’t replicate in the host nucleus and use RNA polymerase II

it instead forms a cytoplasmic pocket that it can replicate in

it can do this because it has a huge coding capacity since it’s geneome is so big so it can afford to do this

Question 12

what are the 3 basic kinds of genes in DNA viruses?

Answer 12

1. immediate early genes (IE genes)
2. early genes (E genes)
3. late genes (L genes)

IE genes –> E genes –> L genes

aka genes are categorized based on when they’re needed during virus replication

Question 13

what are IE genes?

Answer 13

promoters for IE genes are not specific & are recognized in most cells – IE viral promoters are simple promoters, E & L promoters are complex

the DNA virus genome is being recognized really quickly once its in the nucleus by the host transcription factors that drive transcription of the genes marked with promoters

this permits the host transcription machinery to initiate transcription of IE genes

basically IE genes make regulatory proteins at the beginning of the infection that later help make E gene products

Question 14

what do IE genes do?

Answer 14

IE gene products:
1. turn off expression of host genes that interfere with the virus and turn on host genes the virus wants to use

2. turn on expression of E genes
3. turn off their own expression once they’re done

Question 15

what are E gene products?

Answer 15

they modify the host DNA replication machinery, or are DNA polymerases themselves, to allow for the synthesis of viral DNA

they modify the host translation machinery for selective production of viral proteins

they also act to modify the cell so it doesn’t die before the virus replicates

and finally, they modify the transcription machinery further to switch on transcription of the L genes and to turn off their own transcription.

so over all, E gene products are needed to replicate the virus genome and overcome host barriers to infection – they are involved in the synthesis of the virus genomes!!

Question 16

what are L gene products?

Answer 16

L genes encode viral structural proteins!! aka the envelope, capsid, etc. stuff that gets packed into the virion

L gene expression requires E proteins and synthesis of viral DNA – we don’t express L genes till the very end because they’ll just get in the way before

L genes usually only occur after DNA replication!

Question 17

is the adenovirus naked or enveloped?

Answer 17

naked! it has no envelope!

it has fiber knobs on their capsid that binds to the host cell receptor

Question 18

what is the pathway through which the adenovirus enters the cell?

Answer 18

1. virus binds to receptor on host protein via fiber knob on capsid
2. entry and penetration and uncoating – this happens in a pH dependent manner!!
3. genome gets through a nuclear pore so this is where the genome gets inserted into the host nucleus – this is actually where full uncoating happens because the nucleocapsid is getting squeezed through this pore and the genome is being stripped and seperated sorta

Question 19

through what method does the adenovirus replicate?

Answer 19

strand displacement

Question 20

how does strand displacement work?

Answer 20

1. as soon as the genome is uncoated from the capsid, we have the free genome which has terminal repeats
2. an early protein from adenovirus binds to one end of the dsDNA of the adenovirus and splits the strands apart – this E2 also acts as a primer!
3. a viral DNA polymerase binds to E2 primer and replicates the one viral DNA strand

they displaced strand behind

4. the lagging strand connects to itself and forms a circle
5. the E2 protein comes in again and displaces/splits open the circle and binds to the DNA allowing for DNA polymerase to come in again and now replicate the displaced strand

now you have 2 full copies of the viral genome!

Question 21

whats the difference between the latent and eclipse period?

Answer 21

eclipse period is before we start to assemble virions

the latent period is where the virions are assembled but just haven’t been released from the cell

Question 22

which virus family is the one with the largest DNA genome?

Answer 22

poxviridae

Question 23

what is the correct sequence of events during an adenovirus infection?

Answer 23

1. adsorption
2. endosome acidification
3. uncoating
4. DNA synthesis

adenovirus doesn’t have an envelope so they don’t bud!!

Question 24

is the parvovirus single or double stranded?

Answer 24

single stranded

Question 25

are there more adenovirus genes or herpesvirus genes?

Answer 25

herpes virus!

Question 26

what are the characteristics of the largest genomes?

Answer 26

DNA

so linear and double stranded!

Question 27

what’s the simplified summary of DNA viruses?

Answer 27

1. viral DNA enters the nucleus and host enzymes make mRNA from it
2. viral mRNA is translated by host machinery to make viral proteins
3. viral DNA is replicated using host DNA synthesis machinery

Question 28

whats the problem that DNA viruses run into?

Answer 28

only cells that are making DNA have the machinery for DNA synthesis!

so, simple DNA viruses could only replicate in host cells that are cycling aka in S phase!!

however, most human cells are non-dividing, i.e. in G0….

so some viruses acutally figured out how to induce non-proliferating cells to enter the cell cycle and start proliferating while other viruses just encode their own DNA replication machinery so that they can replicate in non-proliferating cells

the good news is that drugs can specifically target viral vs. host DNA replication machinery

Question 29

which DNA virus can only replicate in proliferating cells?

Answer 29

parvovirus

Question 30

which DNA virus can induce non-proliferating cells to enter the cell cycle and start proliferating?

Answer 30

1. polyoma virus
2. papilloma virus
3. adenovirus

Question 31

which DNA viruses can encode their own DNA replication machinery and replicate in non-proliferating cells?

Answer 31

1. herpes virus

2. pox virus