Trkola : Retroviruses

Question 1

What’s a retrovirus genome organisation like ?

Answer 1

LTRs + Gag Pol Env.
gag = structural proteins ( Matrix, Capsid and Nucleocapsid.)
pol : enzymes genes (RT, Integrase, Protease)
env: glycoproteins (Surface unit and Transmembrane unit).

Keep in mind this is general consensus. Many retroviruses have more complex genomes, encoding for accessory proteins.

Question 2

What’s the genome type of retroviruses ?

Answer 2

Positive ssRNA (group 6 Baltimore). Fun thing: it keeps two copies of it in the capsid.

Question 3

Which HIV accessory proteins have a replicative function ?

Answer 3

tat, rev, vpr.

Question 4

Which HIV accessory proteins have an immune evasion function ?

Answer 4

vif, vpu and nef.

Question 5

What’s the three essential tricks of HIV to code sooo many proteins with such a tiny weeny genome ?

Answer 5

Overlapping ORFs + alternative splicing + polyproteins.

Question 6

Where does the RT happen ?

Answer 6

In the cytoplasm. Viral DNA is then translocated to be integrated into the genome before it gets transcribed spliced and all the other bs.

Question 7

When is the HIV virion particularely vulnerable during its replication cycle ?

Answer 7

At the Reverse Transcription phase. The capsid that protects the genome has to partially disassemble for it to happen, which leaves HIV at the mercy of APOBEC for example and other host factors.

Question 8

The HIV1 capsid has two functions, post entry. Which are these ?

Answer 8

It can create pores into it to let only nucleotides in and initiate the RT. As discussed, it also has an occlusion role to hid the genome from cytosolic sensors and nucleases. this is why some antiviral treatments target it.

Question 9

Does the RT only have a polymerase function ?

Answer 9

Nope, it also has RNaseH capability to degrade RNA. This is essential degrade the RNA of the DNA/RNA hybrids and get dsDNA in the end.

Question 10

What’s the primer used by HIV1 to initiate the RT ?

Answer 10

It uses a host tRNA lys, that is actually steals about 20 copies of for assembly to store in the capsid! This binds to the Primer Binding Site (PBS) to initiate RT.

Question 11

What’s the three groups of HIV1 ?

Answer 11

M, O and N.

Question 12

What’s the PIC ?

Answer 12

It’s the pre integration complex: a large complex carrying many signaling sequences to force entry into the nucleus.

Question 13

What’s PIC composition and their roles ?

Answer 13

Matrix, VPR, and Integrases.
Additionally contains cellular proteins as well, p75 for example that is crucial for integration by promoting chromatin association.

Question 14

The integrases also have a role outside of the nucleus. What is it ?

Answer 14

The sequences at the ends of the proviral DNA must be correct and reactive. Integrases binds them to keep them steady and bridge them within the PIC.

Question 15

Is the integration random ?

Answer 15

Nope: retroviruses select regions with a high transcriptional activity

Question 16

How is Tat essential ?

Answer 16

Tat is required for transcription activation by binding to the Transcription Response Element. It’s generated from first mRNA.

Question 17

How is Rev essential ?

Answer 17

It’s required for the generation of genomic (therefore unspliced) RNA. Basically binds to RRE of certain RNAs, preventing one splice site to be exploited.

Question 18

What’s the LTR structure and role ?

Answer 18

LTRs are made of U3, R and U5 regions. Transcription is initiated between U3 and R.

It also contains a few binding sites for cellular TFs within the U3 region.

Question 19

Is there HIV transcription in resting cells ?

Answer 19

Nope. Nucleosomes bind to LTRs and see that it’s not accessible - latency.

Question 20

What cells are used for a latent HIV1 reservoir ?

Answer 20

Resting CD4+ T cells.

Question 21

Why is latency such an annoyance ?

Answer 21

They’re essentially invincible and invisible to the IS and treatments - and resting T cells have a slow decay rate, which makes this reservoir infinite and makes curing HIV1 impossible at the moment.

Question 22

What is tat’s function?

Answer 22

The RNA pol II gets stalled very soon after initiation of transcription. Tat gets activated, binds to the TAR, and recruits elungation factors to un stall it. Activates transcription (very low levels before its expression, enhancer protein).

Question 23

Why is HIV transcription upregulated in activated cells?

Answer 23

Because activated cells recruit a few transcription factors such as NfKb in the nucleus, thus “waking” the virus, and producing tat that’ll trigger the rest.

Question 24

How’s HIV budding ?

Answer 24

Using the cellular export machinery.

Question 25

Give us an ISG capable of inhibiting HIV1 budding - and a countermeasure.

Answer 25

Tetherin ! Vpu counteracts it tho.

Question 26

HIV1 virions need to mature. When and how ?

Answer 26

Mature AFTER budding, in the assembled particle. Essentially the gagpol polyprotein isn’t cleaved yet, leaving the capsid like an IKEA wardrobe.

Question 27

Give us the three classes of antiretroviral drugs.

Answer 27

Protease and maturation inhibitors
RT inhibitors
Integrase inhibitors.

Question 28

What’s the viral set point and what influences it ?

Answer 28

It’s the steady set level at which viremia isn’t achieved. Host genetics and immunity, together with the strain and genetic diversity of HIV, influence it.

Question 29

HTLV regulates a particular cellular process: which and how ?

Answer 29

Regulates cell growth and transformation, with the Tax protein: basically disregulates various receptors and ligands that stimulate growth factor recruitement and activation of TFs. As a result, cells get immortalised, and leukemia develops.