Lecture 7. HIV Replication 1 Flashcards
What genus is HIV apart of?
Lentivirus (which are all retroviruses)
What is the Baltimore classification of HIV?
Class 6 (+ssRNA)
How many people are infected worldwide with HIV?
38 million
How many new HIV infections were there in 2021?
1.5 million
How any people died from AIDS in 2021?
650,000 (15% were children)
What does HIV cause in the immune system?
Destruction of T cells (that normally defend the body against bacteria, fungi and viruses)
When does AIDS develop?
When blood contains less than 200 T cells/μl
What is the set-point?
Without therapy, how long it will take for AIDS to develop in someone who has HIV
The higher the HIV RNA levels in the plasma and the lower the CD4+ T cell count, AIDS will develop faster
What happens in the retroviral replication cycle?
Virus - cell surface interaction
Membrane fusion and capsid release
Reverse transcription of genome RNA
Transfer of proviral DNA to nucleus
Integration of provirus into host chromatin
Viral gene expression and progeny genome synthesis
Assembly of particles and maturation
Release from cell by budding
What steps are the unique points/characteristics of retrovirus replication?
Reverse transcription of genome RNA
Transfer of proviral DNA to nucleus
Integration of provirus into host chromatin
How long is the HIV genome?
~10kb of +ve sense ssRNA
How many genes and proteins does HIV encode?
15 proteins and 9 genes
What is gag?
A polyprotein that encodes the structural proteins of the virus (encoded by HIV)
What does gag encode?
MA = matrix protein (sits just underneath envelope)
CA = Capsid protein (encapsulates viral genome)
NC = nucleocapsid protein (coats the viral RNA)
P6
What is pol?
A polyprotein that encodes the enzymes (encoded by HIV)
What does pol encode?
Protease
Reverse transcriptase
Integrase
What is env and what does it encode for?
A polyprotein that encodes the envelope proteins of the virus (encoded by HIV)
Encodes for the surface and transmembrane parts
How many copies of the viral RNA are there in a single HIV particle?
2 (HIV is diploid)
What is the primary receptor for HIV?
CD4 molecule found on CD4+ T cells (interacts with gp120)
What are the names of the transmembrane and surface subunits found on HIV?
Transmembrane subunit: gp41
Surface subunit: gp120
What happens when gp120 binds to CD4?
Conformational change: the variable regions (V1/V2 and V3) move out and expose highly conserved binding site for coreceptor (also found on the surface of CD4+ T cells)
What are the two coreceptors that can bind to gp120?
CCR5 (chemokine receptor) or CXCR4 (also a chemokine receptor)
What must HIV be bound to?
Both the CD4 and the coreceptor
What does gp41 insert into the membrane?
Fusion peptide
When the α-helices are pulled together, what formation is formed between the membrane of the cell and the membrane of HIV?
“Hairpin formation” - brings membranes close enough to fuse
What does T20 do?
Fusion inhibitor that blocks the conformational change of gp41(prevents hairpin forming)
What does the HIV capsid require the assistance of to breakdown?
Cellular chaperones
What is cyclophilin A involved with?
Cellular protein that acts as a chaperone involved with cellular folding and assembly
How is cyclophilin A incorporated into the capsid structure?
Cycophilin A binds to the capsid protein when the virus is being assembled and incorporated into the capsid
What can and can’t virus particles that lack cyclophilin A do?
Virus particles lacking cyclophilin A fuse and enter but cannot reverse transcribe
What is the role of cyclophilin A within the capsid?
Cyclophilin enables disassembly and uncoating of the capsid
Why is it important that the capsid dissembles?
Reverse transcription cannot happen otherwise (partial disassembly must occur)
Where does the rervese transcriptase enter and why?
Enters cell in particle; incoming genome has no chance to be translated to give new enzyme
IN HIV, what does reverse transcriptase act within?
The partially uncoated/degraded viral core
How many active sites does reverse transcriptase have and what are they?
2
Polymerase active site (attracts metal ions)
RNaseH active site (degrades RNA specifically when in a heteroduplex with a DNA strand)
What is the primer required to start HIV DNA synthesis?
tRNA molecule (for lysine) that binds to the viral RNA at tRNA binding site and creates complimentary DNA that is antiparallel to the original direction of RNA
What does RNaseH do in the process of reverse transcription after DNA synthesis?
Removes the RNA that is complimentary to the newly formed DNA
What happens in the 1st jump of DNA synthesis?
Complimentary DNA binds to the 3’ end of the original RNA sequence
R/repeat regions base pair with each other and now provides more template for DNA synthesis to extend back to the tb (tRNA binding site)
What does RNaseH do after the 1st jump in DNA synthesis?
Removes most of the complimentary RNA to the newly ssDNA
Polypurine regions is more resistant to RNaseH activity and acts as a primer to start synthesising the other strand of DNA
What does RNaseH do after the 2nd DNA sequence has formed in DNA synthesis?
Removes the polypurine stretch and tRNA (all RNA removed, only two partial strands of DNA remain)
Now DNA provirus
What happens in the 2nd jump of DNA synthesis?
The two tb site re-base pair and reverse transcriptase extends both strands of DNA to full length
Extra sequence on each end are called long terminal repeats/LTRs and all DNA has the same sequence of U3, R, U5
Full process of reverse transcription
(-) strand primed by tRNA bound at tb (tRNA binding site)
RNase H exposes the DNA copy of R and U5
Base pairing between R’ and the second copy of R (1st template jump)
Continued (-) strand synthesis and template RNA degradation
Poly purine oligo (polyP) is specially spared degradation to prime (+) strand DNA synthesis
(+) synthesis uses new (-) DNA as template and continues until a modified base in tRNA blocks extension; tRNA degraded by RNaseH
tb and tb’ at 3’ ends of (+) and (-) strands base pair (2nd template jump)
Extension of both strands to completion
What is the role of Vpr?
Key role in nuclear import
What proteins are involved in the importation of the provirus into the genome?
Vpr and MA (matrix protein) which interact with the nuclear pore complex
What is special about the cells HIV infects when compared to other lentiviruses?
They can infect all cells (most lentivirus can only infect dividing cells)
In integration, what is integrase bound to?
A dimer of integrase is bound to both ends of the retroviral DNA at the LTRs
What happens in the joining phase of integration?
Integrase processes each end of the retroviral DNA and then catalyses the joining of the ends to the host cell
How are the nicks formed by the joining phase of integration repaired?
Fixed by host cell DNA repair enzymes (additional sequences can get added in at this stage)
What are the characteristics of integrated proviruses?
Infection is not cytolytic (infection does not cause cells to burst open/lyse, HIV causes apoptosis, but some do not stimulate the immune system)
Provirus will replicate with the host genome at every round of division and propagate to every daughter cell
Provirus can be inherited between generations if virus infects a germ cell
Genomes of humans and other species contain large amounts of vestigial retroviral sequences
What does the U3 region of the 5’ LTR act as?
The enhancer and promotor for viral transcription (transcription start site at R)
What does the U5 region of the 3’ LTR act as?
The U5 region contains the poly A site, the site of cleavage and where poly A tail is added
What does retrovirus transcription create?
Production of full length genomic RNA (from 5’ R to 3’ R)
Splicing in HIV produces subgenomic RNA
