Viral pathogens: classification, biology, disease 1 Flashcards
How are viruses grouped/ how can they be classified?
The Baltimore Classification (Groups I- VII)
What is the structure of a mature HIV-1 particle?
→ The outer envelope of HIV consists of a lipid bilayer with protruding Env spikes (heterotrimers of SU3TM3).
→ Inside the envelope lie shells of Gag proteins. → In the immature particle, Gag itself forms a single shell.
→ Gag is composed of 3 proteins- MA= matrix, CA= capsins and NC= Nucleocapsins
→ MA associates with the membrane CA forms the conical capsid NC coats the viral RNA genome.
→ The core contains two genomic
→ RNA strands (plus strand), tRNALys3, and ~50 copies of each viral enzyme (PR, RT, and IN).
To make proteins required, which 3 polyproteins do we synthesise?
→ Retroviruses synthesise 3 polyproteins:
- Gag; group specific antigen; viral core proteins; MA (matrix), CA (capsid),
NC (nucleocapsid)
Pol; viral enzymes; protease (PR), reverse transcriptase (RT) and integrase
(IN)
Env; envelope glycoprotein; gp120 SU (surface); gp41 TM (transmembrane)
(HIV-1 Env consists of a trimer of gp41 and gp120 peptide subunits and is covered with glycans- post translational modifications)
What are some HIV-1 Regulatory / Accessory Proteins and what do they do?
Tat - potent activator of viral transcription
Rev - mediates unspliced RNA nuclear export
Vif - critical regulator of virus infectivity
Nef - immune modulator, T-cell activation, virus spread (?)
Vpu - immune modulator, virus release
Vpr - cell cycle, virus nuclear import (?)
What do we know about the process of entry of the HIV-1 virus? What does HIV-1 entry require?
HIV-1 entry requires two membrane proteins: CD4 and a chemokine receptor (CCR5/CXCR4)
cell surface receptor CD4 recognises gp120- surface subunit, stimulating the open configuration (?) of the surface subunits. And then it is the interaction of surface subunits with co receptor that stimulates the transmembrane region to go into the cell membrane.
Ultimately you are trying to insert the transmembrane domain of the surface subunit into the lipid bilayer. This causes 6 bundle helix formation and membrane fusion/ (you have 2 envelope trimers which go into the lipid bilayer and this pushes the membrane apart)
HIV-1 is therefore tropic for CD4 expressing cells
such as helper T cells and macrophages; the loss
of which results in immunodeficiency (& AIDS).
Where does the virus go/what happens once it has entered the cell?
→ Once the virus is now in the cell, it needs to move to the site of replication.
→ HIV wants to replicate within the cell nucleus, however because of the large distance, it would take a long time for the virus to enter the nucleus once fused within the membrane of the cell
→ So the virus uses the cell microtubular network to move the core containing the genome to the nuclear membrane (towards the virus rather than virus going towards nucleus). (different methods of this- currently being researched)
Once the virus has got to the nucleus, what process occurs?
Reverse Transcription (process of DNA from RNA)
this is mediated by Reverse Transcriptase:
RT is a heterodimer of p66 and p51 subunits.
Catalytic properties are in p66 subunit, p51 serves structural role and lacks RNAse H domain
RT displays three distinct enzymatic activities:
1. RNA-dependent DNA polymerase
2. RNAse H (cleaves RNA from RNA/DNA hybrid)
3. DNA-dependent DNA polymerase
Essentially, an RNA genome is bound by RNA primer and the reverse transcriptase enzyme acts as a polymerase, making new copies of RNA from an RNA template from the RNA genome. These RNA templates are converted by the same reverse transcriptase enzyme to DNA templates and these becomes double stranded.
Viral DNA integrates into the cell DNA
The HIV DNA genome (provirus) is integrated into the host chromosomes
essentially the cell DNA is cut and viral DNA is placed there instead
The viral integrase enzyme binds both host and viral DNA
LEDGF/P75 binds HIV-1 integrase and facilitates targeting to chromatin
The HIV-1 promoter contains binding sites for transcription factors that
are present in T-lymphocytes
The virus must replicate its viral rna to viral dna using reverse transcriptase!
Where does the virus go/what happens once it has entered the cell?
→ Once the virus is now in the cell, it needs to move to the site of replication.
→ HIV wants to replicate within the cell nucleus, however because of the large distance, it would take a long time for the virus to enter the nucleus once fused within the membrane of the cell
→ So the virus uses the cell microtubular network to move the core containing the genome to the nuclear membrane (towards the virus rather than virus going towards nucleus). (different methods of this- currently being researched)
What binds the Tat protein?
What do we know about Gag and Gag-pol proteins etc?
→ The TAR RNA binds the Tat protein
→ Binding of Tat protein to TAR RNA enhances elongation of RNA pol II
→ The HIV-1provirus generates different mRNAs for the viral proteins
→ Nuclear export of unspliced retrovirus RNA
→ The HIV-1 Rev protein mediates nuclear export of unspliced and singly
spliced viral RNA
→ HIV Rev is essential for the nuclear export of intron-containing viral mRNAs
→ The HIV-1 Rev protein interacts with Crm1 and the RRE RNA
→ The unspliced HIV-1 RNA is the mRNA for Gag and Gag-Pol proteins
→ Dimerisation of the unspliced viral RNA allows packing of two genomes
→ Gag and Gag-Pol proteins assemble viral particles
→ Gag-pol protein is generated by -1 ribosomal frameshifting induced by a ‘slippery’ sequence and an RNA hairpin structure
→ Myristoylation of Glycines in the MA domain of Gag mediates association with the plasma membrane
→ The HIV-1 PT(S)AP motif is required for virus budding and mediates binding of the host Tsg101 protein
→ The ESCRT machinery is hijacked by HIV to perform membrane abscission during viral release
→ Protease releases the individual proteins from
Gag and Gag-Pol polyproteins
Gag processing generates mature virions
