Retroviruses I Flashcards
Why do we care about retroviruses?
- They are sometimes human pathogens (eg HIV)
- They are potential sources of biomedical advances (eg gene therapy)
What do all retroviruses have in common?
All are baltimore type VI. They use reverse transcriptase to produce a DNA transcript from RNA, and insert that into the host genome.
They are also all enveloped!
What is the difference between a simple and complex retrovirus? How closely related are these groups?
This classification only looks at the genome structure–complex retroviruses have more products and alternative splicing. This has little to do with their evolutionary relationships.
What gene of retroviruses constitutes the capsid core?
What is the signifiance of them having 2 ssRNA genomes?
The capsid is made of ‘gag’ products.
This allows them to undergo recombination, making them especially variable.
Describe the genome of a simple retrovirus.
The 5’ end contains R and U5.
This is followed by the gag polyprotein gene–encoding matrix, capsid, nucleocapsid and protease.
This is followed by the pol polyprotein gene–encoding reverse transcriptase and integrase.
This is followd by the env polyprotein gene–encoding the precursor membrane protein (gp160 for HIV).
The 3’ end contains R and U3.
Describe the replication cycle of HIV.
The initial, pre-integration steps (A-E) are typical of any virus: Adsorb, penetrate, uncoat and transit to the nucleus. Reverse transcription must occur before integration.
Steps F-J are post-integration, and are mostly proliferative.
What surface receptor does HIV recognize?
Why would the viral genome keep RT/IN associated during transit to the nucleus?
CD4/CCR5, hence why it targets T-helper cells.
Partly since these are required for integration, but also because their association blocks ribosomes from causing early translation (the viral genome is still polyadenylated RNA at this point, remember).
What is the product of reverse transcriptase action?
RT converts an ssRNA template to a dsDNA fragment. Note that in doing so, it creates LTRs (U3-R-U5) at either end. Note also that going from ssRNA requiers RNA-dependent DNA synthesis AND DNA-dependent DNA synthesis.
Describe the function and mechanism of action of Integrase.
Integrase recognizes the LTRs on a dsDNA strand, and nonspecifically inserts it into the host genome. This process is irreversible–the only good way to rid someone of this DNA is to kill the infected cell.
What is the structure and function of the viral LTR?
The LTR is important for integrase recognition, but also acts as a promoter once integrated into the host genome. Genes downstream of “R” (gag/pol/env) are upregulated. NFkB is important to this function.
Yet, this doesn’t happen on the 3’ end.
Once integrated, viral DNA acts as a template for production of viral mRNAs. Which of these must be spliced?
env mRNA must be spliced for function. Gag-pol stays intact since its cleavage is post-transcriptional (by protease encoded by gag). Some full transcripts are made and unspliced, to act as genome for new virions.
When are the gag-pol products cleaved?
When is the env product cleaved?
Gag-pol is cleaved following budding of a new virion. This causes a change in the structure of the capsid/core, as the capsid and nucleocapsid proteins are “freed”.
Env (gp160) is cleaved (into gp120 and gp41) by a host protease at the endoplasmic reticulum. This is a requisite for functioning virions.
How are full-genome HIV RNAs (and gag-pol) targeted for packaging, while env and host RNAs are not?
The gag-pol gene contains a psi region which is recognized for budding. Env would not have this, full-genome would.
Distinguish between a transforming and non-transforming retrovirus.
Transforming retroviruses carry oncogenes and can rapidly cause tumorigenesis in a host (though most of their virions are defective).
Non-transforming retroviruses may cause cancer by manipulating host DNA and proteins, eg upregulating a promoter.
