Retroviruses I Flashcards
Retroviruses: Group Definition
- Many different viruses that infect insects>>fish>>man
- Acquire host cells sequences - oncogenes
- Insert into host cells chromosome - can activate or inactivate genes >> cancer
- Rapid genome evolution - acquire mutation through replication and recombination
Infection consequences:
- No ill effects
- Tumors - rapid onset or long latency
- Wasting diseases, neurological disorders
- Immune deficiencies - HIV
Difficulty with standard classification
Historically based on pathogenicity or shape, but this classification system does not reflect evolutionary relationships observed in sequence comparisons: Alternative Retrovirus Classification System
Virion Structure and Composition
- Enveloped viruses, env protein embedded in membrane, matrix protein under lipid bilayer
- Capsid core made up of structural proteins - MAtrix CApsid NucleoCapsid, PRotease
- 2 copies of a + ssRNA genome - the only virus that is “diploid” and accounts for recombination potential
Simple retrovirus genomic organization
R:
U5:
The gag gene:
The polymerase gene:
The envelope gene:
U3:
R: “repeat” - it is repeated at both ends
U5: Stands for “unique to 5’ end”
The gag gene: encodes the gag proteins MA, CA, NC, and PR - the proteins are made as a polyprotein that then gets clipped
The polymerase gene: Encodes reverse transcriptase (RT) and integrase (IN) which are made as an extended polyprotein
The envelope gene: Encodes the env protein which is made as a precursor and then gets clipped into the surface (SU) and transmembrane (TM) domains
U3: Unique to 3’ end
Complex Retrovirus Gene Organization
Organized similar to simple retroviruses except numerous additional genes/proteins
mRNAs for the additional genes called “accesory proteins” are generated by complex alternative splicing
Points of Therapeutic Intervention/Replication Cycle
- Adsorption
- Penetration and uncoating
- Reverse Transcription
- Transit to the nucleus
- Integration into host DNA
- Viral RNA synthesis, host pol II
- RNA processing
- Virion protein synthesis
- Assembly and budding
- Capsid maturation (proteolysis)
Adsorption
Virus binds cell via the env protein and a host cell receptor. HIV receptor is CD4/CCR5
Penetration and uncoating
Penetration and Uncoating: Viral envelope fuses with cell membrane either at cell surface or in endosomes after endocytosis
Two antivirals to complete this step
Genomic RNA is only partially uncoated - remains in protein particle in the cytoplasm
- RT, IN and some of the gag proteins remain associated with incoming genomic RNA - convert the ssRNA genome to dsDNA, cause nuclear import, and integration
Reverse Transcription
- The process of converting ssRNA to dsDNA
- Integrated DNA is longer than the template RNA and has U3 and U5 duplicated at the ends to form the long terminal repeat or “LTR”
- Reverse transcription is accomplished in the cytoplasm by the viral enzyme, reverse transcriptase (RT) which has two polymerase functions
- An RNA dependent DNA polymerase
- A DNA dependent DNA polymerase
How does Reverse Transcriptase allow drug resistance
It is an ‘error prone’ polymerase - 5 errors made per genome, which accounts for rapid evolution and drug resistance
Integration
- Carried out by integrase (IN) protein which enters cell with virus and remains associated with dsDNA
- Requires that dsDNA have access to host DNA: HIV can cross nuclear envelope
- Integrase recognizes U3 and U5
- Once integration occurs, virus is a PERMANENT resident of the host cell’s DNA
- Good target for intervention
Proviral Transcription and LTR
Major role of LTR is to direct synthesis of viral RNA
U3 contains binding sites for cellular transcription factors required for high level RNA synthesis
U3 has signals recognized by the cell’s transcription machinery, which directs transcription at the beginning of “R” region (only the 5’ end)
What determines the tissue/cells in which a retrovirus is active
Spectrum of proteins that bind U3
HIV LTR requires the transcription factor NFkB which is only expressed in activated T cells
RNA processing
As pol II transcripts, all viral RNAs are polyadenylated, some must be spliced to generate the env mRNA, but a large portion must remain full length to serve as gag-pol mRNA and as genome for progeny virions
