Retro-transcribing viruses (classes VI specifically)

Everything from RNA Viruses IV - Retroviruses slides

What is the class VI viruses

(+) ssRNA viruses with a DNA intermediate

What is the class VI viral family discussed in class

Retroviridae

Who are the natural hosts of retroviridae

Vertebrates

Do retroviridae have an envelope

Yes

What is the shape of the retroviridae virion

Icosahedral

How big is the retroviridae genome

8-11 kb

What type of genome does retroviridae have

(+) ssRNA

What types of viruses can retroviridae be

Oncogenic or non-oncogenic

What is the main retroviridae discussed in class

HIV-1

What is unique about the retroviral genome found inside the virion

• It requires 2 exact same strands facing the same way, not complementary, antiparallel, or helix

• It comes with its own 5’ cap and poly A tail

What did scientists know by the 1960s about retroviridae

1. The genome is RNA

2. Actinomycin D inhibits virus replication because it binds DNA and disrupts mRNA synthesis

What is a provirus

A virus that integrates its genome into the host genome

Who proposed the provirus theory

Howard Temin did in 1964

What do David Baltimore and Howard Temin discover together in 1970

They discover that there is an enzyme that makes DNA from RNA, which is what we now call reverse transcriptase (RT)

What virus did Temin and Baltimore use to discover RT

Rous sarcoma virus (RSV), which is an oncogenic class VI virus

How does the retrovirus present mRNA for the cell to translate

1. (+) ssRNA gets converted to dsDNA via RT

2. Viral DNA gets transported to the nucleus

3. Integration of viral dsDNA into host’s genome

4. Transcription of viral mRNA by host cell

What viral enzymes are required for retroviridae to present mRNA

RT and integrase

What specific enzymatic activities does RT have

1. RdDp

2. DdDp

3. RNase H - degrades RNA in an RNA:DNA hybrid

What is the tropism for retroviridae

T-cells

What host receptors do retroviridae use to enter the cell

CD4 & CCR5 (coreceptor)

What is unique about HIV

• It integrates its genome into host genome, and therefore is the only RNA virus whose genome is made by cellular transcription, rather than viral transcription processes

• It is the only (+) ssRNA virus whose genome is not directly translated upon entry

How does HIV make dsDNA

1. It uses reverse transcriptase

2. tRNA is used as a primer to make the complementary strand of the RNA into DNA

3. tRNA hops over to the other side to continue synthesizing the rest of the DNA strand

4. As tRNA makes DNA, it degrades the RNA

5. Then another DNA strand is synthesized from the 1st DNA strand made

What does integrase do

It makes a cut in the host genome, pulls it apart, and integrates the viral dsDNA into it

What are the consequences of integration

• Passed onto daughter cells

• Silent

• Production of virions

• Transformation

• Permanent

How are more retroviridae genomes made

Made by the host cell’s RNA polymerase, as it recognizes the viral promoter in the U3 region of the provirus

How are the retroviridae proteins made

• It uses the host cell’s transcription and translational machinery

• The proviral DNA is transcribed from a single promoter in the 5’ LTR into a viral RNA transcript by the cell’s RNA poly II

How do retroviruses make monocistronic mRNAs

Via splicing, ribosomal frameshift, or cleavage by viral protease

What are the regulatory genes of HIV

Tat and Rev

How does tat regulate gene expression for HIV

It binds to TAR, increasing the transcription rate at least 1000 fold

How does rev regulate gene expression for HIV

It binds to the RRE element, facilitating the export of viral RNAs from the nucleus to the cytoplasm

What HIV accessory gene products play a role in modulating host immune response and affects virulence

Nef, vif, vpu, and vpr

What are the essential proteins for HIV

• RT - makes viral dsDNA

• Integrase - integrates viral dsDNA into host DNA

• Protease - cleaves viral polyprotein into smaller proteins, going from immature to mature virus

What proteins are cleaved by HIV protease to form a mature virus

Gag and gag-pol