lect 7: retroviruses

Introduction

  • retroviruses - RNA viruses that have reverse transcriptase (rt)

    • rt converts ssRNA → dsDNA (violates central dogma) 

    • dsDNA integrated into host chr

    • only when integrated is lifecycle active

  • can cause persistent infection

  • nucleocapsid → 2 strands of ssRNA + rt + protein coat

    • the 2 strands are loosely associated via tRNA from the previous host

    • tRNA acts as RNA primer for rt)

  • +ssRNA but genome isn’t transl

  • enveloped virus, have internal P matrix and surface envelop P

  • genome has 2 identical R seq at either end

  • many cancers associated with carcinogens that alter c-onc genes to mut level of expr

Life Cycle

  1. bind and enter

    1. host range - species specificity, specificity within species can attack

    2. cell type specificity - type of cell within a host

  2. uncoat genome - lipid membrane bilayer melts into host cell’s

  3. ssRNA → dsDNA via rt

  4. dsDNA LTR seq (extended versions of the R from ssRNA) acts as insertion seq and integrates into genome by transposition (virus now provirus)

  5. transc to make mRNA

  6. transl to make proteins

  7. assemble virions

  8. budding

  9. release via secretion

    1. don’t lyse cells → persistent infection

Reverse Transcriptase (ssRNA → dsDNA)

  • start: tRNA is bound ~1/3 of the way into the genome

  • rt binds to it and synth DNA strand from tRNA to the 5’ end of +ssRNA (5’ → 3’ on -dsDNA) 

    • -ssDNA strand still has “primer” tRNA attached

  • ribonuclease h (RNAh - acts on heteroduplex) digests the RNA bound to DNA so the RNA past the tRNA binding site is gone

  • the comple R seq in the DNA seq (5’) disconnects and binds to the 3’ R seq

  • the rt (still attached to the DNA seq) then synth 3’ → 5’ (on +ssRNA) / 5’ → 3’ (-ssDNA)

    • end: +RNA and -DNA heteroduplex w/ 1 LTR, ssDNA overhand, and tRNA

  • RNAh digest all +ssDNA except for a GC rich segment that serves as a primer for DNA synth (5’ end)

  • polymerase adds onto the 5’ primer (5’ → 3’) and synth until falls off the end (includes some of the tRNA seq)

    • end w/ -ssDNA + small +ssDNA(+tRNA seg)

  • the longer -ssDNA loops around and binds to the tRNA seg of the +ssDNA

    • displaces the 5’ end of the -ssDNA strand

  • rt transfers to the other strand and completes -ssDNA synth

  • 2 identical LTRs, an integrated tRNA segment, and a dsDNA genome

    • which then goes on to integrate into the host genome

Viral Genome

  • makes 2 kinds of transcripts

    • gag only → mature capsid P, protease

    • gag-pol → gag (see above), pol

      • pol → rt, integrase

  • differential splice to get full transcripts → genomes to get packaged

  • 3 orfs:

    • gag - transc into polyP, cleaved with the encoded protease to make multiple su → nucleocapsid P

    • pol - also transc into polyP; encodes P like rt, protease, and integrase

    • env - encodes envelope components

Phylogeny

  • many classes included

  • not rooted, can’t easily relate them other viruses and the 3 domain tree

  • simple viruses vs complex viruses - whether they have additional genes or not 

    • outside of gag, pol, and env

  • og called RNA tumor viruses bc most have ability to neoplastically transform normal cells → tumor / cancerous

  • 2 types, dept on how quickly and robustly they transform cells

    • acutely transforming viruses - takes days to transform cells, v efficient in culture, have v-onc genes

    • chronically transforming viruses - takes months to develop tumors, low efficiently, only transform cells in whole orgs, don’t have v-onc genes

      • go thru usual process of infection but starts tumor growth when BY CHANCE the genome integrates next to a c-oncogene in genomes

      • the viral enhancer / regulation (in LTR) inc replication and transc of the viral one and can do the same to oncogene, viral enhancer overcomes cellular one

      • if oncogene already in use → chromatin already open → more likely for virus to integrate there

  • 1st discovered was RSV (rous sarcoma virus), acutely transforming virus

RSV / Acutely Transforming Virus

  • discovered in 1911 by peyton rous - injected healthy chickens with cell-free extract of tumor from diseased chicken, which induced cancer and tumor growth

    • first demo of transmissible oncogenetic agent

    • solution with tumor was passed thru filter that excluded bact and cells → only viruses small enough to pass thru

  • has 4 orfs: gag, pol, env, onc

    • extra gene (onc) confers oncogenetic properties

    • has specific names (src, myc, abl, and so on) depending on the specific virus but onc used overall

  • both genomes integrate into host cell’s

  • genome has size constraints so partially/fully delete other genes in genome to make sense

    • survives and can infect bc of the other ssRNA strand in the virus

    • if 1 has the onc gene, then can afford to partially delete others 

    • when packaging: random

      • 2 onc-containing ssRNA → virus nonfunctional

      • 1 onc-containing + 1 not → ideal

      • 2 non-onc ssRNA → functional, infectious, not cause tumor growth

  •  can carry transduced cellular oncogenes (v-onc) that come from transduction (taking in cell DNA during packaging), mut version of c-onc (cellular oncogene)

    • for every v-onc gene in a virus, there’s a c-onc equiv in a cell

  • have onc and v-onc, diff dept their origin

    • onc - general term, sometimes virus evo it, sometimes picked up

    • v-onc - specifically mut version of cellular gene