History says, don’t hope On this side of the grave But then, once in a lifetime

1. History says, don’t hope On this side of the grave But then, once in a lifetime The longed-for tidal wave Of justice can rise up And hope and history rhyme. Seamus Heaney, 1995 Nobel Laureate in Literature 1996 UNC commencement speaker “Voices from Lemnos” http://www.youtube.com/watch?v=RO8MP3wMvqg http://www.ncbi.nlm.nih.gov/pubmed/?term=22728444

2. The dawn of HIV A retrovirus causes AIDS In May 1983: doctors at the Institute Pasteur in France reported that they had isolated a new virus, which they suggested might be the cause of AIDS. Barre-Sinoussi F. … and Montagnier L. (1983), 'Isolation of a T-Lymphotropic retrovirus from a patient at risk for Acquired Immune Deficiency Syndrome (AIDS)', Science, May 20 In May 1983: doctors at the NIH in the US reported that a retrovirus virus related to Human T cell Leukemia virus was present in patients with AIDS. Gelman EP … and Gallo RC. (1983), “Proviral DNA of a retrovirus, human T-cell leukemia virus, in two patients with’AIDS, Science, May 20 January 1985 It becomes clear that LAV and HTLV-III are the same virus and The FDA licenses the first blood test for AIDS http://www.avert.org/his81_86.htm

3. But what is a retrovirus? In May 1983: doctors at the Institute Pasteur in France reported that they had isolated a new virus, which they suggested might be the cause of AIDS. Barre-Sinoussi F. … and Montagnier L. (1983), 'Isolation of a T-Lymphotropic retrovirus from a patient at risk for Acquired Immune Deficiency Syndrome (AIDS)', Science, May 20 In May 1983: doctors at the NIH in the US reported that a retrovirus virus related to Human T cell Leukemia virus was present in patients with AIDS. Gelman EP … and Gallo RC. (1983), “Proviral DNA of a retrovirus, human T-cell leukemia virus, in two patients with’AIDS, Science, May 20 January 1985 It becomes clear that LAV and HTLV-III are the same virus and The FDA licenses the first blood test for AIDS http://www.avert.org/his81_86.htm

4. But what is a retrovirus? http://www.avert.org/his81_86.htm

5. Retroviruses are part of a big family tree! Causes Leukemia! Causes No Disease! Lentiviruses do not cause cancer, and they establish chronic infections that result in a long incubation followed by a chronic symptomatic disease. THE BIOLOGY OF HIV, SIV, AND OTHER LENTIVIRUSES: Harrington and Swanstrom

6. To understand this discovery We need to go back to the beginning http://www.avert.org/his81_86.htm

7. The central dogma-- Don’t forget this! DNA -> RNA -> Proteins

8. We called this step translation DNA -> RNA -> Proteins

9. How about this step? DNA -> RNA -> Proteins

10. It’s called Transcription DNA -> RNA -> Proteins

11. users.ugent.be/.../principles/centraldogma.html

12. As a general rule, one gene encodes one protein -but really one function- (usually!) • Cellular machines are largely made up of proteins. • Proteins are made up of chains of amino acids. • The sequence of these amino acids are "encoded" in the cell's DNA. DNA is transcribed into RNA, which is then translated into protein. • When one gene is mutated, one protein (a machine) is affected (usually disabled).

13. This information flow requires machinery to carry it out DNA RNA Protein Transcription Translation RNA Polymerase Ribosome Replication DNA Polymerase Process in Black, Enzyme in Blue Enzymes are machines (most often made of only proteins) that catalyze a specific biochemical reaction

14. Transcription looks like this

15. Or in a slightly more detailed view

16. Many viruses have genomes like ours, composed of DNA

17. Other viruses have genomes that skip DNA

18. But retroviruses do things differently

19. But retroviruses do things differently RNA DNA RNA Retroviruses. CSHL Press Fig. 1-5

20. This part is “BACKWARDS” RNA DNA RNA 17% of our genome encodes retro-transposons!! Retroviruses. CSHL Press Fig. 1-5

21. How do they do that?? RNA DNA RNA Retroviruses. CSHL Press Fig. 1-5

22. Let’s take a closer look at the virus

23. Let’s take a closer look at the virus

24. How does HIV infect new people?

25. How does HIV infect new people?

26. How does HIV infect new people?

27. How does HIV infect new people?

28. A detailed look at HIV entry gp120 and gp41 made as a precursor protein that is cleaved in the trans-Golgi network Cellular Microbiology (2012) 14(8), 1183–1192

29. Now let’s look closely to what happens when virus enters T cells

31. Retroviruses have stripped down genomes So they make good use of what they have Primer Binding Site for tRNA primer PPT: polypurine tract (RNAse H resistant) — primes + strand synthesis LTR: long terminal repeat — viral integration — transcription from 5’ LTR THE BIOLOGY OF HIV, SIV, AND OTHER LENTIVIRUSES: Harrington and Swanstrom

32. A close look at retroviral replication Comptes Rendus Biologies Volume 325, Issue 1, January 2002, Pages 17–23

33. Template switching results in recombination of viral genomes and increased HIV1 diversity

34. HIV Viral Integration into our genome Cold Spring Harb Perspect Med 2012;2:a006890

35. HIV Viral Integration into our genome 2 cool facts: Lentiviruses can Integrate in non-dividing Cells, because the genome Can be transported into the nucleus Our genomes contain remnants of retroviruses, providing a history of 40 million years of primate evolution. Without deletion, these would represent 40% of genome!!

36. Retroviruses have stripped down genomes So they make good use of what they have Encoded by FL transcript -1 translation frameshift 5% of time Bicistronic mRNA Vif, vpr, tat, rev, nef all encoded by other mRNAs THE BIOLOGY OF HIV, SIV, AND OTHER LENTIVIRUSES: Harrington and Swanstrom

37. Structure of the HIV-1 gag-pol frameshift element Watts JM, Nature. 2009 Aug 6;460(7256):711-6

38. The HIV Virion THE BIOLOGY OF HIV, SIV, AND OTHER LENTIVIRUSES: Harrington and Swanstrom

39. Retroviruses have stripped down genomes So they make good use of what they have

40. Let’s look at reverse transcriptase Science. 1992 Jun 26;256(5065):1783-90

41. It’s a distant relative of DNA polymerase!

42. Encoded in pol are reverse transcriptase, RNAse H, and integrase!

43. Reverse transcriptase, the amazing enzyme that does it all

44. This will be important later!

45. This remarkable reversal of the central dogma was Simultaneously discovered by David Baltimore and Howard Temin And earned them the 1975 Nobel Prize in Medicine or Physiology David Baltimore Howard Temin

46. Now that the provirus is integrated in your DNA, It can generate new viruses

47. This involves transcription, Translation and processing of viral proteins

48. The Gag protein gets cleaved into pieces by an enzyme called a protease THE BIOLOGY OF HIV, SIV, AND OTHER LENTIVIRUSES: Harrington and Swanstrom

49. The Gag protein gets cleaved into pieces by an enzyme called a protease

50. The Gag protein gets cleaved into pieces by an enzyme called a protease Matrix Capsid Gag