1. Viral Genetics BIT 220 Chapter 16

2. Details of the Virus Classified According to a. DNA or RNA b. Enveloped or Non-Enveloped c. Single-stranded or double-stranded Viruses contain only a few genes Reverse transcriptase proteins to inhibit host synthesis to make coat proteins Any other essentials - the virus ‘borrows’ from host cell

3. Obligate parasites Smaller than bacteria Can not replicate without host - autonomous replication in the host Composition -nucleic acid -protein coat -envelope? Where did they come from? first identified ‘bacteriophage’ - virus that infects a bacterium (“eater of bacteria”)

4. Origin of Viruses Do not encode ribosomes or enzymes for energy production Suggests they evolved after cells Evolved from small segments host cell DNA or RNA had regions of homology with host cell DNA - then could recombine and increased in complexity

5. Fig 16.1 Electron micrographs showing the morphologies of a plant virus, an animal virus, and a bacterial virus. © 2003 John Wiley and Sons Publishers Credit: Courtesy of Robley Williams, University of California Berkeley and Harold Fisher, University of Rhode Island.

6. Examples of Viruses

7. Fig 16.2a Electron micrograph showing the structure of bacteriophage T4. © 2003 John Wiley and Sons Publishers Credit: Courtesy of John Finch, Cambridge University.

8. Viruses Simplest of all organisms proteins and nucleic acids T phages (T1-T7) - E. coli phage Components (Figure 16.2) –head: contains several proteins (20 sides) - DNA in head –tail: has 2 hollow tubes (inner needle and outer sheath) –tail fibers: uses to find a bacterial host –base plate (tail pins) - anchor virus to host

9. Fig 16.2 Diagram showing the structure of bacteriophage T4. © 2003 John Wiley and Sons Publishers 20 Sided polyhedron Double-stranded Locate bacterium Anchor to bacterium Needle which injects DNA into bac

10. Fig 16.3 The life cycle of bacteriophage T4. © 2003 John Wiley and Sons Publishers

11. Select Details of Phage Lifecycle A. Bacteriophage DNA enters bacterium B. Viral proteins bind to host polymerase/inhibit host synthesis these proteins also aid in host polymerase recognizing viral genes C. Host DNA is degraded by viral nucleases D. Viral genes encode coat proteins lysozyme (to break host wall for lysis) E. Viruses evade the ‘immune system’ of bacteria glucosylated modified cytosine bases

12. Bacterial Defense Restriction endonucleases (restriction enzymes) - help protect bacteria from invasion by viruses can degrade C- and HMC-containing DNAs Viruses smart - add glucose to HMC residies, so r.e’s can’t break them down (5- hydroxymethylcytosine - cytosine with a CH 2 OH group, contained in viruses

13. Mapping Phage Genome Normally, crossing organisms with different alleles of a gene Don’t have this in viruses Only can been seen with electron microscope need to look at interaction of phage with host cell

14. Phage Plaques Clear area on a lawn of bacteria- results from lysis or killing of contiguous cells Host range - infect some bacterial strains but not others Phage morphology factors: –interaction between phage and bacteria –phage genotype

15.  X174 Genes within genes - 5389 nt; should be 1795 amino acids, but there are 2300 amino acids learned that they contain overlapping genes (translated using different reading frames) See Figures 16.17 and 16.18 - e.g., E gene located entirely within the D gene

16. HIV Human Immunodeficiency Virus Virus that causes AIDS (acquired immune deficiency syndrome) 30 to 40 million infected Prolonged infection Primary effect of HIV infection: reduction in T H cells Slow and steady decline of the immune system

18. Human Immunodeficiency Virus

19. HIV Results of T H cell depletion: –opportunistic infections (pneumonia) –tumors develop HIV mutates rapidly HIV is a retrovirus –genome RNA Member of lentivirus – “slow virus” Enveloped gp120 on virus binds to CD4 –T helper lymphocytes –macrophages gp41 –allows fusion of lipid membranes of virus and host

20. Life Cycle of HIV FIGURE 16.20 (next slide) 1. virus attaches and penetrates host cells 2. Viral RNA converts to viral DNA (PROVIRUS) 3. Viral DNA integrates into human chromosome 4. Infected host cells produce new virus particles 5. New virus particles bud from host cell one-by-one, taking host cell's membrane along as envelope 6. HIV high mutation rate impedes immune response

21. Fig 16.20 Overview of the life cycle of HIV. © 2003 John Wiley and Sons Publishers

22. Rnase H- step 5- degrades RNA in DNA/RNA duplex integrase - enzyme that allows integration of the virus into the host genome Long terminal repeats –required for integration Figures 16.21, 16.22

23. Fig 16.23 Map of the integrated HIV genome showing the location of regulatory genes and genes encoding important viral proteins. © 2003 John Wiley and Sons Publishers

24. Development of HIV Disease Time Periods: 1. weeks 1-3: virus enters body, circulates, and makes infected person contagious 2. weeks 1-8: acute viral syndrome –short term –mild or severe flu-like symptoms –fever, fatigue, rash, aching muscle and joints, sore throat, enlarged lymph nodes

25. Development of HIV Disease 3. 6 weeks - 6 months +: positive HIV antibody test –seronegative: negative test –seropositive: positive test for HIV 4. 2 yrs: onset of longer-lasting symptoms 5. 6 months-15 yrs: development of AIDS yeast infections fungal pneumonia eye infections (CMV virus) tumors (Kaposi’s - skin)

26. Diagnosis of AIDS ELISA test Western Blot PCR test

27. HIV Therapy Strategies Boosting immune response insufficient –once virus in T cells - humoral response ineffective –cytotoxic T cells must kill infected cells, but viral antigens not displayed Interfere with: –HIV attachment to Cells –HIV integration into the host cell genome –Virus replication –Assembly of new virus particles

28. Possible HIV Therapies Preventing assembly of HIV virus –HIV protease inhibitor (Crixivan) Inhibit reverse transcription –AZT (azidothymidine) –Epivir, Retrovir Gene Therapy –Antisense RNA –Introduce into stem cells Preventing entry of HIV into uninfected cells gp120/viral envelope (bind with CD4) –CD4 on the cell surface (bind with mAb) Vaccines – recombinant or attenuated virus (risky?)