Viral Genetics

BIT 220Chapter 16

Details of the VirusClassified According to

a. DNA or RNA

b. Enveloped or Non-Enveloped

c. Single-stranded or double-stranded

Viruses contain only a few genesReverse transcriptaseproteins to inhibit host synthesisto make coat proteins

Any other essentials - the virus ‘borrows’ from host cell

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”)

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

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.

Examples of Viruses

Fig 16.2a Electron micrograph showing the structure of bacteriophage T4.© 2003 John Wiley and Sons Publishers

Credit: Courtesy of John Finch, Cambridge University.

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

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

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

Select Details of Phage Lifecycle

A. Bacteriophage DNA enters bacterium

B. Viral proteins bind to host polymerase/inhibit host synthesisthese proteins also aid in host polymerase recognizing viral genes

C. Host DNA is degraded by viral nucleases

D. Viral genes encode coat proteinslysozyme (to break host wall for lysis)

E. Viruses evade the ‘immune system’ of bacteriaglucosylated modified cytosine bases

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 CH2OH group, contained in viruses

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

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

φX174

• 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

HIVHuman Immunodeficiency Virus

• Virus that causes AIDS (acquired immune deficiency syndrome)

• 30 to 40 million infected• Prolonged infection• Primary effect of HIV infection: reduction

in TH cells• Slow and steady decline of the immune

system

Human Immunodeficiency Virus

HIV• Results of TH 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

Life Cycle of HIVFIGURE 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

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

• 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

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

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

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 AIDSyeast infectionsfungal pneumoniaeye infections (CMV virus)tumors (Kaposi’s - skin)

Diagnosis of AIDS

• ELISA test

• Western Blot

• PCR test

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

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?)