Quiz Ch. 16
Quiz Ch. 17

Viruses: general principles. Bacteriophages

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Last revised: Wednesday, April 5, 2000
Ch. 16, 17 in Prescott et al, Microbiology, 4th Ed.
Note: These notes are provided as a guide to topics the instructor hopes to cover during lecture. Actual coverage will always differ somewhat from what is printed here. These notes are not a substitute for the actual lecture!
Copyright 2000. Thomas M. Terry

Every virus has two stages

  1. a dormant, particulate, transmissible stage called the virion stage
  2. an active, intracellular stage called the infectious stage

Virion Stage

Infectious Stage

Measurement of viral growth

Taxonomy of viruses

Virion Structure

See Lecture notes on "Virus structure"
  1. "Naked" viruses
    1. Helical viruses
      • Tobacco mosaic virus (TMV) is an example of a virus with helical symmetry.
      • A helical array of identical protein subunits surrounds an RNA molecule

        TMV electron micrograph: image from University of Leicester

    2. Icosahedral viruses
      • built from icosahedral (20-sided) assemblies of protein subunits.
      • View animation of icosahedron shape (from Tulane University)
      • Icosahedral shape is the minimum free energy structure for producing a shell of equivalently bonded identical structures.
      • The simplest icosahedral capsids are built up by using 3 identical subunits to form each triangular face, thereby requiring 60 identical subunits to form a complete capsid. A few simple virus particles are constructed in this way, e.g. bacteriophage X174.
      • Most icosahedral viruses have more than 60 subunits, usually some multiple N times 60. N (called the triangulation number) can have values of 1, 3, 4, 7, 9, 12, and more.
      • Visual example: adenovirus diagram
  2. "Enveloped" viruses
    • "Naked" viruses require host death so viruses can be released. This may be wasteful, and may cause premature death of host cell.
    • Alternative strategy: shed virus particles by budding out, continued release from cell membrane. Cell does not die (immediately), continues to serve as factory for virus assembly and release. Virus typically acquires a coating of host cell membrane, modified to include virus-specific proteins. This is the "envelope". Virus may have additional protein coats (often icosahedral) inside the envelope.

      Enveloped Herpes virus, by Linda Stannard
    • Eventually host cell is too depleted to survive. Can see evidence of this as "cytopathic effect" (CPE). Cell then dies.
    • Examples of enveloped viruses include:
      • Retrovirus, including HIV
      • Paramyxovirus, including influenza
      • Rhabdovirus, including rabies
      • Filovirus. Although very "hot" in the news, these viruses are very poorly characterized because of their extreme pathogenicity. They are class IV pathogens, meaning they can only be cultured in total containment facilities, of which there are only two in the U. S. They are thought to be enveloped viruses with - RNA genomes.


        Ebola virus image by Dr. Frederick A. Murphy, University of California, Davis

Virus Genomes


Bacterial Viruses = Phages

Case Study #1: small RNA phage MS2 ---> lytic infection

Case study #2: large phage T4 ---> lytic infection

Case Study #3: lysogenic phage Lambda ---> lytic or lysogenic infection

  1. View animation of stages in Phage lambda infection and induction
  2. Lambda has ds DNA, injected into cell as linear molecule. Enough DNA for ~ 55 proteins. (see section 8.12 in text, also class handout)
  3. View image of phage lambda
  4. Phage has two possible outcomes: lytic infection or lysogeny = "silent" partnership with cell, virus DNA becomes integrated into host chromosome and gets duplicated and passed on to all cell offspring.
  5. DNA has "sticky ends". ~20 bases at each end are single stranded. The two ends are complementary, DNA can circularize once in cell. DNA ligase can seal two ends to make covalently closed circle.
  6. Lambda has 3 promoter sites. Two of these allow transcription of lytic genes. Other promoter leads to transcription of a repressor protein (Lambda repressor) that can bind to the two lytic promoters, block all lytic genes. Repressor does not block its own promoter, so cell continues to synthesize small quantity of repressor (~10-20 copies/cell).
  7. One early lambda protein is Integrase; causes specific recombination event at region where both Lambda DNA and host DNA have same 13 base pairs. (homologous sequence).
  8. If Lambda repressor is expressed before transcription of late lytic pathway genes occurs, then Lambda remains in host DNA indefinitely, gets replicated just like host genes.
  9. Induction: under "nasty" environmental conditions where DNA damage occurs (e.g. UV light or certain chemicals), can stop repressor synthesis. If this occurs, lytic promoters are no longer blocked, lytic genes get transcribed and translated, and cell becomes phage factory, leads to lytic production of lambda viruses.

Bacterial defenses against infection

Cell surfaces: possibilities of mutation

  1. Virus must attach to some specific cell surface protein or polysaccharide. But these are specified by genes, and genes can mutate. In population, will always find some variant strains with slightly different cell surfaces, may not bind virus well.
  2. When phage first discovered, thought this could be effective weapon against bacterial disease. But frequency of resistant bacterial strains was too high, any given strain of virus quickly became useless as resistant survivors propagated.

Nucleases: endo- and exo-DNases and RNases

  1. All bacteria seem to have nucleases that can attack DNA (called DNases) and RNA (called RNases).
  2. Exoenzymes attack free 5' or 3' ends of DNA, RNA molecules. Bacteria are protected since DNA (and plasmids) are always circular. RNases are present, and in fact destroy mRNA eventually (bacteria are always making new RNAs, very responsive to enviroment changes).
  3. Endonucleases are potentially lethal weapons. Called restriction enzymes. Attack at specific sequence: e.g., in E. coli, enzyme called EcoRI will attack any sequence with 5' G-A-A-T-T-C 3' (cuts DNA between G and A).
  4. Why doesn't this kill cell? Because cell also has a second enzyme, called modification enzyme, that protects all host DNA sequences of this type. Typically adds a methyl (-CH3) group to one base at the cutting site. The methylated base is modified, and protected from the restriction enzyme. When foreign DNA comes into cell (e.g. virus DNA), if restriction site if present it will be cut and ----- requiem for the virus!

The importance of Restriction Enzymes

Restriction enzymes are responsible for the genetic revolution. They make reproducible, specific cuts with surgical precision. Major industry has emerged in biochemical supply companies to harvest bacteria, purify restriction enzymes, and sell these to research and applied industries. Big $$$$$$$.

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