Lecture 17: RNA Coliphages

1. A representative collection: MS2 (close relative of f2, fr, R17), ø6, Qß

2. General Gross Anatomy
   1. Icosahedral: about 26-27 nm diameter (1/10 the wavelength of visible light!)
      1. Coat: Two groups of identical capsomers (180 capsomers (14 kdal); 4 megadaltons)
         1. Apical (12 groups of 5)
         2. Facetal (20 groups of 6)
      2. Capsomers
         1. MS2: 129 aa (close relatives have up to only 2 replacements)
         2. Qß: 132 aa (about 15% the same sequence as MS2)

   2. Growth Cycle
      1. Latent Period: about 30 to 40 minutes
      2. Burst size: about 10,000!

   3. RNA: 1.2 to 1.6 megadaltons (3.5 to 4.7 kb = 1200 to 1600 aa = 4 or 5 proteins)
      1. Single piece of RNA: therefore a polycistronic message
      2. MS2 RNA = 3569 bases long
      3. Termini: 5' pppGGGGŠŠŠŠŠCCCA 3'
         (This 3' end is identical with all ssRNA viruses - plant, animal, microbial.)
         (This should also remind you of tRNA's 3'-terminus.)
      4. 74% double-helix; many sections are twisted into hairpins (again, like tRNA)

3. An RNA-Genome Operating in a DNA-Dominated Universe
   1. The Host's Machinery ('The DNA-Dominated Universe')

   2. The Strategy of the RNA Genome
      1. Escape from restriction endonucleases, where dsDNA is the target
      2. Miniaturization of genetic requirements
         1. Small number of requirements
         2. Compactness of the genetic code
            • How to fit more genes into less space
            • UGA, the weak terminator in Qß
      3. Parasitization of host proteins to yield a major portion of RNA-dependent RNA polymerase ("RNA replicase" = "replicase")
      4. The genetically encoded clock in MS2 (later)
         

   3. Packaging

4. In vitro Evolution with Qß (á la Don Mills)
   1. Cell-free genomic-RNA synthesis (á la Norman Pace)
      1. Materials and Methods
      2. Infective RNA

   2. A "Darwinian Experiment"
      1. Methods of serial transfer
      2. After 75 transfers, only 17% of the self-replicating genome remained.