RNA phages


Valegard, K., Murray, J.B., Stonehouse, H.J., van den Worm, S., Stockley, P.G., Liljas, L. The three-dimensional structures of two complexes between recombinant MS2 capsids and RNA operator fragments reveal sequence-specific protein-RNA interactions. J. Mol. Biol. 270, 724-38 (1997)
Van Duin, J. Single stranded RNA bacteriophages. in Viruses of Procaryotes. vol. 1, ed. Calendar. pp. 117-167 (1987)
Van Duin, J. Single stranded RNA bacteriophages in Encyclopedia of Virology, 2nd edition (1999)
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I- A useful model system for plus stranded RNA plant viruses

1- Were the first reasonably well understood viruses
2- Grow rapidly and are easily manipulated
3- A reference for comparing to plant viruses
II - General properties

1- Discovered about 1960 (sewage)
2- Icosahedral, 25nm diameter, contain 3.5-4.5 Kb of plus stranded RNA
3- Family (leviviridae) with 2 genera
a- Leviviruses, R17 (first RNA virus to be sequenced)
b- Alloleviviruses, Qβ (RNA replicase well studied)
4- Infection process

a- Attach to pili (sex factors)
b- Pili retract
c- RNA and "maturation" protein enter cell, capsid left behind
5- One step growth
a- Latent period of about 1 hr
b- Burst size of 104!
III- Proteins

1- Coat (12K), 180 copies per virion - mutants produce no virions
2- "Maturation" or tail protein (40K) -1 copy per virion - mutants give noninfectious, unstable virions. No comparable protein in plant viruses
3- RNA replicase (63K) - Virus subunit combines with 3 host subunits- deficient mutants synthesize no detectable protein or RNA
4- Lysis protein (8K) - small - overlaps coat protein gene in R17. Mutants do not lyse
5- "Readthrough" protein - only in Qβ , produced by readthrough of coat protein termination codon (UGA); virion constituent, essential for infection
6- Genetic map - 5'-maturation protein-coat protein-replicase-3'
IV- In vitro translation

1- Ribosomes preferentially translate the coat protein gene
2- RNA structure blocks translation of maturation protein, replicase
3- Translation of coat protein "unblocks" translation of replicase, lysis protein
4- Coat protein (cp) represses (blocks) translation of replicase
V- Regulation of translation

1- Translation of replicase (and R17 lysis protein) requires cp translation
2- Replicase and ribosome compete for cp initiation site
3- Coat protein represses replicase translation (well characterized RNA-protein complex)
4- Replicase translation favored early, coat protein translation favored late