cis-Acting Elements within an RNA Coliphage Genome: Fold as You Please, but Fold You Must

Using an in vivocomplementation system, we conducted a mutational analysis of the bacteriophage Qβ readthrough cistron. In the Qβ cDNA-containing plasmid, pQβm100, we constructed six defined Qβ deletion cDNA genomes, each missing between 86 and 447 nucleotides from within the readthrough cistron. These deletion plasmids were introduced into host cells that are constitutively supplied with Qβ readthrough protein from the plasmid pQβRT. Under these conditions, all six deletion genomes spontaneously generated phage particles, each exhibiting a characteristic plaque phenotype and virus forming potential. Isolated readthrough-defective phage particles were subsequently used to infect host cells that carried helper readthrough protein. Passaged viruses yielded both larger plaques and higher titers, compared with those of the parent phages. Sequence analysis revealed that the genomes of the passaged viruses had deleted additional regions of readthrough RNA sequence. We discuss the possibilities that (1) the disruption of a well-defined structural domain in Qβ RNA was selectively disadvantagous to phage infection, and that (2) the evolved viral populations were selected by virtue of their ability to restore critical integrity of short and/or long-range nucleotide interactions within this region of Qβ RNA.