Spontaneous deletion mutants of bacteriophage Pf3: mapping of signals involved in replication and assembly

Defective deletion mutants (miniphages) arise spontaneously during serial propagation of the filamentous bacteriophage Pf3. They contain a circular single-stranded (ss) DNA molecule which is up to 80% smaller than the wild-type single-stranded genome. Analysis of the genomic structure of three of these miniphages revealed that they consist of sequences that in the wild-type genome are flanked by direct repeats 5-8 nucleotides long; only one copy of these repeats was found again in the miniphage genome. One miniphage genome contained a tandemly duplicated sequence, and from its structure we concluded that the duplication had occurred after a primary deletion event. Also, short direct repeats must have been involved in the duplication process. We conclude that the deletion and duplication events have occurred by an identical recombination process, probably the "slipped mispairing" mechanism. In the presence of helper functions, the three miniphage genomes are replicated and assembled into ssDNA containing virus-like particles. Hence, the assembly signal and the replication origins for viral and complementary strand synthesis are located within the region shared by all three miniphage genomes, i.e., nucleotides 4092-4678 of the wild-type genome (Luiten et al., 1985).