Plasmid deletion formation in recE4 and addB72 mutants of Bacillus subtilis

Plasmid deletion formation was compared in wild-type, recE4, and addB72 strains of Bacillus subtilis. Deletion frequencies in plasmid pGP1, as monitored with a penP-lacZ fusion, were low in recE4 and high in addB72, in comparison to the wild-type strain. In the wild-type and recE4 strains, deletions between directly repeated sequences were rare. In contrast, about half of the deletions in the addB72 mutant resulted from recombination at direct repeats of 5 bp or more. The sequences at or near the left deletion endpoints showed striking similarities in the three strains. (1) 5'-T-T-T-3', or the complement 5'-A-A-A-3', was frequently located at these sites. (2) 5'-T-G-T-A-3' was found close to most of these termini. (3) Nearly all left termini occurred in a region rich in hyphenated dyad symmetry, which includes the penP transcription/translation regulatory sequences. It is assumed that DNA secondary structures, together with a sequence preference, specify the majority of the left deletion termini, which we speculate to be target sites for topoisomerase I. The right termini of deletions in the wild-type and addB72 mutant were frequently located close to a loose octanucleotide consensus sequence: 5'-G/C-G/C-G/C-G-A/T-A/T-A/T-A/G-3'. In contrast, in the recE4 mutant, the sequence 5'-C-A-G/C-G/C-G/C-G/C-T/G-3' was more frequently found at this position.