Plasmid deletion formation in Bacillus subtilis

Plasmid pGP1 carrying a penP-lacZ fusion was used to study structural plasmid instability in Bacillus subtilis. In only one of 28 sequenced deletion junction points in the penP-lacZ region short direct repeats (10 bp) and flanking imperfect inverted repeats (12 bp) were associated with endpoints. In 27 deletions no repeated sequences of more than 3 bp were present at the endpoints. In 15 of these the sequence 5'-T-G-T-A-3' was found within 10 bp from the left endpoint. At the left cleavage sites the sequence 5'-T-T-T-3', or the 5'-A-A-A-3' complement thereof, was frequently observed. Most of the left deletion endpoints were located in potential stem-loop structures in the penP transcription/translation regulatory region, which is very rich in hyphenated dyad symmetry. Near the right deletion endpoints a sequence consisting of four G/C residues, followed by three or four A/T residues, was found in 15 cases. It is speculated that DNA topoisomerase I is involved in the formation of the deletions studied.