Division inhibition gene dicF of Escherichia coli reveals a widespread group of prophage sequences in bacterial genomes.

The genomes of various eubacteria were analyzed by Southern blot hybridization to detect sequences related to the segment of the defective lambdoid prophage Kim which encodes DicF RNA, an antisense inhibitor of cell division gene ftsZ in Escherichia coli K-12. Among the homologous sequences found, one fragment from E. coli B, similar to a piece of Rac prophage, and two fragments from Shigella flexneri were cloned and sequenced. dicF-like elements similar to transcriptional terminators were found in each sequence, but unlike dicF these had no effect on division in E. coli K-12. Like dicF, these sequences are flanked by secondary structures which form potential sites for RNase III recognition. Coding sequences located upstream from the dicF-like feature in E. coli B are related to gene sieB of bacteriophage lambda, while sequences downstream of the S. flexneri elements are similar to the immunity region of satellite bacteriophage P4. Under hybridization conditions in which only strong sequence homologies were detected in E. coli B and S. flexneri, the genomes of a large variety of microorganisms, including some gram-positive bacteria, hybridized to the dicF probe. Our results suggest that dicF and its flanking regions are markers of a widespread family of prophage-like elements of different origins.