BACTERIAL INTERSPERSED MOSAIC ELEMENTS (BIMES) ARE A MAJOR SOURCE OF SEQUENCE POLYMORPHISM IN ESCHERICHIA-COLI INTERGENIC REGIONS INCLUDINGSPECIFIC ASSOCIATIONS WITH A NEW INSERTION-SEQUENCE

A significant fraction of Escherichia coli intergenic DNA sequences is composed of two families of repeated bacterial interspersed mosaic el ements (BIME-1 and BIME-2). In this study, we determined the sequence organization of six intergenic regions in 51 E. coli and Shigella natu ral isolates. Each region contains a BIME in E. coli K-12. We found th at multiple sequence variations are located within or near these BIMEs in the different bacteria. Events included excisions of a whole BIME- 1, expansion/deletion within a BIME-2 and insertions of non-BIME seque nces like the boxC repeat or a new IS element, named IS1397. Remarkabl y, 14 out of 14 IS1397 integration sites correspond to a BIME sequence , strongly suggesting that this IS element is specifically associated with BIMEs, and thus inserts only in extragenic regions. Unlike BIMEs, IS1397 is not detected in all E. coli isolates. Possible relationship s between the presence of this IS element and the evolution of BIMEs a re discussed.