INTEGRATION HOST FACTOR BINDS TO A UNIQUE CLASS OF COMPLEX REPETITIVEEXTRAGENIC DNA-SEQUENCES IN ESCHERICHIA-COLI

Interspersed repeated DNA sequences are characteristic features of bot h prokaryotic and eukaryotic genomes. REP sequences are defined as con served repetitive extragenic palindromic sequences and are found in Es cherichia coli, Salmonella typhimurium and other closely related enter ic bacteria. These REP sequences may participate in the folding of the bacterial chromosome. In this work we describe a unique class of 28 c onserved complex REP clusters, about 100 bp long, in which two inverte d REPs are separated by a singular integration host factor (IHF) recog nition sequence. We term these sequences RIP (for repetitive IHF-bindi ng palindromic) elements and demonstrate that IHF binds to them specif ically. It is estimated that there are about 70 RIP elements in E. col i. Our analysis shows that the RIP elements are evenly distributed aro und the bacterial chromosome. The possible function of the RIP element is discussed.