Short repeated palindromes in enterobacteria

Bacterial Interspersed Mosaic Elements (BIMEs)

BIMEs are protein binding sites

There is no global function known for BIMEs, although some of them have been shown to act as bidirectional transcription terminators (Gilson et al. 1986a) or mRNA stabilisators (Newbury et al. 1987a, Newbury et al. 1987b, Stern et al. 1988). Several proteins have been shown to specifically interact with BIME motifs. The DNA Polymerase I (Pol I) has been shown to specifically interact with PU sequences (in a BIME-2 structure) in vitro (Gilson et al. 1986b, Gilson et al. 1990). This interaction has never been tested in vivo, and it is not known whether Pol I can also interact with PUs in other BIME structures. The interaction of DNA gyrase with BIME-2 DNA at PU sequences has been shown both in vitro (Yang and Ames, 1988) and in vivo (Espéli and Boccard, 1997).
The Integration Host Factor (IHF) is the third protein known to interact with BIMEs. IHF-binding sites are found in the L motif, which is part of BIME-1 and of some atypical BIMEs. BIMEs containing IHF binding sites are referred to as Reiterative IHF BIME (RIB, Boccard and Prentki, 1993) or Repetitive IHF-binding Palindromic (RIP, Oppenheim et al. 1993) elements. IHF has been shown to interact both in vitro and in vivo with RIBs (Engelhorn et al. 1995).

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