Rep-elements of the Escherichia coli genome and transcription signals: positional and functional analysis

In the intergenic regions of the Escherichia coli genome there are 356 REP-elements, containing 1-12 repeated sequences with degenerated consensus. Their biological role is poorly understood, but multiplicity in the genome, preferential localization between convergent genes and ability to form hairpin structures have led to the assumption that REP-elements participate in the transcription termination and processes affecting stability of the corresponding RNAs. Though the direct experiments did not confirm the ability of the model REP-sequence to stop RNA synthesis leaving some ambiguity regarding their primary function. In this study, positional and functional analysis was undertaken for the entire set of annotated REP-sequences and the reduced efficiency of RNA synthesis behind the many REP-modules was observed. However, some REP-modules had no effect on the transcription processivity, assuming the inclusion of REP-sequences into RNA and the possibility of their regulatory action. We also observed REP-associated transcription activation and found overlapping promoters. The most unexpected was specific distribution of REP-sequences nearby promoter islands, which indicates their insulator-like action maintaining functional autonomy of the “islands” and assumes functional significance of “island”-born RNAs.