Promoter islands in the genome of E. coli: comparative analysis against AT-rich sequences

The functional properties of E. coli genome promoter islands (PIs), i.e. regions with abnormally high contents of transcription signals, were compared to those of genomic areas, abnormally enriched with A/T-pairs. It was found that two representative sets of these regions partially overlap, and their functional properties are similar in many parameters. At the same time, promoter islands are characterized by a higher potential for synthesis of short oligonucleotides, as compared to AT-rich sequences. Such RNAs may be the target products of these unusual sites or byproducts of their suppressed state. The islands are richer in inverted repeats than AT-rich regions, and much richer compared with regular promoters. Considering that such structural elements commonly serve as targets for interactions with dimers or tetramers of regulatory proteins, it can be assumed that transcription initiation from island-embedded promoters is under the control of cell regulatory networks. The resulting RNA products might, therefore, be required for normal cell functioning. This idea is also supported by experimentally confirmed high yield of oligonucleotide product from the island promoter inside the yjgL gene.