Promoter Islands in the Genome of E. coli: Comparative Analysis against AT-Rich Sequences
Glazunova O.A., Kiselev S.S., Shavkunov K.S., Bykov A.A., Panyukov V.V., Ozoline O.N.
Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow region, 142290, Russia
Pushchino State Institute of Natural Sciences, Pushchino, Moscow region, 142290, Russia
Nizhny Novgorod State University, Biological Faculty, Nizhny Novgorod, 603950, Russia
Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow region, 142290, Russia
Abstract. The functional properties of E. coli genome promoter islands, which are special regions with abnormally high contents of transcription signals, are compared to those of genomic areas, which are unusually rich in A/T-pairs. It was shown that computational sets of regions for both types partially overlap by certain criteria, while their functional properties are much alike. 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 dimer or tetramer forms of regulatory proteins, it can be assumed that transcription initiation from island-embedded promoters is under control of the regulatory network of cells. Thus, the resulting RNA products might 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.
Key words: promoter islands, AT-rich genomic regions, abortive synthesis, untranslated RNA, horizontal gene transfer.