Mixed promoter islands as genomic regions with specific structural and functional properties

The study is aimed at unusual genomic regions of E. coli — mixed promoter islands, which possess high density of potential transcription initiation points. They were predicted by promoter finder PlatPromU, without the consideration of conservative elements, recognized by $\sigma$-subunits of RNA polymerase, thus they are supposed to interact with polymerase, which has different $\sigma$-factors. We found that the structural and functional properties of mixed promoter islands are very similar to those of promoter islands, previously revealed by the algorithm PlatProm, which was adjusted to the search for $\sigma^{70}$-specific promoters of E. coli. Thus, both types of islands are preferentially located in the regulatory regions of genes acquired by horizontal transfer. Their double helix is characterized by a higher degree of curvature and twisting, compared to normal promoters. Both types of islands have a higher capacity to form complexes with RNAP, than normal promoters, but lower ability to initiate productive transcription. This suppression can be largely explained by the advanced ability of islands to interact with the histone-like inhibitory protein H-NS. However, RNA synthesis from the promoter island associated with the gene appY, increased upon its transfer into the plasmid pET28b-eGFP and showed dependence not only from the presence of H-NS binding sites, but also from the spatial configuration of the neighboring areas. That means that conformational changes in the genome can increase the transcriptional activity from the islands, delivering the products of adjacent genes for metabolic needs of the bacterial cell.