Promoter islandsas a platform for interaction with nucleoid proteins and transcription factors

Abstract

Seventy-eight promoter islands with an extraordinarily high density of potential promoters have been recently found in the genome of Escherichia coli. It has been shown that RNA polymerase binds internal promoters of these islands and produces short oligonucleotides, while the synthesis of normal mRNAs is suppressed. This quenching may be biologically relevant, as most islands are associated with foreign genes, which expression may deplete cellular resources. However, a molecular mechanism of silencing with the participation of these promoter-rich regions remains obscure. It has been demonstrated that all islands interact with histone-like protein H-NS--a specific sentinel of foreign genes. In this study, we demonstrated the inhibitory effect of H-NS using Δhns mutant of Escherichia coli and showed that deletion of dps, encoding another protein of bacterial nucleoid, tended to decrease rather than increase the amount of island-specific transcripts. This observation precluded consideration of promoter islands as sites for targeted heterochromatization only and a computer search for the binding sites of 53 transcription factors (TFs) revealed six proteins, which may specifically regulate their transcriptional output.

Genomic Looping: A Key Principle of Chromatin Organization

“…Binding sites determined by DNA footprint assays for FIS and IHF are indicated by boxes along the linear chromosome, whereas binding regions detected by ChIP-seq [Kahramanoglou et al, 2011;Prieto et al, 2012] are indicated by bars parallel to the chromosome. sites of spurious transcription (arising from weak promoters) of noncoding and antisense RNAs or due to inefficient Rho-dependent termination [Peters et al, 2012;Purtov et al, 2014;Saxena and Gowrishankar, 2011;Singh and Grainger, 2013]. In agreement with the proposed effect of pausing on transcript elongation, H-NS contributes to the suppression of antisense transcription by binding close to intragenic Rho-binding sites and facilitating Rho termination [Peters et al, 2012].…”

Visualizing the activity of Escherichia coli divergent promoters and probing their dependence on superhelical density using dual-colour fluorescent reporter vector

“…Which ones of numerous potential start points are utilized by RNA polymerase in the “island” and how efficiently different promoters of the “island” initiate productive and abortive RNA synthesis may depend on conditions. Transcription within “island” is often blocked by H-NS at the step of short oligonucleotide synthesis121323. These short RNAs are produced from multiple promoters and the excess of such products can mask functional promoter integrated into regulatory networks of the cell.…”

“…Particular importance in this regard may have areas with unusually high density of potential promoters (“promoter islands”). Seventy-eight such “islands” were recently found10 and partly characterized1213 in the genome of E.coli . Topological drift in these regions in response to multiple functional interactions with proteins of transcription machinery is expected with the highest probability.…”

REP-elements of the Escherichia coli Genome and Transcription Signals: Positional and Functional Analysis

“…4. Низкая продуктивность островков предполагает наличие специальных механизмов, подавляющих способность их промоторов инициировать транскрипцию. Некоторые из этих механизмов уже установлены (избыточная позитивная суперскрученность двойной спирали [14,23] и способность связываться с гистон-подобным белком бактериального нуклеоида H-NS [24]). Однако причастность REP-элементов к терминации транскрипции (рис.…”