Bacterial nucleoid protein Dps binds structured RNA molecules

Architectural protein Dps of bacterial nucleoid employs side lysine groups at its N-terminal modules for interacting with the sugar-phosphate backbone of the DNA. Electrostatic nature of interaction assumes the potential ability of Dps to bind with any nucleotide sequence, including RNA. The available data also indicate that Dps exhibits enhanced affinity to branched DNA structures. In RNA molecules such structures are formed more frequently than in DNA. Hence, the aim of this investigation was to study the ability of purified Dps immobilized on acrylate spheres to bind short RNAs isolated from bacterial cells. It appeared that transport and small regulatory RNAs forming stable secondary structures are the preferred targets for such interaction. Among RNAs identified in complexes with Dps 8 transcripts corresponded to intergenic spaces, which might indicate the presence of novel genes. Moreover, 9–13 nucleotide long products, belonging to small untranslated RNAs SdsR and RyeA and transcribed from both strands of the same locus, were registered. Since the amount of longer transcripts from this region was at least five-fold lower, it can be presumed that pairs of counter-synthesized products form partly complementary duplexes subjected to the controlled processing. The selectivity of Dps to these molecules, as well as to other structured RNAs, indicates a possibility of its involvement not only in bacterial genome condensation, but also in maintaining the functional state of the transcriptome.