Bacterial nucleoid protein Dps binds structured RNA molecules
Bykov A.A., Shavkunov K.S., Panyukov V.V., Ozoline O.N.
Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow region, Russia
Pushchino State Institute of Natural Sciences, Pushchino, Moscow region, Russia
Pushchino Scientific Center of Russian Academy of Sciences, Pushchino, Moscow region, Russia
Institute of Mathematical Problems of Biology - the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Pushchino, Moscow region, Russia
Abstract. Architectural protein Dps of the bacterial nucleoid employs side groups of lysines 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 studying the ability of purified Dps immobilized on acrylate spheres to bind with short RNAs isolated from bacterial cells. It appeared that transport and small regulatory RNAs forming stable secondary structures are preferential 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, products 9-13 nucleotides long belonging to small untranslated RNAs SdsR and RyeA and transcribed from both strands of the same locus were registered. Since the number of longer transcripts from this region was at least five-fold lower, it can be presumed that two counter-synthesized products form a partly complementary duplex subjected to 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.
Key words: Dps, Dps-RNA complexes, pull-down assay, RNA-seq.