Bacterium Aggregatibacter actinomycetemcomitans is the major cause of localized aggressive periodontitis (LAP). This disease causes rapid destruction of the dental tissue and occurs early in life. The RNA-protein interaction plays a key role in the proteins synthesis, which directs processes in cells. The bioinformatics analysis previously indicated that certain A. actinomycetemcomitans synthesized proteins may interact with RNA molecules of the eukaryotic host. Our goal was to analyze the interaction of the proteins DnaK, HU, YjgF and Pnp with the eukaryotic RNA molecules. These proteins were identified in the outer membrane vesicles released from the bacterium and are putative RNA binding proteins. The recombinant proteins and the RNA molecules were isolated from the human cell lines. The proteins were then immobilized onto the Ni-NTA agarose. Immobilized proteins were afterwards exposed to the isolated RNA and the RNAs bound to proteins were later eluted with elution buffer. The mRNA molecules were converted into cDNA molecules that we tried to identify. The performed affinity isolation of the target RNA molecules proved to be difficult and this methoddid not prove the binding of the selected proteins to the RNA molecules. In the continuation of the study, the binding of the DnaK protein with RNA molecules was analyzed. Measurements of the tryptophan spectrum of DnaK protein, in the presence or in the absence of RNA molecules, indicate that DnaK protein interacts with RNA molecules. According to the data obtained, we assume that binding the RNA molecules to the DnaK protein changes the conformation of the protein in such a way that the triptofan residue is brought to the surface.
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