Probing the functional motifs of Escherichia coli 5S rRNA in relation to 16S rRNA using a SELEX experiment

Abstract

The function of 5S rRNA, a constituent of a large subunit of ribosome, is not dearly known yet. To identify RNA motifs interacting with 5S rRNA, and thereby to get an insight into the function of 5S rRNA in the ribosome, a SELEX (Systematic Evolution of Ligands by Exponential Enrichment) experiment was performed. RNA molecules binding to Escherichia coli 5S rRNA were selected from a 48-mer random sequence library through 12 rounds of selection, cloned, and sequenced. Two groups of the selected RNA molecules had the consensus sequences GCGG and GUGAAA, respectively, which are present in the segment, G(688) through A(696), of E. coli 16S rRNA. The gel mobility shift assay showed that 5S rRNA interacted with the 16S rRNA fragment containing the GCGG and GUGAAA sequences. The enzymatic protection experiment shows that the A(29)CCUGA(34) and G(51)AAGUG(56) sequences of 5S rRNA and the C(680)AGG(683) and G(688)CGG(691) sequences of the 16S rRNA fragment are involved in the interaction between the two RNA molecules. On the basis of this observation, we suggest that 5S rRNA and 16S rRNA play a role for the association of two ribosomal subunits.