The Escherichia coli ribosomal RNA leader nut region interacts specifically with mature 16S RNA.

All ribosomal RNAs are preceded by leader sequences not present in the final ribosome particles. The highly conserved leader sequences of bacterial rRNAs are known to be important for the folding and assembly of functional ribosomes. Very likely transient binding of the leader to mature parts of the 16S RNA occurs during transcription. To better understand the mechanistic details of these functions we have performed a secondary structural analysis of E. coli ribosomal RNA leader transcripts by chemical modification and enzymatic hydrolysis studies. The data were combined with results from thermodynamic stability calculations to yield a generalized structural model. The same secondary structure of the leader core, comprising the nut-like sequences up to the mature 5' end of the 16S RNA, was deduced, irrespective if transcripts started at promoter P1 or 120 nucleotides downstream at P2. Employing gelshift and cross-linking studies we were able to demonstrate that a part of the leader core, namely the nut-like sequence elements bind directly to specific regions within the mature 16S RNA. The sites of RNA-RNA cross-linking could be localized by sequencing. They map in the 16S RNA 5' domain at nucleotide positions G27 to G42, C48, G68, G117 and G126. The results may explain the recently observed scaffolding function of the leader RNA during ribosome biogenesis.