Nucleic Acids Research, Vol 27, Issue 22 4353-4362, Copyright © 1999 by Oxford University Press
W Besancon and R Wagner
The co-transcribed leader sequences of bacterial rRNA are known to affect
the structure and function of the small ribosomal subunits. Base changes in
the leader nut -like sequence elements have been shown to cause misfolded
but correctly processed 16S rRNA structures at low growth temperature.
Transient interactions of leader sequences with the nascent 16S rRNA are
considered to guide rRNA folding and to facilitate correct structure
formation. In order to understand this chaperone-like activity of the
leader RNA we have analyzed the thermodynamic stabilities of wild-type and
mutant leader transcripts. We show here that base changes cause subtle
differences in the melting profiles of the corresponding leader
transcripts. Furthermore, we show that direct interaction between leader
transcripts and the 16S rRNA is limited to the 5'-domain of the 16S rRNA
for both wild-type and mutant leaders. Binding studies of mutant and
wild-type leader transcripts to 16S rRNA revealed small changes in the
affinities and the thermal stabilities as a consequence of the base
changes. Different complex stabilities as a function of the Mg(2+) ion
concentration indicated that mutant and wild- type leader transcripts
interact differently with the 16S rRNA, consistent with a less stable and
tightly folded structure of the mutant leader. Employing time-resolved
oligonucleotide hybridization assays we could show different folding
kinetics for 16S rRNA molecules when linked to wild-type leader, mutant
leader or in the absence of leader RNA. The studies help to understand how
bacterial rRNA leader transcripts may affect the folding of the small
subunit rRNA.
ARTICLES
Characterization of transient RNA-RNA interactions important for the facilitated structure formation of bacterial ribosomal 16S RNA
Institut fur Physikalische Biologie, Heinrich-Heine-Universitat Dusseldorf, Universitatsstrasse 1, D-40225 Dusseldorf, Germany.
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