Bulged residues promote the progression of a looploop interaction to a stable and inhibitory antisensetarget RNA complex
Authors: Wagner E.G.H.; Kolb F.A.; Westhof E.; Ehresmann C.; Ehresmann B.; Romby P.
Source: Nucleic Acids Research, Volume 29, Number 15, 1 August 2001 , pp. 3145-3153(9)
Publisher: Oxford University Press
Abstract:In several groups of bacterial plasmids, antisense RNAs regulate copy number through inhibition of replication initiator protein synthesis. These RNAs are characterized by a long hairpin structure interrupted by several unpaired residues or bulged loops. In plasmid R1, the inhibitory complex between the antisense RNA (CopA) and its target mRNA (CopT) is characterized by a four-way junction structure and a side-by-side helical alignment. This topology facilitates the formation of a stabilizer intermolecular helix between distal regions of both RNAs, essential for in vivo control. The bulged residues in CopA/CopT were shown to be required for high in vitro binding rate and in vivo activity. This study addresses the question of why removal of bulged nucleotides blocks stable complex formation. Structure mapping, modification interference, and molecular modeling of bulged-less mutant CopACopT complexes suggests that, subsequent to looploop contact, helix propagation is prevented. Instead, a fully base paired looploop interaction is formed, inducing a continuous stacking of three helices. Consequently, the stabilizer helix cannot be formed, and stable complex formation is blocked. In contrast to the four-way junction topology, the looploop interaction alone failed to prevent ribosome binding at its loading site and, thus, inhibition of RepA translation was alleviated.
Document Type: Original article
Publication date: 2001-08-01
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