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Bulged residues promote the progression of a loop–loop interaction to a stable and inhibitory antisense–target 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 CopA–CopT complexes suggests that, subsequent to loop–loop contact, helix propagation is prevented. Instead, a fully base paired loop–loop 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 loop–loop interaction alone failed to prevent ribosome binding at its loading site and, thus, inhibition of RepA translation was alleviated.Document Type: Original article
Affiliations: 1: Institute of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, Husargatan 3, S-75124 Uppsala, Sweden
Publication date: 2001-08-01
- Nucleic Acids Research (NAR) is a fully Open Access journal, providing rapid publication of leading edge research into the nucleic acids under the following categories: chemistry, computational biology, genomics, molecular biology, nucleic acid enzymes, RNA and structural biology. There is a Survey and Summary section, and methods papers are published
in NAR Methods Online. Each year the first issue is devoted to biological databases, and a later issue to relevant web-based software resources.
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- In this Subject: Anatomy & Physiology
- By this author: Wagner E.G.H. ; Kolb F.A. ; Westhof E. ; Ehresmann C. ; Ehresmann B. ; Romby P.
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