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Four-way junctions in antisense RNA-mRNA complexes involved in plasmid replication control: a common theme?
F A Kolb1, E Westhof, B Ehresmann
1UPR 9002 du CNRS, Institut de Biologie Moléculaire et Cellulaire, 15 Rue R. Descartes, Strasbourg Cedex, F-67084, France.
Journal of Molecular Biology
|June 9, 2001
Summary
Antisense RNAs regulate bacterial plasmid copy number by inhibiting protein synthesis. Similar structural features, including a four-way junction, are found in complexes of antisense RNA and target mRNA across different plasmids, ensuring efficient control.
Area of Science:
- Molecular Biology
- Bacterial Genetics
- RNA Structure and Function
Background:
- Antisense RNAs are crucial regulators of bacterial plasmid copy number.
- They function by inhibiting the synthesis of replication initiator proteins.
Purpose of the Study:
- To investigate the structural similarities of antisense RNA-target mRNA complexes in different bacterial plasmids.
- To understand the conserved mechanisms of RNA-based gene regulation in plasmids.
Main Methods:
- Lead-induced cleavage assays to map RNA structures.
- Ribonuclease (RNase) V(1) probing to identify double-stranded regions.
- Molecular modeling to visualize complex topology.
Main Results:
- The inhibitory complex between antisense RNA (CopA) and target mRNA (CopT) in plasmid R1 forms a four-way junction with side-by-side helical alignment.
- A similar topology, including the four-way junction and ion-binding sites, was observed for the Inc/RepZ complex in plasmid Col1b-P9.
- Conserved structural features and binding pathways were identified across multiple plasmid systems.
Conclusions:
- Bacterial plasmids utilize conserved structural features in antisense and target RNAs for efficient copy number control.
- The identified four-way junction and binding sites are key to the inhibitory mechanism.
- These findings provide insights into the general principles of antisense RNA-mediated gene regulation in bacteria.