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Structural lability in stem-loop 1 drives a 5' UTR-3' UTR interaction in coronavirus replication
Lichun Li1, Hyojeung Kang, Pinghua Liu
1Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA.
Journal of Molecular Biology
|February 22, 2008
Summary
Coronaviruses utilize a dynamic leader RNA structure (SL1) in their 5' untranslated region (UTR) for subgenomic RNA synthesis. This structure
Area of Science:
- Virology
- Molecular Biology
- RNA Structure
Background:
- Coronaviruses possess a leader RNA in the 5' untranslated region (UTR) with two stem-loop structures, SL1 and SL2.
- The structural and functional roles of these elements in viral replication are not fully understood.
Purpose of the Study:
- To investigate the functional and structural properties of the SL1 stem-loop in the 5' UTR of coronaviral genomes.
- To elucidate the role of SL1 lability in mediating interactions essential for subgenomic RNA synthesis.
Main Methods:
- Genetic selection experiments to identify compensatory mutations.
- Thermal denaturation and imino proton solvent exchange to assess RNA stability.
- Analysis of viral genomes for conserved structural features.
Main Results:
- SL1 is functionally and structurally bipartite, with the upper region requiring base pairing.
- A deletion of nucleotide A35 destabilizes SL1, leading to selection for second-site mutations that restore stability.
- These compensatory mutations in SL1 are associated with specific mutations in the 3' UTR.
- The lower half of SL1 exhibits instability, crucial for interaction with the 3' UTR.
Conclusions:
- A "dynamic SL1" model is proposed, where optimized lability at the base of SL1 facilitates 5'-3' UTR interaction.
- This interaction is critical for stimulating subgenomic RNA synthesis.
- General structural characteristics of SL1, rather than sequence, appear conserved across coronaviruses.
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