Research
Comparison between the HCV IRES domain IV RNA structure and the Iron Responsive Element
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* Corresponding author: William B Lott b.lott@qut.edu.au
1 Molecular Biology Program, New Mexico State University, Las Cruces, NM 88003-8001, USA
2 Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM 88003-8001, USA
3 Institute for Health and Biomedical Innovation, School of Life Sciences, Queensland University of Technology, Brisbane, QLD 4001, Australia
Journal of Negative Results in BioMedicine 2009, 8:4 doi:10.1186/1477-5751-8-4
Published: 18 February 2009Abstract
Background
Serum ferritin and hepatic iron concentrations are frequently elevated in patients who are chronically infected with the hepatitis C virus (HCV), and hepatic iron concentration has been used to predict response to interferon therapy, but these correlations are not well understood. The HCV genome contains an RNA structure resembling an iron responsive element (IRE) in its internal ribosome entry site (IRES) structural domain IV (dIV). An IRE is a stem loop structure used to control the expression of eukaryotic proteins involved in iron homeostasis by either inhibiting ribosomal binding or protecting the mRNA from nuclease degradation. The HCV structure, located within the binding site of the 40S ribosomal subunit, might function as an authentic IRE or by an IRE-like mechanism.
Results
Electrophoretic mobility shift assays showed that the HCV IRES domain IV structure does not interact with the iron regulatory protein 1 (IRP1) in vitro. Systematic HCV IRES RNA mutagenesis suggested that IRP1 cannot accommodate the shape of the wild type HCV IRES dIV RNA structure.
Conclusion
The HCV IRES dIV RNA structure is not an authentic IRE. The possibility that this RNA structure is responsible for the observed correlations between intracellular iron concentration and HCV infection parameters through an IRE-like mechanism in response to some other cellular signal remains to be tested.