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Journal of Virology, September 2008, p. 9008-9022, Vol. 82, No. 18
0022-538X/08/$08.00+0     doi:10.1128/JVI.02326-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

A Hepatitis C Virus cis-Acting Replication Element Forms a Long-Range RNA-RNA Interaction with Upstream RNA Sequences in NS5B {triangledown} ,{dagger}

Sinéad Diviney,1 Andrew Tuplin,1 Madeleine Struthers,1 Victoria Armstrong,2 Richard M. Elliott,2 Peter Simmonds,3 and David J. Evans1*

Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom,1 Department of Biomolecular Sciences, University of St. Andrews, Fife KY16 9ST, United Kingdom,2 Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, United Kingdom3

Received 26 October 2007/ Accepted 2 July 2008

The genome of hepatitis C virus (HCV) contains cis-acting replication elements (CREs) comprised of RNA stem-loop structures located in both the 5' and 3' noncoding regions (5' and 3' NCRs) and in the NS5B coding sequence. Through the application of several algorithmically independent bioinformatic methods to detect phylogenetically conserved, thermodynamically favored RNA secondary structures, we demonstrate a long-range interaction between sequences in the previously described CRE (5BSL3.2, now SL9266) with a previously predicted unpaired sequence located 3' to SL9033, approximately 200 nucleotides upstream. Extensive reverse genetic analysis both supports this prediction and demonstrates a functional requirement in genome replication. By mutagenesis of the Con-1 replicon, we show that disruption of this alternative pairing inhibited replication, a phenotype that could be restored to wild-type levels through the introduction of compensating mutations in the upstream region. Substitution of the CRE with the analogous region of different genotypes of HCV produced replicons with phenotypes consistent with the hypothesis that both local and long-range interactions are critical for a fundamental aspect of genome replication. This report further extends the known interactions of the SL9266 CRE, which has also been shown to form a "kissing loop" interaction with the 3' NCR (P. Friebe, J. Boudet, J. P. Simorre, and R. Bartenschlager, J. Virol. 79:380-392, 2005), and suggests that cooperative long-range binding with both 5' and 3' sequences stabilizes the CRE at the core of a complex pseudoknot. Alternatively, if the long-range interactions were mutually exclusive, the SL9266 CRE may function as a molecular switch controlling a critical aspect of HCV genome replication.

* Corresponding author. Mailing address: Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom. Phone: 44 24765 74183. Fax: 44 24765 23701. E-mail: d.j.evans{at}warwick.ac.uk

{triangledown} Published ahead of print on 9 July 2008.

{dagger} Supplemental material for this article may be found at http://jvi.asm.org/.

Journal of Virology, September 2008, p. 9008-9022, Vol. 82, No. 18
0022-538X/08/$08.00+0     doi:10.1128/JVI.02326-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.



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