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A hepatitis C virus cis-acting replication element forms a long-range RNA-RNA interaction with upstream RNA sequences in NS5B

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Diviney, Sinéad, Tuplin, Andrew, Struthers, Madeleine, Armstrong, Victoria, Elliott, Richard M., Simmonds, Peter and Evans, D. J. (David J.). (2008) A hepatitis C virus cis-acting replication element forms a long-range RNA-RNA interaction with upstream RNA sequences in NS5B. Journal of Virology, Vol.82 (No.18). pp. 9008-9022. ISSN 0022-538X

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Official URL: http://dx.doi.org/10.1128/JVI.02326-07

Abstract

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' non-coding regions (NCR), and in the NS5B coding sequence. Through the application of several algorithmically-independent bioinformatic methods to detect phylogenetically-conserved, thermodynamically-favoured 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 (8), and suggests that cooperative long-range binding with both 5' and 3' sequences stabilises the CRE at the core of a complex pseudoknot. Alternatively, if the long-range interactions are mutually exclusive, the SL9266 CRE may function as a molecular switch controlling a critical aspect of HCV genome replication.

Item Type:

Journal Article

Subjects:

Q Science > QR Microbiology

Divisions:

Faculty of Science > Life Sciences (2010- ) > Biological Sciences ( -2010)

Library of Congress Subject Headings (LCSH):

Hepatitis C virus -- Genetics

Journal or Publication Title:

Journal of Virology

Publisher:

American Society for Microbiology

ISSN:

0022-538X

Official Date:

September 2008

Dates:

Date	Event
September 2008	Published

Volume:

Vol.82

Number:

No.18

Page Range:

pp. 9008-9022

Identification Number:

10.1128/JVI.02326-07

Status:

Peer Reviewed

Access rights to Published version:

Open Access

Funder:

Medical Research Council (Great Britain) (MRC), GlaxoSmithKline

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