Analysis of natural variants of the hepatitis C virus internal ribosome entry site reveals that primary sequence plays a key role in cap-independent translation

Barría MI; González A; Vera-Otarola, J; León U; Vollrath, V; Marsac D.; Monasterio O.; Perez-Acle, T; Soza A.; Lopez-Lastra, M

Abstract

The HCV internal ribosome entry site (IRES) spans a region of ~340 nt that encompasses most of the 5' untranslated region (5'UTR) of the viral mRNA and the first 24-40 nt of the core-coding region. To investigate the implication of altering the primary sequence of the 5'UTR on IRES activity, naturally occurring variants of the 5'UTR were isolated from clinical samples and analyzed. The impact of the identified mutations on translation was evaluated in the context of RLuc/FLuc bicistronic RNAs. Results show that depending on their location within the RNA structure, these naturally occurring mutations cause a range of effects on IRES activity. However, mutations within subdomain IIId hinder HCV IRES-mediated translation. In an attempt to explain these data, the dynamic behavior of the subdomain IIId was analyzed by means of molecular dynamics (MD) simulations. Despite the loss of function, MD simulations predicted that mutant G266A/G268U possesses a structure similar to the wt-RNA. This prediction was validated by analyzing the secondary structure of the isolated IIId RNAs by circular dichroism spectroscopy in the presence or absence of Mg 2+ ions. These data strongly suggest that the primary sequence of subdomain IIId plays a key role in HCV IRES-mediated translation. © 2008 The Author(s).

Más información

Título según WOS: Analysis of natural variants of the hepatitis C virus internal ribosome entry site reveals that primary sequence plays a key role in cap-independent translation
Título según SCOPUS: Analysis of natural variants of the hepatitis C virus internal ribosome entry site reveals that primary sequence plays a key role in cap-independent translation
Título de la Revista: NUCLEIC ACIDS RESEARCH
Volumen: 37
Número: 3
Editorial: OXFORD UNIV PRESS
Fecha de publicación: 2009
Página de inicio: 957
Página final: 971
Idioma: English
URL: http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkn1022
DOI:

10.1093/nar/gkn1022

Notas: ISI, SCOPUS