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Identification of novel RNA secondary structures within the hepatitis C virus genome reveals a cooperative involvement in genome packaging

The specific packaging of the hepatitis C virus (HCV) genome is hypothesised to be driven by Core-RNA interactions. To identify the regions of the viral genome involved in this process, we used SELEX (systematic evolution of ligands by exponential enrichment) to identify RNA aptamers which bind spec...

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Autores principales: Stewart, H., Bingham, R.J., White, S. J., Dykeman, E. C., Zothner, C., Tuplin, A. K., Stockley, P. G., Twarock, R., Harris, M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4789732/
https://www.ncbi.nlm.nih.gov/pubmed/26972799
http://dx.doi.org/10.1038/srep22952
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author Stewart, H.
Bingham, R.J.
White, S. J.
Dykeman, E. C.
Zothner, C.
Tuplin, A. K.
Stockley, P. G.
Twarock, R.
Harris, M.
author_facet Stewart, H.
Bingham, R.J.
White, S. J.
Dykeman, E. C.
Zothner, C.
Tuplin, A. K.
Stockley, P. G.
Twarock, R.
Harris, M.
author_sort Stewart, H.
collection PubMed
description The specific packaging of the hepatitis C virus (HCV) genome is hypothesised to be driven by Core-RNA interactions. To identify the regions of the viral genome involved in this process, we used SELEX (systematic evolution of ligands by exponential enrichment) to identify RNA aptamers which bind specifically to Core in vitro. Comparison of these aptamers to multiple HCV genomes revealed the presence of a conserved terminal loop motif within short RNA stem-loop structures. We postulated that interactions of these motifs, as well as sub-motifs which were present in HCV genomes at statistically significant levels, with the Core protein may drive virion assembly. We mutated 8 of these predicted motifs within the HCV infectious molecular clone JFH-1, thereby producing a range of mutant viruses predicted to possess altered RNA secondary structures. RNA replication and viral titre were unaltered in viruses possessing only one mutated structure. However, infectivity titres were decreased in viruses possessing a higher number of mutated regions. This work thus identified multiple novel RNA motifs which appear to contribute to genome packaging. We suggest that these structures act as cooperative packaging signals to drive specific RNA encapsidation during HCV assembly.
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spelling pubmed-47897322016-03-16 Identification of novel RNA secondary structures within the hepatitis C virus genome reveals a cooperative involvement in genome packaging Stewart, H. Bingham, R.J. White, S. J. Dykeman, E. C. Zothner, C. Tuplin, A. K. Stockley, P. G. Twarock, R. Harris, M. Sci Rep Article The specific packaging of the hepatitis C virus (HCV) genome is hypothesised to be driven by Core-RNA interactions. To identify the regions of the viral genome involved in this process, we used SELEX (systematic evolution of ligands by exponential enrichment) to identify RNA aptamers which bind specifically to Core in vitro. Comparison of these aptamers to multiple HCV genomes revealed the presence of a conserved terminal loop motif within short RNA stem-loop structures. We postulated that interactions of these motifs, as well as sub-motifs which were present in HCV genomes at statistically significant levels, with the Core protein may drive virion assembly. We mutated 8 of these predicted motifs within the HCV infectious molecular clone JFH-1, thereby producing a range of mutant viruses predicted to possess altered RNA secondary structures. RNA replication and viral titre were unaltered in viruses possessing only one mutated structure. However, infectivity titres were decreased in viruses possessing a higher number of mutated regions. This work thus identified multiple novel RNA motifs which appear to contribute to genome packaging. We suggest that these structures act as cooperative packaging signals to drive specific RNA encapsidation during HCV assembly. Nature Publishing Group 2016-03-14 /pmc/articles/PMC4789732/ /pubmed/26972799 http://dx.doi.org/10.1038/srep22952 Text en Copyright © 2016, Macmillan Publishers Limited http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Article
Stewart, H.
Bingham, R.J.
White, S. J.
Dykeman, E. C.
Zothner, C.
Tuplin, A. K.
Stockley, P. G.
Twarock, R.
Harris, M.
Identification of novel RNA secondary structures within the hepatitis C virus genome reveals a cooperative involvement in genome packaging
title Identification of novel RNA secondary structures within the hepatitis C virus genome reveals a cooperative involvement in genome packaging
title_full Identification of novel RNA secondary structures within the hepatitis C virus genome reveals a cooperative involvement in genome packaging
title_fullStr Identification of novel RNA secondary structures within the hepatitis C virus genome reveals a cooperative involvement in genome packaging
title_full_unstemmed Identification of novel RNA secondary structures within the hepatitis C virus genome reveals a cooperative involvement in genome packaging
title_short Identification of novel RNA secondary structures within the hepatitis C virus genome reveals a cooperative involvement in genome packaging
title_sort identification of novel rna secondary structures within the hepatitis c virus genome reveals a cooperative involvement in genome packaging
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4789732/
https://www.ncbi.nlm.nih.gov/pubmed/26972799
http://dx.doi.org/10.1038/srep22952
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