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Nucleic Acids Research Advance Access originally published online on November 22, 2007
Nucleic Acids Research 2008 36(3):712-725; doi:10.1093/nar/gkm1051
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Nucleic Acids Research, 2008, Vol. 36, No. 3 712-725
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

RNA

RNA chaperoning and intrinsic disorder in the core proteins of Flaviviridae

Roland Ivanyi-Nagy1, Jean-Pierre Lavergne2, Caroline Gabus1, Damien Ficheux2 and Jean-Luc Darlix1,*

1LaboRetro INSERM #758, Ecole Normale Supérieure de Lyon, IFR 128 Biosciences Lyon-Gerland, 69364 Lyon Cedex 07 and 2Institut de Biologie et Chimie des Protéines, CNRS-UMR 5086, Université Claude Bernard Lyon I, IFR 128 Biosciences Lyon-Gerland, 69367 Lyon Cedex 07, France

*To whom correspondence should be addressed. Tel: +33 4 72 72 81 69; Fax: +33 4 72 72 81 37; Email: jldarlix{at}ens-lyon.fr

Received August 14, 2007. Revised October 8, 2007. Accepted November 6, 2007.

RNA chaperone proteins are essential partners of RNA in living organisms and viruses. They are thought to assist in the correct folding and structural rearrangements of RNA molecules by resolving misfolded RNA species in an ATP-independent manner. RNA chaperoning is probably an entropy-driven process, mediated by the coupled binding and folding of intrinsically disordered protein regions and the kinetically trapped RNA. Previously, we have shown that the core protein of hepatitis C virus (HCV) is a potent RNA chaperone that can drive profound structural modifications of HCV RNA in vitro. We now examined the RNA chaperone activity and the disordered nature of core proteins from different Flaviviridae genera, namely that of HCV, GBV-B (GB virus B), WNV (West Nile virus) and BVDV (bovine viral diarrhoea virus). Despite low-sequence similarities, all four proteins demonstrated general nucleic acid annealing and RNA chaperone activities. Furthermore, heat resistance of core proteins, as well as far-UV circular dichroism spectroscopy suggested that a well-defined 3D protein structure is not necessary for core-induced RNA structural rearrangements. These data provide evidence that RNA chaperoning—possibly mediated by intrinsically disordered protein segments—is conserved in Flaviviridae core proteins. Thus, besides nucleocapsid formation, core proteins may function in RNA structural rearrangements taking place during virus replication.


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