New insight into the structure of RNA in red clover necrotic mosaic virus and the role of divalent cations revealed by small-angle neutron scattering

Stanton L. Martin; Lilin He; Flora Meilleur; Richard H. Guenther; Tim L. Sit; Steven A. Lommel; William T. Heller

doi:10.1007/s00705-013-1650-6

New insight into the structure of RNA in red clover necrotic mosaic virus and the role of divalent cations revealed by small-angle neutron scattering

Stanton L. Martin, Lilin He, Flora Meilleur, Richard H. Guenther, Tim L. Sit, Steven A. Lommel, William T. Heller

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Abstract

Red clover necrotic mosaic virus (RCNMV) is a 36-nm-diameter, T = 3 icosahedral plant virus with a genome that is split between two single-stranded RNA molecules of approximately 3.9 kb and 1.5 kb, as well as a 400-nucleotide degradation product. The structure of the virus capsid and its response to removing Ca²⁺ and Mg²⁺ was previously studied by cryo-electron microscopy (cryo-EM) (Sherman et al. J Virol 80:10395-10406, 2006) but the structure of the RNA was only partially resolved in that study. To better understand the organization of the RNA and conformational changes resulting from the removal of divalent cations, small-angle neutron scattering with contrast variation experiments were performed. The results expand upon the cryo-EM results by clearly showing that virtually all of the RNA is contained in a thin shell that is in contact with the interior domains of the viral capsid protein, and they provide new insight into changes in the RNA packing that result from removal of divalent cations.

Original language	English
Pages (from-to)	1661-1669
Number of pages	9
Journal	Archives of Virology
Volume	158
Issue number	8
DOIs	https://doi.org/10.1007/s00705-013-1650-6
State	Published - Aug 2013

Funding

This research was supported by the Laboratory Directed Research and Development Program of Oak Ridge National Laboratory (ORNL). The research at ORNL’s Center for Structural Molecular Biology (FWP ERKP291) was supported by the U.S. Department of Energy’s Office of Biological and Environmental Research. Work at HFIR was sponsored by the Scientific User Facilities Division, Office of Basic Energy Sciences, U.S. Department of Energy. Oak Ridge National Laboratory is managed by UT-Battelle, LLC for the U.S. Department of Energy under contract No. DO-AC05-00OR22725. This manuscript has been authored by UT-Battelle, LLC, under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains, and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes.

Funders	Funder number
Scientific User Facilities Division
U.S. Department of Energy
Basic Energy Sciences	DE-AC05-00OR22725
Biological and Environmental Research
Oak Ridge National Laboratory

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title = "New insight into the structure of RNA in red clover necrotic mosaic virus and the role of divalent cations revealed by small-angle neutron scattering",

abstract = "Red clover necrotic mosaic virus (RCNMV) is a 36-nm-diameter, T = 3 icosahedral plant virus with a genome that is split between two single-stranded RNA molecules of approximately 3.9 kb and 1.5 kb, as well as a 400-nucleotide degradation product. The structure of the virus capsid and its response to removing Ca2+ and Mg2+ was previously studied by cryo-electron microscopy (cryo-EM) (Sherman et al. J Virol 80:10395-10406, 2006) but the structure of the RNA was only partially resolved in that study. To better understand the organization of the RNA and conformational changes resulting from the removal of divalent cations, small-angle neutron scattering with contrast variation experiments were performed. The results expand upon the cryo-EM results by clearly showing that virtually all of the RNA is contained in a thin shell that is in contact with the interior domains of the viral capsid protein, and they provide new insight into changes in the RNA packing that result from removal of divalent cations.",

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AU - He, Lilin

AU - Meilleur, Flora

AU - Guenther, Richard H.

AU - Sit, Tim L.

AU - Lommel, Steven A.

AU - Heller, William T.

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AB - Red clover necrotic mosaic virus (RCNMV) is a 36-nm-diameter, T = 3 icosahedral plant virus with a genome that is split between two single-stranded RNA molecules of approximately 3.9 kb and 1.5 kb, as well as a 400-nucleotide degradation product. The structure of the virus capsid and its response to removing Ca2+ and Mg2+ was previously studied by cryo-electron microscopy (cryo-EM) (Sherman et al. J Virol 80:10395-10406, 2006) but the structure of the RNA was only partially resolved in that study. To better understand the organization of the RNA and conformational changes resulting from the removal of divalent cations, small-angle neutron scattering with contrast variation experiments were performed. The results expand upon the cryo-EM results by clearly showing that virtually all of the RNA is contained in a thin shell that is in contact with the interior domains of the viral capsid protein, and they provide new insight into changes in the RNA packing that result from removal of divalent cations.

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New insight into the structure of RNA in red clover necrotic mosaic virus and the role of divalent cations revealed by small-angle neutron scattering

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