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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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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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Acknowledgements

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.

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Authors and Affiliations

  1. Department of Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA

    Stanton L. Martin, Richard H. Guenther, Tim L. Sit & Steven A. Lommel

  2. Center for Structural Molecular Biology and Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA

    Lilin He & William T. Heller

  3. Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA

    Lilin He, Flora Meilleur & William T. Heller

  4. Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA

    Flora Meilleur

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  1. Stanton L. Martin
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Correspondence to William T. Heller.

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S. L. Martin and L. He contributed equally to this work.

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Martin, S.L., He, L., Meilleur, F. et al. 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. Arch Virol 158, 1661–1669 (2013). https://doi.org/10.1007/s00705-013-1650-6

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