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Elife. 2017 Sep 18;6. pii: e27453. doi: 10.7554/eLife.27453.

Protein-mediated RNA folding governs sequence-specific interactions between rotavirus genome segments.

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Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom.
Department of Chemistry, Center for NanoScience, Nanosystems Initiative Munich (NIM) and Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilian University of Munich, Munich, Germany.
York Centre for Complex Systems Analysis, University of York, York, United Kingdom.
Department of Mathematics, University of York, York, United Kingdom.
Department of Biology, University of York, York, United Kingdom.


Segmented RNA viruses are ubiquitous pathogens, which include influenza viruses and rotaviruses. A major challenge in understanding their assembly is the combinatorial problem of a non-random selection of a full genomic set of distinct RNAs. This process involves complex RNA-RNA and protein-RNA interactions, which are often obscured by non-specific binding at concentrations approaching in vivo assembly conditions. Here, we present direct experimental evidence of sequence-specific inter-segment interactions between rotavirus RNAs, taking place in a complex RNA- and protein-rich milieu. We show that binding of the rotavirus-encoded non-structural protein NSP2 to viral ssRNAs results in the remodeling of RNA, which is conducive to formation of stable inter-segment contacts. To identify the sites of these interactions, we have developed an RNA-RNA SELEX approach for mapping the sequences involved in inter-segment base-pairing. Our findings elucidate the molecular basis underlying inter-segment interactions in rotaviruses, paving the way for delineating similar RNA-RNA interactions that govern assembly of other segmented RNA viruses.


Fluorescence Cross-Correlation Spectroscopy; RNA folding; RNA-RNA interactions; Rotavirus; Virus assembly; biophysics; infectious disease; microbiology; structural biology; virus

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