Principles of RNA recruitment to viral ribonucleoprotein condensates in a segmented dsRNA virus

  1. Sebastian Strauss
  2. Julia Acker
  3. Guido Papa
  4. Daniel Desiró
  5. Florian Schueder
  6. Alexander Borodavka  Is a corresponding author
  7. Ralf Jungmann  Is a corresponding author
  1. Max Planck Institute of Biochemistry, Germany
  2. University of Cambridge, United Kingdom
  3. MRC Laboratory of Molecular Biology, United Kingdom

Abstract

Rotaviruses transcribe eleven distinct RNAs that must be co-packaged prior to their replication to make an infectious virion. During infection, nontranslating rotavirus transcripts accumulate in cytoplasmic protein-RNA granules known as viroplasms that support segmented genome assembly and replication via a poorly understood mechanism. Here we analysed the RV transcriptome by combining DNA-barcoded smFISH of rotavirus-infected cells. Rotavirus RNA stoichiometry in viroplasms appears to be distinct from the cytoplasmic transcript distribution, with the largest transcript being the most enriched in viroplasms, suggesting a selective RNA enrichment mechanism. While all eleven types of transcripts accumulate in viroplasms, their stoichiometry significantly varied between individual viroplasms. Accumulation of transcripts requires the presence of 3' untranslated terminal regions and viroplasmic localisation of the viral polymerase VP1, consistent with the observed lack of polyadenylated transcripts in viroplasms. Our observations reveal similarities between viroplasms and other cytoplasmic RNP granules and identify viroplasmic proteins as drivers of viral RNA assembly during viroplasm formation.

Data availability

RNA-Seq data have been uploaded, and the SRA Illumina reads data are available under the accession number PRJNA702157 (SRR13723918, RNA-Seq of Bovine Rotavirus A: Strain RF).SRA Metadata:BioProject: PRJNA702157 (Bovine rotavirus strain RF transcriptome of MA104 cells)BioSample: SAMN17926863 (Viral sample from Bovine rotavirus A)SRA: SRR13723918 (RNA-Seq of Bovine Rotavirus A: Strain RF)All data generated during this study are included in the manuscript and supporting files. Source data files have been provided for all figures.

The following data sets were generated
The following previously published data sets were used
    1. Andrew Yates et al
    (2020) ENSEMBL 2020
    http://ftp.ensembl.org/pub/release-102/.

Article and author information

Author details

  1. Sebastian Strauss

    Max Planck Institute of Biochemistry, Munich, Germany
    Competing interests
    The authors declare that no competing interests exist.
  2. Julia Acker

    Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  3. Guido Papa

    MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5215-0014
  4. Daniel Desiró

    Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  5. Florian Schueder

    Max Planck Institute of Biochemistry, Munich, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3412-5066
  6. Alexander Borodavka

    Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
    For correspondence
    ab2677@cam.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5729-2687
  7. Ralf Jungmann

    Max Planck Institute of Biochemistry, Munich, Germany
    For correspondence
    jungmann@biochem.mpg.de
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4607-3312

Funding

Wellcome Trust (213437/Z/18/Z)

  • Alexander Borodavka

Deutsche Forschungsgemeinschaft (SFB1032)

  • Ralf Jungmann

European Research Council (MolMap 680241)

  • Ralf Jungmann

Max Planck Institute for Biochemistry

  • Sebastian Strauss

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Miles P Davenport, University of New South Wales, Australia

Version history

  1. Preprint posted: March 22, 2021 (view preprint)
  2. Received: March 23, 2021
  3. Accepted: January 26, 2023
  4. Accepted Manuscript published: January 26, 2023 (version 1)
  5. Version of Record published: February 13, 2023 (version 2)
  6. Version of Record updated: April 17, 2023 (version 3)

Copyright

© 2023, Strauss et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Sebastian Strauss
  2. Julia Acker
  3. Guido Papa
  4. Daniel Desiró
  5. Florian Schueder
  6. Alexander Borodavka
  7. Ralf Jungmann
(2023)
Principles of RNA recruitment to viral ribonucleoprotein condensates in a segmented dsRNA virus
eLife 12:e68670.
https://doi.org/10.7554/eLife.68670

Share this article

https://doi.org/10.7554/eLife.68670

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