Cryo-electron tomography reveals novel features of a viral RNA replication compartment

  1. Kenneth J Ertel
  2. Desirée Benefield
  3. Daniel Castaño-Diez
  4. Janice Pennington
  5. Mark Horswill
  6. Johan A den Boon
  7. Marisa Otegui
  8. Paul Ahlquist  Is a corresponding author
  1. Janelia Research Campus, Howard Hughes Medical Institute, United States
  2. University of Wisconsin-Madison, United States
  3. University of Basel, Switzerland

Abstract

Positive-strand RNA viruses, the largest genetic class of viruses, include numerous important pathogens such as Zika virus. These viruses replicate their RNA genomes in novel, membrane-bounded mini-organelles, but the organization of viral proteins and RNAs in these compartments is largely unknown. We used cryo-electron tomography to reveal many previously unrecognized features of Flock house nodavirus (FHV) RNA replication compartments. These spherular invaginations of outer mitochondrial membranes are packed with electron-dense RNA fibrils and their volumes are closely correlated with RNA replication template length. Each spherule's necked aperture is crowned by a striking cupped ring structure containing multifunctional FHV RNA replication protein A. Subtomogram averaging of these crowns revealed twelve-fold symmetry, concentric flanking protrusions, and a central electron density. Many crowns were associated with long cytoplasmic fibrils, likely to be exported progeny RNA. These results provide new mechanistic insights into positive-strand RNA virus replication compartment structure, assembly, function and control.

Article and author information

Author details

  1. Kenneth J Ertel

    Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Desirée Benefield

    Institute for Molecular Virology, University of Wisconsin-Madison, Madison, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Daniel Castaño-Diez

    BioEM lab, Biozentrum, University of Basel, Basel, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  4. Janice Pennington

    Institute for Molecular Virology, University of Wisconsin-Madison, Madison, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Mark Horswill

    Institute for Molecular Virology, University of Wisconsin-Madison, Madison, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Johan A den Boon

    Institute for Molecular Virology, University of Wisconsin-Madison, Madison, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Marisa Otegui

    Department of Botany, University of Wisconsin-Madison, Madison, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Paul Ahlquist

    Institute for Molecular Virology, University of Wisconsin-Madison, Madison, United States
    For correspondence
    ahlquist@wisc.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4584-9318

Funding

Howard Hughes Medical Institute (Investigator)

  • Paul Ahlquist

Morgridge Institute for Research (Investigator)

  • Paul Ahlquist

National Science Foundation (DBI 1126441)

  • Marisa Otegui
  • Paul Ahlquist

National Science Foundation (MCB 1614965)

  • Marisa Otegui

Rowe Family Virology Venture Fund (Investigator)

  • Paul Ahlquist

National Institutes of Health (T32 AI078985)

  • Desirée Benefield

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

Reviewing Editor

  1. Wesley I Sundquist, University of Utah School of Medicine, United States

Publication history

  1. Received: February 10, 2017
  2. Accepted: June 20, 2017
  3. Accepted Manuscript published: June 27, 2017 (version 1)
  4. Version of Record published: July 18, 2017 (version 2)

Copyright

© 2017, Ertel 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. Kenneth J Ertel
  2. Desirée Benefield
  3. Daniel Castaño-Diez
  4. Janice Pennington
  5. Mark Horswill
  6. Johan A den Boon
  7. Marisa Otegui
  8. Paul Ahlquist
(2017)
Cryo-electron tomography reveals novel features of a viral RNA replication compartment
eLife 6:e25940.
https://doi.org/10.7554/eLife.25940

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