Abstract

A founding paradigm in virology is that the spatial unit of the viral replication cycle is an individual cell. Multipartite viruses have a segmented genome where each segment is encapsidated separately. In this situation the viral genome is not recapitulated in a single virus particle but in the viral population. How multipartite viruses manage to efficiently infect individual cells with all segments, thus with the whole genome information, is a long-standing but perhaps deceptive mystery. By localizing and quantifying the genome segments of a nanovirus in host plant tissues we show that they rarely co-occur within individual cells. We further demonstrate that distinct segments accumulate independently in different cells and that the viral system is functional through complementation across cells. Our observation deviates from the classical conceptual framework in virology and opens an alternative possibility (at least for nanoviruses) where the infection can operate at a level above the individual cell level, defining a viral multicellular way of life.

Data availability

All data are available in the manuscript and in Supplemental Information.Raw data of all quantified green and red fluorescence within individual cells of infected plants are provided as a separate EXCEL supplementary file: Table S4.To allow repeat/reproduce all correlation tests, the 508 raw/unprocessed images (.lsm format) used for preparing all figures and for fluorescence quantification in individual cells have been deposited in the public repository figshare. They can be accessed at the DOI: 10.6084/m9.figshare.5981968

The following data sets were generated

Article and author information

Author details

  1. Anne Sicard

    UMR BGPI, INRA, Centre Occitanie Montpellier, Montpellier, France
    Competing interests
    The authors declare that no competing interests exist.
  2. Elodie Pirolles

    UMR BGPI, INRA, Centre Occitanie Montpellier, Montpellier, France
    Competing interests
    The authors declare that no competing interests exist.
  3. Romain Gallet

    UMR BGPI, INRA, Centre Occitanie Montpellier, Montpellier, France
    Competing interests
    The authors declare that no competing interests exist.
  4. Marie-Stéphanie Vernerey

    UMR BGPI, INRA, Centre Occitanie Montpellier, Montpellier, France
    Competing interests
    The authors declare that no competing interests exist.
  5. Michel Yvon

    UMR BGPI, INRA, Centre Occitanie Montpellier, Montpellier, France
    Competing interests
    The authors declare that no competing interests exist.
  6. Cica Urbino

    UMR BGPI, INRA, Centre Occitanie Montpellier, Montpellier, France
    Competing interests
    The authors declare that no competing interests exist.
  7. Michel Peterschmitt

    UMR BGPI, INRA, Centre Occitanie Montpellier, Montpellier, France
    Competing interests
    The authors declare that no competing interests exist.
  8. Serafin Gutierrez

    UMR BGPI, INRA, Centre Occitanie Montpellier, Montpellier, France
    Competing interests
    The authors declare that no competing interests exist.
  9. Yannis Michalakis

    MIVEGEC (CNRS/IRD/UM), Centre National de la Recherche Scientifique, Montpellier, France
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1929-0848
  10. Stéphane Blanc

    UMR BGPI, INRA, Centre Occitanie Montpellier, Montpellier, France
    For correspondence
    stephane.blanc@inra.fr
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3412-0989

Funding

Institut National de la Recherche Agronomique

  • Anne Sicard
  • Elodie Pirolles
  • Romain Gallet
  • Marie-Stéphanie Vernerey
  • Michel Yvon
  • Serafin Gutierrez
  • Stéphane Blanc

Centre National de la Recherche Scientifique

  • Elodie Pirolles
  • Yannis Michalakis

Institut de Recherche pour le developpement

  • Yannis Michalakis

Agence Nationale de la Recherche (ANR-14-CE02-0014)

  • Anne Sicard
  • Elodie Pirolles
  • Romain Gallet
  • Marie-Stéphanie Vernerey
  • Michel Yvon
  • Yannis Michalakis
  • Stéphane Blanc

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

Copyright

© 2019, Sicard 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.

Metrics

  • 19,048
    views
  • 1,547
    downloads
  • 51
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Anne Sicard
  2. Elodie Pirolles
  3. Romain Gallet
  4. Marie-Stéphanie Vernerey
  5. Michel Yvon
  6. Cica Urbino
  7. Michel Peterschmitt
  8. Serafin Gutierrez
  9. Yannis Michalakis
  10. Stéphane Blanc
(2019)
A multicellular way of life for a multipartite virus
eLife 8:e43599.
https://doi.org/10.7554/eLife.43599

Share this article

https://doi.org/10.7554/eLife.43599

Further reading

    1. Genetics and Genomics
    2. Microbiology and Infectious Disease
    Dániel Molnár, Éva Viola Surányi ... Judit Toth
    Research Article

    The sustained success of Mycobacterium tuberculosis as a pathogen arises from its ability to persist within macrophages for extended periods and its limited responsiveness to antibiotics. Furthermore, the high incidence of resistance to the few available antituberculosis drugs is a significant concern, especially since the driving forces of the emergence of drug resistance are not clear. Drug-resistant strains of Mycobacterium tuberculosis can emerge through de novo mutations, however, mycobacterial mutation rates are low. To unravel the effects of antibiotic pressure on genome stability, we determined the genetic variability, phenotypic tolerance, DNA repair system activation, and dNTP pool upon treatment with current antibiotics using Mycobacterium smegmatis. Whole-genome sequencing revealed no significant increase in mutation rates after prolonged exposure to first-line antibiotics. However, the phenotypic fluctuation assay indicated rapid adaptation to antibiotics mediated by non-genetic factors. The upregulation of DNA repair genes, measured using qPCR, suggests that genomic integrity may be maintained through the activation of specific DNA repair pathways. Our results, indicating that antibiotic exposure does not result in de novo adaptive mutagenesis under laboratory conditions, do not lend support to the model suggesting antibiotic resistance development through drug pressure-induced microevolution.

    1. Cell Biology
    2. Microbiology and Infectious Disease
    Clément Mazeaud, Stefan Pfister ... Laurent Chatel-Chaix
    Research Article

    Zika virus (ZIKV) infection causes significant human disease that, with no approved treatment or vaccine, constitutes a major public health concern. Its life cycle entirely relies on the cytoplasmic fate of the viral RNA genome (vRNA) through a fine-tuned equilibrium between vRNA translation, replication, and packaging into new virions, all within virus-induced replication organelles (vROs). In this study, with an RNA interference (RNAi) mini-screening and subsequent functional characterization, we have identified insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) as a new host dependency factor that regulates vRNA synthesis. In infected cells, IGF2BP2 associates with viral NS5 polymerase and redistributes to the perinuclear viral replication compartment. Combined fluorescence in situ hybridization-based confocal imaging, in vitro binding assays, and immunoprecipitation coupled to RT-qPCR showed that IGF2BP2 directly interacts with ZIKV vRNA 3’ nontranslated region. Using ZIKV sub-genomic replicons and a replication-independent vRO induction system, we demonstrated that IGF2BP2 knockdown impairs de novo vRO biogenesis and, consistently, vRNA synthesis. Finally, the analysis of immunopurified IGF2BP2 complex using quantitative mass spectrometry and RT-qPCR revealed that ZIKV infection alters the protein and RNA interactomes of IGF2BP2. Altogether, our data support that ZIKV hijacks and remodels the IGF2BP2 ribonucleoprotein complex to regulate vRO biogenesis and vRNA neosynthesis.