Alphavirus nsP3 organizes into tubular scaffolds essential for infection and the cytoplasmic granule architecture
Alphaviruses, such as chikungunya virus (CHIKV), are mosquito-borne viruses that represent a significant threat to human health due to the current context of global warming. Efficient alphavirus infection relies on the activity of the non-structural protein 3 (nsP3), a puzzling multifunctional molecule whose role in infection remains largely unknown. NsP3 is a component of the plasma membrane-bound viral RNA replication complex (vRC) essential for RNA amplification and is also found in large cytoplasmic aggregates of unknown function<sub>.</sub> Here, we report the cryo-electron microscopy (cryo-EM) structure of the CHIKV nsP3 at 2.35 Å resolution. We show that nsP3 assembles into tubular structures made by a helical arrangement of its alphavirus unique domain (AUD). The nsP3 helical scaffolds are consistent with crown structures found on tomographic reconstructions of the mature viral RCs. In addition, nsP3 helices assemble into cytoplasmic granules organized in a network of tubular structures that contain viral genomic RNA and capsid as well as host factors required for productive infection. Structure-guided mutagenesis identified residues that prevent or disturb nsP3 assemblies, resulting in impaired viral replication or transcription. Altogether, our results reveal an unexpected nsP3-dependent molecular organization essential for different phases of alphavirus infection.
Authors
- Andrei Karpov (ORCID: https://orcid.org/0000-0002-1654-3021)
- Laurine Couture (ORCID: https://orcid.org/0000-0002-9000-7438)
- Michael Hons (ORCID: https://orcid.org/0000-0002-8317-7631)
- Claire Zimberger (ORCID: https://orcid.org/0000-0002-2499-9176)
- Juan Reguera (ORCID: https://orcid.org/0000-0003-4977-7948)
- Céline Amadori (ORCID: https://orcid.org/0000-0002-2958-6098)
- Ali Amara (ORCID: https://orcid.org/0000-0002-0283-1815)
- Laurent Meertens (ORCID: https://orcid.org/0000-0003-2811-3675)
- Ambroise Desfosses (ORCID: https://orcid.org/0000-0002-6525-5042)
- Rhian Jones (ORCID: https://orcid.org/0000-0001-5513-5939)
- Beate Mareike Kümmerer (ORCID: https://orcid.org/0000-0002-9011-2764)
- Denis Ptchelkine (ORCID: https://orcid.org/0000-0001-8821-3200)
- Vasiliya Kril (ORCID: https://orcid.org/0000-0002-4394-4146)
- Julien Burlaud‐Gaillard (ORCID: https://orcid.org/0000-0001-5171-9873)
- Philippe Roingeard (ORCID: https://orcid.org/0000-0001-9131-3341)
- Alexandra L Thienel (ORCID: https://orcid.org/0009-0009-1698-5290)
- Yara Bouery
Institutions
- Université de Tours (FR)
- Centre National de la Recherche Scientifique (FR)
- University of Bonn (DE)
- Inserm (FR)
- Université Paris Cité (FR)
- Aix-Marseille Université (FR)
- Commissariat à l'Énergie Atomique et aux Énergies Alternatives (FR)
- Deutsches Elektronen-Synchrotron DESY (DE)
- CEA Grenoble (FR)
- European Molecular Biology Laboratory (FR)
- Theories and Approaches of Genomic Complexity (FR)
- Hôpital Saint-Louis (FR)
- Institut de Biologie Structurale (FR)
- Centre for Structural Systems Biology (DE)
- Living Systems (United States) (US)
- Université Grenoble Alpes (FR)
Publication Details
- Journal
- Nature Communications
- Published
- 2024-09-16
- DOI
- https://doi.org/10.1038/s41467-024-51952-z
- Citations
- 31
- Primary Topic
- Mosquito-borne diseases and control
- Type
- article
- Field-Weighted Citation Impact
- 16.29
Funders
- Aix-Marseille Université
- Deutsche Forschungsgemeinschaft
- Agence Nationale de la Recherche
- Institut National de la Santé et de la Recherche Médicale
- Centre National de la Recherche Scientifique
- Tartu Ülikool
- French Infrastructure for Integrated Structural Biology
- Inserm Transfert