The SARS-CoV-2 accessory protein Orf3a is not an ion channel, but does interact with trafficking proteins
- Janelia Research Campus, United States
- Universidad Austral de Chile, Chile
- University of Pennsylvania, United States
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, United States
Abstract
The severe acute respiratory syndrome associated coronavirus 2 (SARS-CoV-2) and SARS-CoV-1 accessory protein Orf3a colocalizes with markers of the plasma membrane, endocytic pathway, and Golgi apparatus. Some reports have led to annotation of both Orf3a proteins as viroporins. Here we show that neither SARS-CoV-2 nor SARS-CoV-1 Orf3a form functional ion conducting pores and that the conductances measured are common contaminants in overexpression and with high levels of protein in reconstitution studies. Cryo-EM structures of both SARS-CoV-2 and SARS-CoV-1 Orf3a display a narrow constriction and the presence of a positively-charged aqueous vestibule, which would not favor cation permeation. We observe enrichment of the late endosomal marker Rab7 upon SARS-CoV-2 Orf3a overexpression, and co-immunoprecipitation with VPS39. Interestingly, SARS-CoV-1 Orf3a does not cause the same cellular phenotype as SARS-CoV-2 Orf3a and does not interact with VPS39. To explain this difference, we find that a divergent, unstructured loop of SARS-CoV-2 Orf3a facilitates its binding with VPS39, a HOPS complex tethering protein involved in late endosome and autophagosome fusion with lysosomes. We suggest that the added loop enhances SARS-CoV-2 Orf3a's ability to co-opt host cellular trafficking mechanisms for viral exit or host immune evasion.
Data availability
All constructs and stable cell lines generated are available upon request. Atomic coordinates and cryo-EM density maps of have been deposited with the Protein Data Bank and Electron Microscopy Data Bank with the accession numbers: 8EQJ (SARS-CoV-2 Orf3a, LE/Lyso, MSP1D1 nanodisc; EMD-28538), 8EQT (SARS-CoV-2 Orf3a, PM, MSP1D1 nanodisc; EMD-28545), 8EQU (SARS-CoV-2 Orf3a, LE/Lyso, Saposin A nanodisc; EMD-28546) and 8EQS (SARS-CoV-1 Orf3a, LE/Lyso, MSP1D1 nanodisc; EMD-28544).
Article and author information
Author details
Patrick R Houlihan
Sebastian E Brauchi
Funding
National Institute of Health (GM133172,HL147379)
- Dejian Ren
Australian National Health and Medical Research Council (APP1162427)
- Ben Cristofori-Armstrong
Comisión National de Investigación de Cientifica y Tecnologíca (2117080)
- Deny Cabezas-Bratesco
Millennium Nucleus of Ion Channels -- Associated Diseases (NCN19_168)
- Sebastian E Brauchi
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Kenton J Swartz, National Institute of Neurological Disorders and Stroke, National Institutes of Health, United States
Version history
- Preprint posted: September 3, 2022 (view preprint)
- Received: October 26, 2022
- Accepted: January 25, 2023
- Accepted Manuscript published: January 25, 2023 (version 1)
- Version of Record published: February 9, 2023 (version 2)
- Version of Record updated: February 13, 2023 (version 3)
Copyright
This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.
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The SARS-CoV-2 accessory protein Orf3a is not an ion channel, but does interact with trafficking proteins
eLife 12:e84477.
https://doi.org/10.7554/eLife.84477
Further reading
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The receptor tyrosine kinase ROR2 mediates noncanonical WNT5A signaling to orchestrate tissue morphogenetic processes, and dysfunction of the pathway causes Robinow syndrome, Brachydactyly B and metastatic diseases. The domain(s) and mechanisms required for ROR2 function, however, remain unclear. We solved the crystal structure of the extracellular cysteine-rich (CRD) and Kringle (Kr) domains of ROR2 and found that, unlike other CRDs, the ROR2 CRD lacks the signature hydrophobic pocket that binds lipids/lipid-modified proteins, such as WNTs, suggesting a novel mechanism of ligand reception. Functionally, we showed that the ROR2 CRD, but not other domains, is required and minimally sufficient to promote WNT5A signaling, and Robinow mutations in the CRD and the adjacent Kr impair ROR2 secretion and function. Moreover, using function-activating and -perturbing antibodies against the Frizzled (FZ) family of WNT receptors, we demonstrate the involvement of FZ in WNT5A-ROR signaling. Thus, ROR2 acts via its CRD to potentiate the function of a receptor super-complex that includes FZ to transduce WNT5A signals.
