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Zimmer MM, Kibe A, Rand U, Pekarek L, Ye L, Buck S, Smyth RP, Cicin-Sain L, Caliskan N. The short isoform of the host antiviral protein ZAP acts as an inhibitor of SARS-CoV-2 programmed ribosomal frameshifting. Nat Commun 2021; 12:7193. [PMID: 34893599 PMCID: PMC8664833 DOI: 10.1038/s41467-021-27431-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 11/18/2021] [Indexed: 12/20/2022] Open
Abstract
Programmed ribosomal frameshifting (PRF) is a fundamental gene expression event in many viruses, including SARS-CoV-2. It allows production of essential viral, structural and replicative enzymes that are encoded in an alternative reading frame. Despite the importance of PRF for the viral life cycle, it is still largely unknown how and to what extent cellular factors alter mechanical properties of frameshift elements and thereby impact virulence. This prompted us to comprehensively dissect the interplay between the SARS-CoV-2 frameshift element and the host proteome. We reveal that the short isoform of the zinc-finger antiviral protein (ZAP-S) is a direct regulator of PRF in SARS-CoV-2 infected cells. ZAP-S overexpression strongly impairs frameshifting and inhibits viral replication. Using in vitro ensemble and single-molecule techniques, we further demonstrate that ZAP-S directly interacts with the SARS-CoV-2 RNA and interferes with the folding of the frameshift RNA element. Together, these data identify ZAP-S as a host-encoded inhibitor of SARS-CoV-2 frameshifting and expand our understanding of RNA-based gene regulation.
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Affiliation(s)
- Matthias M Zimmer
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Zentrum für Infektionsforschung (Helmholtz Centre for Infection Research), Josef-Schneider-Strasse 2, 97080, Würzburg, Germany
| | - Anuja Kibe
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Zentrum für Infektionsforschung (Helmholtz Centre for Infection Research), Josef-Schneider-Strasse 2, 97080, Würzburg, Germany
| | - Ulfert Rand
- Helmholtz Zentrum für Infektionsforschung, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Lukas Pekarek
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Zentrum für Infektionsforschung (Helmholtz Centre for Infection Research), Josef-Schneider-Strasse 2, 97080, Würzburg, Germany
| | - Liqing Ye
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Zentrum für Infektionsforschung (Helmholtz Centre for Infection Research), Josef-Schneider-Strasse 2, 97080, Würzburg, Germany
| | - Stefan Buck
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Zentrum für Infektionsforschung (Helmholtz Centre for Infection Research), Josef-Schneider-Strasse 2, 97080, Würzburg, Germany
| | - Redmond P Smyth
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Zentrum für Infektionsforschung (Helmholtz Centre for Infection Research), Josef-Schneider-Strasse 2, 97080, Würzburg, Germany
- Medical Faculty, Julius-Maximilians University Würzburg, 97074, Würzburg, Germany
| | - Luka Cicin-Sain
- Helmholtz Zentrum für Infektionsforschung, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Neva Caliskan
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Zentrum für Infektionsforschung (Helmholtz Centre for Infection Research), Josef-Schneider-Strasse 2, 97080, Würzburg, Germany.
- Medical Faculty, Julius-Maximilians University Würzburg, 97074, Würzburg, Germany.
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Dodero-Rojas E, Onuchic JN, Whitford PC. Sterically confined rearrangements of SARS-CoV-2 Spike protein control cell invasion. eLife 2021; 10:70362. [PMID: 34463614 PMCID: PMC8456623 DOI: 10.7554/elife.70362] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/06/2021] [Indexed: 12/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is highly contagious, and transmission involves a series of processes that may be targeted by vaccines and therapeutics. During transmission, host cell invasion is controlled by a large-scale (200–300 Å) conformational change of the Spike protein. This conformational rearrangement leads to membrane fusion, which creates transmembrane pores through which the viral genome is passed to the host. During Spike-protein-mediated fusion, the fusion peptides must be released from the core of the protein and associate with the host membrane. While infection relies on this transition between the prefusion and postfusion conformations, there has yet to be a biophysical characterization reported for this rearrangement. That is, structures are available for the endpoints, though the intermediate conformational processes have not been described. Interestingly, the Spike protein possesses many post-translational modifications, in the form of branched glycans that flank the surface of the assembly. With the current lack of data on the pre-to-post transition, the precise role of glycans during cell invasion has also remained unclear. To provide an initial mechanistic description of the pre-to-post rearrangement, an all-atom model with simplified energetics was used to perform thousands of simulations in which the protein transitions between the prefusion and postfusion conformations. These simulations indicate that the steric composition of the glycans can induce a pause during the Spike protein conformational change. We additionally show that this glycan-induced delay provides a critical opportunity for the fusion peptides to capture the host cell. In contrast, in the absence of glycans, the viral particle would likely fail to enter the host. This analysis reveals how the glycosylation state can regulate infectivity, while providing a much-needed structural framework for studying the dynamics of this pervasive pathogen.
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Affiliation(s)
- Esteban Dodero-Rojas
- Center for Theoretical Biological Physics, Rice University, Houston, United States
| | - Jose N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, United States.,Department of Physics and Astronomy, Rice University, Houston, United States.,Department of Chemistry, Rice University, Houston, United States.,Department of Biosciences, Rice University, Houston, United States
| | - Paul Charles Whitford
- Center for Theoretical Biological Physics, Northeastern University, Boston, United States.,Department of Physics, Northeastern University, Boston, United States
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Tharayil A, Rajakumari R, Chirayil CJ, Thomas S, Kalarikkal N. A short review on nanotechnology interventions against COVID-19. EMERGENT MATERIALS 2021; 4:131-141. [PMID: 33554045 PMCID: PMC7856851 DOI: 10.1007/s42247-021-00163-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/12/2021] [Indexed: 05/02/2023]
Abstract
The COVID-19 has affected all major aspects of the society in a global perspective. The role of nanotechnology is much sought after in fighting this pandemic. Advanced materials based on nanotechnology are the basis of several technologies starting from masks and personal protection equipment to specific diagnostic tools that could diminish the impact of COVID-19. Development of nanotechnology-based products is therefore an absolute necessity for fight against COVID-19. We examine the fundamental concepts related to virology, histopathologic findings and how nanotechnology can help in fighting the disease. In this review we discuss the state of the art and ongoing nanotechnology-based strategies like antiviral coatings, 3D printing and therapeutics to fight against this deadly disease. The importance of using nanoparticles in point of care tests and biosensors is also highlighted.
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Affiliation(s)
- Abhimanyu Tharayil
- School of Energy Materials, Mahatma Gandhi University, Kottayam, Kerala 686560 India
| | - R. Rajakumari
- International and Inter-University Centre for Nanoscience and Nanotechnology, Mahatma Gandhi University, Kottayam, Kerala 686560 India
| | | | - Sabu Thomas
- School of Energy Materials, Mahatma Gandhi University, Kottayam, Kerala 686560 India
- International and Inter-University Centre for Nanoscience and Nanotechnology, Mahatma Gandhi University, Kottayam, Kerala 686560 India
- School of Chemical Sciences, Mahatma Gandhi University, Kottayam, Kerala 686560 India
| | - Nandakumar Kalarikkal
- International and Inter-University Centre for Nanoscience and Nanotechnology, Mahatma Gandhi University, Kottayam, Kerala 686560 India
- School of Pure and Applied Physics, Mahatma Gandhi University, Kottayam, Kerala 686560 India
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