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Zhang J, Cruz-Cosme R, Zhang C, Liu D, Tang Q, Zhao RY. Endoplasmic reticulum-associated SARS-CoV-2 ORF3a elicits heightened cytopathic effects despite robust ER-associated degradation. mBio 2024; 15:e0303023. [PMID: 38078754 PMCID: PMC10790703 DOI: 10.1128/mbio.03030-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has tragically claimed millions of lives through coronavirus disease 2019 (COVID-19), and there remains a critical gap in our understanding of the precise molecular mechanisms responsible for the associated fatality. One key viral factor of interest is the SARS-CoV-2 ORF3a protein, which has been identified as a potent inducer of host cellular proinflammatory responses capable of triggering the catastrophic cytokine storm, a primary contributor to COVID-19-related deaths. Moreover, ORF3a, much like the spike protein, exhibits a propensity for frequent mutations, with certain variants linked to the severity of COVID-19. Our previous research unveiled two distinct types of ORF3a mutant proteins, categorized by their subcellular localizations, setting the stage for a comparative investigation into the functional and mechanistic disparities between these two types of ORF3a variants. Given the clinical significance and functional implications of the natural ORF3a mutations, the findings of this study promise to provide invaluable insights into the potential roles undertaken by these mutant ORF3a proteins in the pathogenesis of COVID-19.
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Affiliation(s)
- Jiantao Zhang
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Ruth Cruz-Cosme
- Department of Microbiology, Howard University College of Medicine, Washington, DC, USA
| | - Chenyu Zhang
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Dongxiao Liu
- Department of Microbiology, Howard University College of Medicine, Washington, DC, USA
| | - Qiyi Tang
- Department of Microbiology, Howard University College of Medicine, Washington, DC, USA
| | - Richard Y. Zhao
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Institute of Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Research & Development Service, VA Maryland Health Care System, Baltimore, Maryland, USA
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Wang X, Yang Y, Sun Z, Zhou X. Crystal structure of the membrane (M) protein from a bat betacoronavirus. PNAS NEXUS 2023; 2:pgad021. [PMID: 36874273 PMCID: PMC9982069 DOI: 10.1093/pnasnexus/pgad021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 12/20/2022] [Accepted: 01/26/2023] [Indexed: 02/01/2023]
Abstract
The membrane (M) protein is the most abundant structural protein of coronaviruses including MERS-CoV, SARS-CoV, and SARS-CoV-2, and plays a central role in virus assembly through its interaction with various partner proteins. However, mechanistic details about how M protein interacts with others remain elusive due to lack of high-resolution structures. Here, we present the first crystal structure of a betacoronavirus M protein from Pipistrellus bat coronavirus HKU5 (batCOV5-M), which is closely related to MERS-CoV, SARS-CoV, and SARS-CoV-2 M proteins. Furthermore, an interaction analysis indicates that the carboxy-terminus of the batCOV5 nucleocapsid (N) protein mediates its interaction with batCOV5-M. Combined with a computational docking analysis an M-N interaction model is proposed, providing insight into the mechanism of M protein-mediated protein interactions.
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Affiliation(s)
- Xiaodong Wang
- State Key Laboratory of Biotherapy, Department of Integrated Traditional Chinese and Western Medicine, Rare Diseases Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yuwei Yang
- State Key Laboratory of Biotherapy, Department of Integrated Traditional Chinese and Western Medicine, Rare Diseases Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Ziyi Sun
- State Key Laboratory of Biotherapy, Department of Integrated Traditional Chinese and Western Medicine, Rare Diseases Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xiaoming Zhou
- State Key Laboratory of Biotherapy, Department of Integrated Traditional Chinese and Western Medicine, Rare Diseases Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
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Veneziano C, Marascio N, De Marco C, Quaresima B, Biamonte F, Trecarichi EM, Santamaria G, Quirino A, Torella D, Quattrone A, Matera G, Torti C, De Filippo C, Costanzo FS, Viglietto G. The Spread of SARS-CoV-2 Omicron Variant in CALABRIA: A Spatio-Temporal Report of Viral Genome Evolution. Viruses 2023; 15:v15020408. [PMID: 36851622 PMCID: PMC9963258 DOI: 10.3390/v15020408] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/25/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
We investigated the evolution of SARS-CoV-2 spread in Calabria, Southern Italy, in 2022. A total of 272 RNA isolates from nasopharyngeal swabs of individuals infected with SARS-CoV-2 were sequenced by whole genome sequencing (N = 172) and/or Sanger sequencing (N = 100). Analysis of diffusion of Omicron variants in Calabria revealed the prevalence of 10 different sub-lineages (recombinant BA.1/BA.2, BA.1, BA.1.1, BA.2, BA.2.9, BA.2.10, BA.2.12.1, BA.4, BA.5, BE.1). We observed that Omicron spread in Calabria presented a similar trend as in Italy, with some notable exceptions: BA.1 disappeared in April in Calabria but not in the rest of Italy; recombinant BA.1/BA.2 showed higher frequency in Calabria (13%) than in the rest of Italy (0.02%); BA.2.9, BA.4 and BA.5 emerged in Calabria later than in other Italian regions. In addition, Calabria Omicron presented 16 non-canonical mutations in the S protein and 151 non-canonical mutations in non-structural proteins. Most non-canonical mutations in the S protein occurred mainly in BA.5 whereas non-canonical mutations in non-structural or accessory proteins (ORF1ab, ORF3a, ORF8 and N) were identified in BA.2 and BA.5 sub-lineages. In conclusion, the data reported here underscore the importance of monitoring the entire SARS-CoV-2 genome.
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Affiliation(s)
- Claudia Veneziano
- Department of Experimental and Clinical Medicine, “Magna Graecia” University of Catanzaro, 88100 Catanzaro, Italy
- Interdepartmental Center of Services (CIS), Molecular Genomics and Pathology, “Magna Græcia” University of Catanzaro, 88100 Catanzaro, Italy
| | - Nadia Marascio
- Department of Health Sciences, “Magna Graecia” University of Catanzaro, 88100 Catanzaro, Italy
| | - Carmela De Marco
- Department of Experimental and Clinical Medicine, “Magna Graecia” University of Catanzaro, 88100 Catanzaro, Italy
- Interdepartmental Center of Services (CIS), Molecular Genomics and Pathology, “Magna Græcia” University of Catanzaro, 88100 Catanzaro, Italy
| | - Barbara Quaresima
- Department of Experimental and Clinical Medicine, “Magna Graecia” University of Catanzaro, 88100 Catanzaro, Italy
- Interdepartmental Center of Services (CIS), Molecular Genomics and Pathology, “Magna Græcia” University of Catanzaro, 88100 Catanzaro, Italy
| | - Flavia Biamonte
- Department of Experimental and Clinical Medicine, “Magna Graecia” University of Catanzaro, 88100 Catanzaro, Italy
- Interdepartmental Center of Services (CIS), Molecular Genomics and Pathology, “Magna Græcia” University of Catanzaro, 88100 Catanzaro, Italy
| | - Enrico Maria Trecarichi
- Department of Medical and Surgical Sciences, “Magna Graecia” University of Catanzaro, 88100 Catanzaro, Italy
- “Mater Domini” University Hospital of Catanzaro, 88100 Catanzaro, Italy
| | - Gianluca Santamaria
- Department of Experimental and Clinical Medicine, “Magna Graecia” University of Catanzaro, 88100 Catanzaro, Italy
| | - Angela Quirino
- Department of Health Sciences, “Magna Graecia” University of Catanzaro, 88100 Catanzaro, Italy
- “Mater Domini” University Hospital of Catanzaro, 88100 Catanzaro, Italy
| | - Daniele Torella
- Department of Experimental and Clinical Medicine, “Magna Graecia” University of Catanzaro, 88100 Catanzaro, Italy
- “Mater Domini” University Hospital of Catanzaro, 88100 Catanzaro, Italy
| | - Aldo Quattrone
- Neuroscience Research Center, “Magna Graecia” University of Catanzaro, 88100 Catanzaro, Italy
| | - Giovanni Matera
- Department of Health Sciences, “Magna Graecia” University of Catanzaro, 88100 Catanzaro, Italy
- “Mater Domini” University Hospital of Catanzaro, 88100 Catanzaro, Italy
| | - Carlo Torti
- Department of Medical and Surgical Sciences, “Magna Graecia” University of Catanzaro, 88100 Catanzaro, Italy
- “Mater Domini” University Hospital of Catanzaro, 88100 Catanzaro, Italy
| | | | - Francesco Saverio Costanzo
- Department of Experimental and Clinical Medicine, “Magna Graecia” University of Catanzaro, 88100 Catanzaro, Italy
- Interdepartmental Center of Services (CIS), Molecular Genomics and Pathology, “Magna Græcia” University of Catanzaro, 88100 Catanzaro, Italy
- “Mater Domini” University Hospital of Catanzaro, 88100 Catanzaro, Italy
| | - Giuseppe Viglietto
- Department of Experimental and Clinical Medicine, “Magna Graecia” University of Catanzaro, 88100 Catanzaro, Italy
- “Mater Domini” University Hospital of Catanzaro, 88100 Catanzaro, Italy
- Correspondence:
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