Author Correction: Cryo-EM structure of SARS-CoV-2 ORF3a in lipid nanodiscs

Kern, David; Sorum, Ben; Mali, Sonali; Hoel, Christopher; Sridharan, Savitha; Remis, Jonathan; Toso, Daniel B.; Kotecha, Abhay; Bautista, Diana M.; Brohawn, Stephen G.

doi:10.1038/s41594-021-00642-1

Cited by 7 publications

(6 citation statements)

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“…We identified 9% of isolates with non-canonical mutations in the gene encoding ORF3a. ORF3a is a viral potassium ion channel (viroporin) that inhibits autophagy and activates the inflammasome and apoptosis [ 62 , 63 ]. We found 11 non-canonical mutations that, to our knowledge, have been poorly characterized so far, except for the L108F and F207L mutations.…”

Section: Resultsmentioning

confidence: 99%

The Spread of SARS-CoV-2 Omicron Variant in CALABRIA: A Spatio-Temporal Report of Viral Genome Evolution

Veneziano

Marascio

Marco

et al. 2023

Viruses

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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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Section: Resultsmentioning

confidence: 99%

The Spread of SARS-CoV-2 Omicron Variant in CALABRIA: A Spatio-Temporal Report of Viral Genome Evolution

Veneziano

Marascio

Marco

et al. 2023

Viruses

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“…This result may explain why molecular replacement for batCOV5-M xtal failed when using SARS2-M AF as a template, but succeeded with the batCOV5-M CTD-xtal structure. Intriguingly, a structural comparison analysis using the Dali server 31 indicates the batCOV5-M xtal structure shares fold with the cryo-EM structure of SARS-COV-2 ORF3a protein (termed SARS2-ORF3a EM , PDB: 6XDC), which is a cation channel and also a homodimer 32 . Indeed, superposition of the two dimer structures yielded an all-C α RMSD of 3.75 Å, suggesting that the overall folding of the two structures is alike (Fig.…”

Section: Main Textmentioning

confidence: 99%

Crystal structure of the membrane (M) protein from a SARS-COV-2-related coronavirus

Wang

Yang

Sun

et al. 2022

Preprint

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The membrane (M) protein is the most abundant structural protein of coronaviruses including 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 coronavirus M protein from Pipistrellus bat coronavirus HKU5 (batCOV5-M), which is closely related to SARS-COV-2 M protein. The batCOV5-M structure reveals a homodimeric configuration with each protomer containing a short amino-terminus, a three-helix transmembrane domain and a β-sandwich carboxy-terminal domain. An interaction analysis demonstrates that the last 17 residues of the batCOV5 nucleocapsid (N) protein mediate its interaction with batCOV5-M. Combined with a computational docking analysis an M-N interaction model is proposed, in which dimerization of batCOV5-M forms a nearly horizontal binding groove for the carboxy-end of N protein.

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“…ORF3a is unique to SARS-CoV and SARS-CoV-2 among the seven known human coronaviruses ( 6 ), which indicates the clinical importance of ORF3a in causing severe human diseases like SARS or COVID-19. Indeed, clinical investigations have unveiled a significant presence of anti-ORF3a antibodies in COVID-19 patients, with sera from these patients exhibiting heightened levels of IgG and IgA reactivity specifically against ORF3a ( 7 , 8 ).…”

Section: Introductionmentioning

confidence: 99%

“…Through that study that was expanded in this study, we examined subcellular localization of those ORF3a mutants in pulmonary and renal epithelial cell lines and uncovered two distinct types of ORF3a mutations based on their subcellular localizations, i.e., the lysosomal membrane-associated ORF3a proteins that we termed as the L-ORF3a protein and the ORF3a proteins that are present in the ER that we coined as the E-ORF3a protein. Notably, some of those E-ORF3a proteins that reside in ER are naturally occurring ORF3a mutants such as the Y233N mutant or the G188 deletion mutant (∆G188) where several natural mutant variants (G188C/D/V) were present, and this glycine residue is critical for intracellular transport of ORF3a ( 1 , 5 , 6 , 14 ). However, the functional differences of these two types of ORF3a mutant proteins on host cellular responses and functional outcomes remain unexplored.…”

Section: Introductionmentioning

confidence: 99%

Endoplasmic reticulum-associated SARS-CoV-2 ORF3a elicits heightened cytopathic effects despite robust ER-associated degradation

Zhang,

Cruz-Cosme,

Zhang

et al. 2024

mBio

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ORF3a protein plays a vital role in viral pathogenesis and coronavirus disease 2019 (COVID-19). Like the spike protein, ORF3a mutates frequently, and certain variants are associated with the severity of COVID-19. Given the clinical significance and functional implications of ORF3a mutations, we conducted a comprehensive mutagenesis study targeting various known functional elements and revealed two distinctive types of ORF3a proteins based on their subcellular localizations: ORF3a proteins primarily localize on the lysosomal membrane (L-ORF3a) and those present in the endoplasmic reticulum (E-ORF3a). The objective of this study was to contrast the functional and mechanistic distinctions between these two types of ORF3a proteins. We examined six distinct ORF3a mutants and assessed their effects on cellular oxidative stress, nuclear factor kappa B-induced cytokine production, and cell death. Mechanistically, we explored ORF3a-induced ER stress, autophagy, and interactions with relevant cellular proteins. Our findings indicate that ORF3a proteins induce cytopathic effects through a similar mechanism, irrespective of their subcellular location. However, E-ORF3a proteins elicit more pronounced cytopathic effects despite their lower abundance and minimal impact on ER stress and autophagy when compared to L-ORF3a proteins. This discrepancy is attributed to ER-associated degradation since ORF3a proteins bind to a ubiquitin E3 ligase TRIM59. Inhibition of the 26S proteasome partially restores the protein levels of E-ORF3a and cellular ER stress response. This suggests that even a small quantity of ORF3a can lead to significant cytopathic effects due to the delicate nature of ER. Our study underscores the intricate interplay of dynamic cellular signaling within these two subcellular compartments in response to ORF3a. 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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Author Correction: Cryo-EM structure of SARS-CoV-2 ORF3a in lipid nanodiscs

Cited by 7 publications

References 0 publications

The Spread of SARS-CoV-2 Omicron Variant in CALABRIA: A Spatio-Temporal Report of Viral Genome Evolution

The Spread of SARS-CoV-2 Omicron Variant in CALABRIA: A Spatio-Temporal Report of Viral Genome Evolution

Crystal structure of the membrane (M) protein from a SARS-COV-2-related coronavirus

Endoplasmic reticulum-associated SARS-CoV-2 ORF3a elicits heightened cytopathic effects despite robust ER-associated degradation

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