A key role for the carboxy-terminal tail of the murine coronavirus nucleocapsid protein in coordination of genome packaging

Kuo, Lili; Koetzner, Cheri A.; Masters, Paul S.

doi:10.1016/j.virol.2016.04.009

Cited by 38 publications

(45 citation statements)

References 40 publications

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“…Thus, the SARS-CoV N protein likely would not have evolved to recognize the MHV PS. This outcome was reinforced by the subsequent demonstration that a mutant with a substitution of the even more divergent N protein CTD of the alphacoronavirus TGEV also exhibited a packaging-defective phenotype (Kuo et al, 2016b).…”

Section: Studies Implicating Roles For Both the Ctd And Domain N3 Of mentioning

confidence: 99%

“…In the M protein, the aminoterminal ectodomain (ecto) is connected to the carboxy-terminal endodomain (endo) by three transmembrane segments (Tm). Red, loci of substitutions or point mutations of N protein, in either the CTD (Kuo et al, 2014) or in N3 (Kuo et al, 2016b), which separately abolish packaging selectivity in viruses that contain a wt PS. Green, loci of critical residues in N protein (Hurst et al, 2005;Verma et al, 2006) and M protein (Escors et al, 2001;Kuo and Masters, 2002;Verma et al, 2007) essential for N-M virion assembly interactions (arrow).…”

Section: Earlier Studies Of Ps Binding By N Proteinmentioning

confidence: 99%

“…A separate region of the N molecule was later shown to also be involved in PS recognition (Kuo et al, 2016b). This finding resulted from examination of the effect of complete or partial replacement of the MHV M protein by the M protein of SARS-CoV.…”

Section: Studies Implicating Roles For Both the Ctd And Domain N3 Of mentioning

confidence: 99%

“…One model, which is derived from the genetic studies (Kuo et al, 2014 andKuo et al, 2016b), builds upon the known roles of the CTD as an RNA-binding module (Chang et al, 2014) and of domain N3 as the sole region of N that interacts with M protein (Hurst et al, 2005;Verma et al, 2006;Kuo et al, 2016a). In this proposed mechanism, the largely acidic domain N3 is originally sequestered by the CTD and then becomes dislodged, directly or indirectly, only as a result of the CTD binding to the PS (Fig.…”

Section: Primary Ps Recognition By N Proteinmentioning

confidence: 99%

“…5C). This model would seem to be ruled out by the existence of N3 mutants that have fully retained normal N-M assembly but have lost selective gRNA packaging (Kuo et al, 2016b). Nevertheless, it has been shown that not only the two structural domains, the NTD and CTD, but also unstructured segments of N, including N3, contribute to the affinity of RNA binding (Chang et al, 2009).…”

Section: Complex Formation Between N and M Proteins Followed By Recomentioning

confidence: 99%

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Coronavirus genomic RNA packaging

2019

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RNA viruses carry out selective packaging of their genomes in a variety of ways, many involving a genomic packaging signal. The first coronavirus packaging signal was discovered nearly thirty years ago, but how it functions remains incompletely understood. This review addresses the current state of knowledge of coronavirus genome packaging, which has mainly been studied in two prototype species, mouse hepatitis virus and transmissible gastroenteritis virus. Despite the progress that has been made in the mapping and characterization of some packaging signals, there is conflicting evidence as to whether the viral nucleocapsid protein or the membrane protein plays the primary role in packaging signal recognition. The different models for the mechanism of genomic RNA packaging that have been prompted by these competing views are described. Also discussed is the recent exciting discovery that selective coronavirus genome packaging is critical for in vivo evasion of the host innate immune response.

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Section: Studies Implicating Roles For Both the Ctd And Domain N3 Of mentioning

confidence: 99%

Section: Earlier Studies Of Ps Binding By N Proteinmentioning

confidence: 99%

Section: Studies Implicating Roles For Both the Ctd And Domain N3 Of mentioning

confidence: 99%

Section: Primary Ps Recognition By N Proteinmentioning

confidence: 99%

Section: Complex Formation Between N and M Proteins Followed By Recomentioning

confidence: 99%

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Coronavirus genomic RNA packaging

2019

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Porcine deltacoronavirus nucleocapsid protein antagonizes IFN-β production by impairing dsRNA and PACT binding to RIG-I

et al. 2019

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Porcine deltacoronavirus (PDCoV) is an emerging swine enteropathogenic coronavirus that causes watery diarrhea, vomiting and mortality in newborn piglets. Previous studies have suggested that PDCoV infection antagonizes RIG-I-like receptor (RLR)-mediated IFN-β production to evade host innate immune defense, and PDCoV-encoded nonstructural protein nsp5 and accessory protein NS6 are associated with this process. However, whether the structural protein(s) of PDCoV also antagonize IFN-β production remains unclear. In this study, we found that PDCoV nucleocapsid (N) protein, the most abundant viral structural protein, suppressed Sendai virus (SEV)-induced IFN-β production and transcription factor IRF3 activation, but did not block IFN-β production induced by overexpressing RIG-I/MDA5. Furthermore, study revealed that PDCoV N protein interacted with RIG-I and MDA5 in an in vitro overexpression system and evident interactions between N protein and RIG-I could be detected in the context of PDCoV infection, which interfered with the binding of dsRNA and protein activator of protein kinase R (PACT) to RIG-I. Together, our results demonstrate that PDCoV N protein is an IFN antagonist and utilizes diverse strategies to attenuate RIG-I recognition and activation.Publisher's Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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Structural and conformational analysis of SARS CoV 2 N-CTD revealing monomeric and dimeric active sites during the RNA-binding and stabilization: Insights towards potential inhibitors for N-CTD

Chauhan

Avti

Shekhar

et al. 2021

Computers in Biology and Medicine

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The advent of SARS-CoV-2 has become a universal health issue with no appropriate cure available to date. The coronavirus nucleocapsid (N) protein combines viral genomic RNA into a ribonucleoprotein and protects the viral genome from the host's nucleases. Structurally, the N protein comprises two independent domains: the N-terminal domain (NTD) for RNA-binding and C-terminal domain (CTD) involved in RNA-binding, protein dimerization, and nucleocapsid stabilization. The present study explains the structural aspects associated with the involvement of nucleocapsid C-terminal domain in the subunit assembly that helps the RNA binding and further stabilizing the virus assembly by protecting RNA from the hosts exonucleases degradation. The molecular dynamics (MD) simulations of the N-CTD and RNA complex suggests two active sites (site I: a monomer) and (site II: a dimer) with stable structural stability (RMSD: ∼2Å), Cα fluctuations (RMSF: ∼3Å) and strong protein-ligand interactions and the same were confirmed through the SiteMap module of Schrodinger. Virtual screening of 2456 FDA-approved drugs using structure-based docking identified top two leads distinctively against Site-I (monomer): Ceftaroline fosamil (MMGBSA = -47.12 kcal/mol) and Cefoperazone (-45.84 kcal/mol); and against Site-II (dimer): Boceprevir, (an antiviral protease inhibitor, -106.78 kcal/mol) and Ceftaroline fosamil (-99.55 kcal/mol). The DCCM and PCA of drugs Ceftaroline fosamil (PC1+PC2= 71.9%) and Boceprevir (PC1 +PC2= 61.6%) show significant correlated residue motions which suggests highly induced conformational changes in the N-CTD dimer. Therefore, we propose N-CTD as a druggable target with structural insights having two active binding sites (monomer and dimer) involved in specific RNA binding and stability. The RNA binding site with Ceftaroline fosamil binding can prevent viral assembly and can act as an antiviral for coronavirus.

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A key role for the carboxy-terminal tail of the murine coronavirus nucleocapsid protein in coordination of genome packaging

Cited by 38 publications

References 40 publications

Coronavirus genomic RNA packaging

Coronavirus genomic RNA packaging

Porcine deltacoronavirus nucleocapsid protein antagonizes IFN-β production by impairing dsRNA and PACT binding to RIG-I

Structural and conformational analysis of SARS CoV 2 N-CTD revealing monomeric and dimeric active sites during the RNA-binding and stabilization: Insights towards potential inhibitors for N-CTD

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