Nucleocapsid proteins: roles beyond viral <scp>RNA</scp> packaging

Ding, Beichen; Qin, Yali; Chen, Mingzhou

doi:10.1002/wrna.1326

Cited by 18 publications

(12 citation statements)

References 117 publications

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“…Previous studies, including our own, have examined fundamental properties of nucleocapsid or nucleoproteins (N) from RNA viruses, which revealed overlapping and unique functions (Arragain et al, 2019; Ding et al, 2016; Lu et al, 2020; Luo et al, 2020; Raymond et al, 2010; Su et al, 2018; Wan et al, 2017). These include the insights into RNA binding, oligomerization, as well as potential roles in RNA synthesis and immune evasion.…”

Section: Introductionmentioning

confidence: 99%

Characterization of SARS-CoV-2 N protein reveals multiple functional consequences of the C-terminal domain

Qavi

Hachim

et al. 2020

Preprint

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SummaryNucleocapsid protein (N) is the most abundant viral protein encoded by SARS-CoV-2, the causative agent of COVID-19. N plays key roles at different steps in the replication cycle and is used as a serological marker of infection. Here we characterize the biochemical properties of SARS-CoV-2 N. We define the N domains important for oligomerization and RNA binding that are associated with spherical droplet formation and suggest that N accessibility and assembly may be regulated by phosphorylation. We also map the RNA binding interface using hydrogen-deuterium exchange mass spectrometry. Finally, we find that the N protein C-terminal domain is the most immunogenic by sensitivity, based upon antibody binding to COVID-19 patient samples from the US and Hong Kong. Together, these findings uncover domain-specific insights into the significance of SARS-CoV-2 N and highlight the diagnostic value of using N domains as highly specific and sensitive markers of COVID-19.

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Section: Introductionmentioning

confidence: 99%

Characterization of SARS-CoV-2 N protein reveals multiple functional consequences of the C-terminal domain

Qavi

Hachim

et al. 2020

Preprint

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“…Nucleocapsid (N) protein is encoded by a highly variable region of the genes N gene, responsible for the formation of the helical nucleocapsid. N protein can elicit both cellmediated and humoral immune response and thus has potential value in vaccine development (Ding et al, 2016). In the N gene, one nucleotide change was detected at position G2881A found in 152 samples, and two nucleotides changes in the adjacent codons found in 149 samples.…”

Section: Discussionmentioning

confidence: 99%

The genetic variant analyses of SARS-CoV-2 strains; circulating in Bangladesh

Mahmud

Taznin²,

Sarkar

et al. 2020

Preprint

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Genomic mutation of the virus may impact the viral adaptation to the local environment, their transmission, disease manifestation, and the effectiveness of existing treatment and vaccination. The objectives of this study were to characterize genomic variations, non-synonymous amino acid substitutions, especially in target proteins, mutation events per samples, mutation rate, and overall scenario of coronaviruses across the country. To investigate the genetic diversity, a total of 184 genomes of virus strains sampled from different divisions of Bangladesh with sampling dates between the 10th of May 2020 and the 27th of June 2020 were analyzed. To date, a total of 634 mutations located along the entire genome resulting in non-synonymous 274 amino acid substitutions in 22 different proteins were detected with nucleotide mutation rate estimated to be 23.715 substitutions per year. The highest non-synonymous amino acid substitutions were observed at 48 different positions of the papain-like protease (nsp3). Although no mutations were found in nsp7, nsp9, nsp10, and nsp11, yet orf1ab accounts for 56% of total mutations. Among the structural proteins, the highest non-synonymous amino acid substitution (at 36 positions) observed in spike proteins, in which 9 unique locations were detected relative to the global strains, including 516E>Q in the boundary of the ACE2 binding region. The most dominated variant G614 (95%) based in spike protein is circulating across the country with co-evolving other variants including L323 (94%) in RNA dependent RNA polymerase (RdRp), K203 (82%) and R204 (82%) in nucleocapsid, and F120 (78%) in NSP2. These variants are mostly seen as linked mutations and are part of a haplotype observed in Europe. Data suggest effective containment of clade G strains (4.8%) with sub-clusters GR 82.4%, and GH clade 6.4%.HighlightsWe have sequenced 137 and analyzed 184 whole-genomes sequences of SARS-CoV-2 strains from different divisions of Bangladesh.A total of 634 mutation sites across the SARS-CoV-2 genome and 274 non-synonymous amino acid substitutions were detected.The mutation rate of SARS-CoV-2 estimated to be 23.715 nucleotide substitutions per year.Nine unique variants were detected based on non-anonymous amino acid substitutions in spike protein relative to the global SARS-CoV-2 strains.

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“…CoV N proteins share a similar overall topology structure and a highly conserved function of packaging the viral genome with structural proteins to form ribonucleoprotein complexes for viral assembly [46]. Nevertheless, they also manifested inhibitory trends in innate immune mediation and the strategies they exploit are complicated.…”

Section: Discussionmentioning

confidence: 99%

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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Nucleocapsid proteins: roles beyond viral RNA packaging

Cited by 18 publications

References 117 publications

Characterization of SARS-CoV-2 N protein reveals multiple functional consequences of the C-terminal domain

Characterization of SARS-CoV-2 N protein reveals multiple functional consequences of the C-terminal domain

The genetic variant analyses of SARS-CoV-2 strains; circulating in Bangladesh

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

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