The SARS-CoV-2 nucleocapsid protein: its role in the viral life cycle, structure and functions, and use as a potential target in the development of vaccines and diagnostics

Virology Journal, Journal Year: 2023, Volume and Issue: 20(1)

Published: Jan. 10, 2023

Coronavirus disease 2019 (COVID-19) continues to take a heavy toll on personal health, healthcare systems, and economies around the globe. Scientists are expending tremendous effort develop diagnostic technologies for detecting positive infections within shortest possible time, vaccines drugs specifically prevention treatment of COVID-19 disease. At same emerging novel variants have raised serious concerns about vaccine efficacy. The SARS-CoV-2 nucleocapsid (N) protein plays an important role in coronavirus life cycle, participates various vital activities after virus invasion. It has attracted large amount attention drug development. Here, we summarize latest research N protein, including its structure function, post-translational modifications addition involvement liquid-liquid phase separation (LLPS) use as basis development techniques.

Language: Английский

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A conserved oligomerization domain in the disordered linker of coronavirus nucleocapsid proteins

Science Advances, Journal Year: 2023, Volume and Issue: 9(14)

Published: April 5, 2023

The nucleocapsid (N-)protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a key role in viral assembly and scaffolding the RNA. It promotes liquid-liquid phase separation (LLPS), forming dense droplets that support ribonucleoprotein particles with as-of-yet unknown macromolecular architecture. Combining biophysical experiments, molecular dynamics simulations, analysis mutational landscape, we describe heretofore oligomerization site contributes to LLPS, is required for higher-order protein-nucleic acid complexes, coupled large-scale conformational changes N-protein upon nucleic binding. self-association interface located leucine-rich sequence intrinsically disordered linker between folded domains formed by transient helices assembling into trimeric coiled-coils. Critical residues stabilizing hydrophobic electrostatic interactions adjacent are highly protected against mutations viable SARS-CoV-2 genomes, motif conserved across related coronaviruses, thus presenting target antiviral therapeutics.

Language: Английский

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The Mutational Landscape of SARS-CoV-2

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(10), P. 9072 - 9072

Published: May 22, 2023

Mutation research is crucial for detecting and treating SARS-CoV-2 developing vaccines. Using over 5,300,000 sequences from genomes custom Python programs, we analyzed the mutational landscape of SARS-CoV-2. Although almost every nucleotide in genome has mutated at some time, substantial differences frequency regularity mutations warrant further examination. C>U are most common. They found largest number variants, pangolin lineages, countries, which indicates that they a driving force behind evolution Not all genes have same way. Fewer non-synonymous single variations encode proteins with critical role virus replication than ancillary roles. Some genes, such as spike (S) nucleocapsid (N), show more others. prevalence target regions COVID-19 diagnostic RT-qPCR tests generally low, cases, primers bind to N gene, it significant. Therefore, ongoing monitoring crucial. The Portal provides access database mutations.

Language: Английский

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The disordered N-terminal tail of SARS-CoV-2 Nucleocapsid protein forms a dynamic complex with RNA

Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 52(5), P. 2609 - 2624

Published: Dec. 28, 2023

Abstract The SARS-CoV-2 Nucleocapsid (N) protein is responsible for condensation of the viral genome. Characterizing mechanisms controlling nucleic acid binding a key step in understanding how realized. Here, we focus on role RNA domain (RBD) and its flanking disordered N-terminal (NTD) tail, using single-molecule Förster Resonance Energy Transfer coarse-grained simulations. We quantified contact site size affinity acids concomitant conformational changes occurring region. found that NTD increases RBD by about 50-fold. Binding both nonspecific specific results modulation tail configurations, which respond an length-dependent manner. Not only does increase RNA, but mutations occur Omicron variant modulate interactions, indicating functional tail. Finally, NTD-RBD preferentially interacts with single-stranded resulting protein:RNA complexes are flexible dynamic. speculate this mechanism interaction enables to search genome bind high-affinity motifs.

Language: Английский

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Assembly of SARS-CoV-2 nucleocapsid protein with nucleic acid

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: 52(11), P. 6647 - 6661

Published: April 8, 2024

Abstract The viral genome of SARS-CoV-2 is packaged by the nucleocapsid (N-)protein into ribonucleoprotein particles (RNPs), 38 ± 10 which are contained in each virion. Their architecture has remained unclear due to pleomorphism RNPs, high flexibility N-protein intrinsically disordered regions, and highly multivalent interactions between RNA binding sites both N-terminal (NTD) C-terminal domain (CTD). Here we explore critical interaction motifs RNPs applying a combination biophysical techniques ancestral mutant proteins different nucleic acids an vitro assay for RNP formation, examining protein variants assembly assay. We find that acid-bound dimers oligomerize via recently described protein–protein interface presented transient helix its long linker region NTD CTD. resulting hexameric complexes stabilized protein-nucleic acid establish crosslinks dimeric subunits. Assemblies CTD offering more than one site stem–loop RNA. Our study suggests model where scaffolding at density on followed cooperative multimerization through linker.

Language: Английский

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Phosphorylation in the Ser/Arg-rich region of the nucleocapsid of SARS-CoV-2 regulates phase separation by inhibiting self-association of a distant helix

Journal of Biological Chemistry, Journal Year: 2024, Volume and Issue: 300(6), P. 107354 - 107354

Published: May 7, 2024

The nucleocapsid protein (N) of SARS-CoV-2 is essential for virus replication, genome packaging, evading host immunity, and maturation. N a multidomain composed an independently folded monomeric N-terminal domain that the primary site RNA binding, dimeric C-terminal efficient phase separation condensate formation with RNA. domains are separated by disordered Ser/Arg-rich region preceding self-associating Leu-rich helix. Phosphorylation in Ser/Arg infected cells decreases viscosity N:RNA condensates promoting viral replication immune evasion. molecular level effect phosphorylation, however, missing from our current understanding. Using NMR spectroscopy analytical ultracentrifugation we show phosphorylation destabilizes helix 30 amino acids distant site. gel shift assays demonstrate binding linker dampened whereas to full-length not significantly affected presumably due retained strong interactions domain. Introducing switchable replace confirms importance self-association droplet suggests only increases solubility positively charged elongated as observed other proteins but can also inhibit These data highlight both at local sites hydrophobic regulating liquid-liquid entire protein.

Language: Английский

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Incipient functional SARS-CoV-2 diversification identified through neural network haplotype maps

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(10)

Published: Feb. 28, 2024

Since its introduction in the human population, SARS-CoV-2 has evolved into multiple clades, but events intrahost diversification are not well understood. Here, we compare three-dimensional (3D) self-organized neural haplotype maps (SOMs) of from thirty individual nasopharyngeal diagnostic samples obtained within a 19-day interval Madrid (Spain), at time transition between clades 19 and 20. SOMs have been trained with repertoire present mutant spectra nsp12- spike (S)-coding regions. Each SOM consisted dominant neuron (displaying maximum frequency), surrounded by low-frequency cloud. The sequence master (dominant) was either identical to that reference Wuhan-Hu-1 genome or differed it one nucleotide position. Six different deviant sequences were identified among neurons. Some substitutions clouds affected critical sites nsp12-nsp8-nsp7 polymerase complex resulted altered kinetics RNA synthesis an vitro primer extension assay. Thus, analysis mutations relevant modification viral synthesis, quasispecies. These most likely occurred during several COVID-19 patients, initial stage pandemic, brief period.

Language: Английский

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Assembly of SARS-CoV-2 ribonucleosomes by truncated N∗ variant of the nucleocapsid protein

Journal of Biological Chemistry, Journal Year: 2023, Volume and Issue: 299(12), P. 105362 - 105362

Published: Oct. 19, 2023

The nucleocapsid (N) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) compacts the RNA genome into viral ribonucleoprotein (vRNP) complexes within virions. Assembly vRNPs is inhibited by phosphorylation N serine/arginine (SR) region. Several SARS-CoV-2 variants concern carry mutations that reduce and enhance efficiency packaging. Variants dominant B.1.1 lineage also encode a truncated protein, termed

Language: Английский

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More or less deadly? A mathematical model that predicts SARS-CoV-2 evolutionary direction

Computers in Biology and Medicine, Journal Year: 2023, Volume and Issue: 153, P. 106510 - 106510

Published: Jan. 6, 2023

SARS-CoV-2 has caused tremendous deaths globally. It is of great value to predict the evolutionary direction SARS-CoV-2. In this paper, we proposed a novel mathematical model that could trend We focus on mutational effects viral assembly capacity. A robust coarse-grained constructed simulate virus dynamics in host body. Both virulence and transmissibility can be quantified model. delicate equilibrium point optimizes numerically obtained. Based model, might further decrease, accompanied by an enhancement transmissibility. However, not continuous; its will disappear but remains at relatively stable range. which simulates packing process also proposed. explained why few mutations would lead significant divergence clinical performance, both overall particle formation quantity virulence. This research provides attempt elucidate driving force RNA evolution.

Language: Английский

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Modulation of biophysical properties of nucleocapsid protein in the mutant spectrum of SARS-CoV-2

eLife, Journal Year: 2024, Volume and Issue: 13

Published: Feb. 6, 2024

Genetic diversity is a hallmark of RNA viruses and the basis for their evolutionary success. Taking advantage uniquely large genomic database SARS-CoV-2, we examine impact mutations across spectrum viable amino acid sequences on biophysical phenotypes highly expressed multifunctional nucleocapsid protein. We find variation in physicochemical parameters its extended intrinsically disordered regions (IDRs) sufficient to allow local plasticity, but also observe functional constraints that similarly occur related coronaviruses. In experiments with several N-protein species carrying associated major variants, point IDRs can have nonlocal modulate thermodynamic stability, secondary structure, protein oligomeric state, particle formation, liquid-liquid phase separation. Omicron variant, distant different compensatory effects shifting delicate balance interactions controlling assembly properties, include creation new protein-protein interaction interface N-terminal IDR through defining P13L mutation. A picture emerges where genetic accompanied by significant characteristics species, particular IDRs.

Language: Английский

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