Unlocking the puzzle: non-defining mutations in SARS-CoV-2 proteome may affect vaccine effectiveness DOI Creative Commons

Eugenia Ulzurrun,

Ana Grande-Pérez, Daniel del Hoyo

и другие.

Frontiers in Public Health, Год журнала: 2024, Номер 12

Опубликована: Авг. 15, 2024

Introduction SARS-CoV-2 variants are defined by specific genome-wide mutations compared to the Wuhan genome. However, non-clade-defining may also impact protein structure and function, potentially leading reduced vaccine effectiveness. Our objective is identify across entire viral genome rather than focus on individual that be associated with failure examine physicochemical properties of resulting amino acid changes. Materials methods Whole-genome consensus sequences from COVID-19 patients were retrieved GISAID database. Analysis focused Dataset_1 (7,154 genomes Italy) Dataset_2 (8,819 Spain). Bioinformatic tools identified changes codon frequencies 10% or higher, organized into sets based identical combinations. Results Non-defining in belonging clades 21 L (Omicron), 22B/22E 22F/23A (Omicron) 21J (Delta) failure. Four significantly linked low coverage: one clade 21L L3201F (ORF1a), A27- (S) G30- (N); two shared 22B 22E (S), I68- R346T set 22F 23A containing F486P (N). Booster doses showed a slight improvement protection against Omicron clades. Regarding exhibited combination non-clade P2046L P2287S L829I (ORF1b), T95I Y145H R158- Q9L (N), was Discussion Vaccine coverage associations appear influenced harbored marketed vaccines. An analysis revealed primarily hydrophobic polar substitutions occurred. results suggest non-defining proteome could affect extent vaccine. In addition, alteration characteristics acids disrupt function both.

Язык: Английский

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

Ai Nguyen,

Huaying Zhao,

Dulguun Myagmarsuren

и другие.

eLife, Год журнала: 2024, Номер 13

Опубликована: Фев. 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.

Язык: Английский

Процитировано

9
Efficient overexpression and purification of SARS-CoV-2 Nucleocapsid proteins in Escherichia coli DOI Creative Commons
Emma L. Brudenell, Manoj Baliram Pohare, Domen Zafred

и другие.

Biochemical Journal, Год журнала: 2024, Номер 481(11), С. 669 - 682

Опубликована: Май 7, 2024

The fundamental biology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid protein (Ncap), its use in diagnostic assays and potential application as a vaccine component have received considerable attention since the outbreak Covid19 pandemic late 2019. Here we report scalable expression purification soluble, immunologically active, SARS-CoV-2 Ncap Escherichia coli. Codon-optimised synthetic genes encoding original sequence four common variants with an N-terminal 6His affinity tag (sequence MHHHHHHG) were cloned into inducible vector carrying regulated bacteriophage T5 promoter controlled by lac operator binding sites. constructs used to express proteins protocols developed which allow efficient production purified yields over 200 mg per litre culture media. These deployed ELISA comparison their responses human sera. Our results suggest that there was no detectable difference between 6His-tagged untagged but may be slight loss sensitivity sera other isolates.

Язык: Английский

Процитировано

3
Variant mutation G215C in SARS-CoV-2 nucleocapsid enhances viral infection via altered genomic encapsidation DOI Creative Commons

Hannah C. Kubinski,

Hannah W. Despres, Bryan A. Johnson

и другие.

PLoS Biology, Год журнала: 2025, Номер 23(4), С. e3003115 - e3003115

Опубликована: Апрель 29, 2025

The evolution of SARS-CoV-2 variants and their respective phenotypes represents an important set tools to understand basic coronavirus biology as well the public health implications individual mutations in concern. While outside spike are not studied, entire viral genome is undergoing evolutionary selection, with several containing central disordered linker region nucleocapsid (N) protein. Here, we identify a mutation (G215C), characteristic Delta variant, that introduces novel cysteine into this domain, which results formation more stable N-N dimer. Using reverse genetics, determined residue necessary sufficient for dimer WA1 background, where it significantly increased growth both vitro vivo. Mechanistically, show N:G215C mutant has encapsidation measured by RNA binding N, N incorporation virions, electron microscopy showing virions larger, elongated morphologies.

Язык: Английский

Процитировано

0
Intrinsic Factors Behind Long COVID: VI. Combined Impact of G3BPs and SARS‐CoV‐2 Nucleocapsid Protein on the Viral Persistence and Long COVID DOI

Ahmed Eltayeb,

Alberto Rubio‐Casillas, Vladimir N. Uversky

и другие.

Journal of Cellular Biochemistry, Год журнала: 2025, Номер 126(5)

Опубликована: Май 1, 2025

The efficient transmission of SARS-CoV-2 caused the COVID-19 pandemic, which affected millions people around globe. Despite extensive efforts, specific therapeutic interventions and preventive measures against its consequences, such as long COVID, have not yet been identified due to lack a comprehensive knowledge biology. Therefore, deeper understanding sophisticated strategies employed by bypass host antiviral defense systems is needed. One these inhibition Ras GTPase-activating protein-binding protein (GAP SH3-binding or G3BP)-dependent immune response nucleocapsid (N) protein. This disrupts formation stress granules (SGs), are crucial for defense. By preventing SG formation, virus enhances replication evades host's response, leading increased disease severity. Given involvement G3BP1 in ability interact with viral proteins, along role N virus, we hypothesize that proteins may potential pathogenesis COVID. current direct evidence linking their interactions functions suggest possible connection warrants further investigation.

Язык: Английский

Процитировано

0
Evolution of Virus-like Features and Intrinsically Disordered Regions in Retrotransposon-derived Mammalian Genes DOI Creative Commons
Rachele Cagliani, Diego Forni, Alessandra Mozzi

и другие.

Molecular Biology and Evolution, Год журнала: 2024, Номер 41(8)

Опубликована: Авг. 1, 2024

Abstract Several mammalian genes have originated from the domestication of retrotransposons, selfish mobile elements related to retroviruses. Some proteins encoded by these maintained virus-like features; including self-processing, capsid structure formation, and generation different isoforms through −1 programmed ribosomal frameshifting. Using quantitative approaches in molecular evolution biophysical analyses, we studied 28 retrotransposon-derived genes, with a focus on features. By analyzing rate synonymous substitutions, show that frameshifting mechanism three (PEG10, PNMA3, PNMA5) is conserved across mammals originates alternative proteins. These were targets positive selection primates, one positively selected sites affects B-cell epitope spike domain PNMA5 capsid, finding reminiscent observations infectious viruses. More generally, found vary their intrinsically disordered region content this directly associated evolutionary rates. Most are located regions some them impact protein posttranslational modifications, such as autocleavage phosphorylation. Detailed analyses properties showed preferentially targeted lower conformational entropy. Furthermore, introduces variation binary sequence patterns orthologues, well chain compaction. Our results shed light trajectories unique class suggest novel approach study how characteristics affected evolution.

Язык: Английский

Процитировано

2
A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding DOI Creative Commons
Karthikeyan Dhamotharan, Sophie Marianne Korn, Anna Wacker

и другие.

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Дек. 9, 2024

Abstract The SARS-CoV-2 nucleocapsid protein is indispensable for viral RNA genome processing. Although the N-terminal domain (NTD) suggested to mediate specific RNA-interactions, high-resolution structures with are still lacking. Available hybrid of NTD ssRNA and dsRNA provide valuable insights; however, precise mechanism complex formation remains elusive. Similarly, molecular impact mutations that have emerged since 2019 has not yet been fully explored. Using crystallography solution NMR, we investigate how influence structural integrity RNA-binding. We find both features rely on a core network residues conserved in Betacoronaviruses , crucial stability communication among flexible loop-regions facilitate RNA-recognition. Our comprehensive analysis demonstrates contacts within this guide selective RNA-interactions. propose renders evolutionarily robust plasticity its versatile processing roles.

Язык: Английский

Процитировано

1
Assembly reactions of SARS-CoV-2 nucleocapsid protein with nucleic acid DOI Open Access
Huaying Zhao, Abdullah M. Syed, Mir M. Khalid

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Ноя. 23, 2023

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 mutant proteins different nucleic acids an vitro assay for RNP formation, examining 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 multi-valent protein-nucleic acid establish crosslinks dimeric subunits. Assemblies CTD offering more than one site stem-loop RNA. Our study suggests model where N- scaffolding at density on followed cooperative multimerization through linker.

Язык: Английский

Процитировано

3
How mutations affect function DOI Creative Commons
Thomas E. Kuhlman

eLife, Год журнала: 2024, Номер 13

Опубликована: Июнь 28, 2024

A new study reveals how naturally occurring mutations affect the biophysical properties of nucleocapsid proteins in SARS-CoV-2.

Язык: Английский

Процитировано

0
Unlocking the puzzle: non-defining mutations in SARS-CoV-2 proteome may affect vaccine effectiveness DOI Creative Commons

Eugenia Ulzurrun,

Ana Grande-Pérez, Daniel del Hoyo

и другие.

Frontiers in Public Health, Год журнала: 2024, Номер 12

Опубликована: Авг. 15, 2024

Introduction SARS-CoV-2 variants are defined by specific genome-wide mutations compared to the Wuhan genome. However, non-clade-defining may also impact protein structure and function, potentially leading reduced vaccine effectiveness. Our objective is identify across entire viral genome rather than focus on individual that be associated with failure examine physicochemical properties of resulting amino acid changes. Materials methods Whole-genome consensus sequences from COVID-19 patients were retrieved GISAID database. Analysis focused Dataset_1 (7,154 genomes Italy) Dataset_2 (8,819 Spain). Bioinformatic tools identified changes codon frequencies 10% or higher, organized into sets based identical combinations. Results Non-defining in belonging clades 21 L (Omicron), 22B/22E 22F/23A (Omicron) 21J (Delta) failure. Four significantly linked low coverage: one clade 21L L3201F (ORF1a), A27- (S) G30- (N); two shared 22B 22E (S), I68- R346T set 22F 23A containing F486P (N). Booster doses showed a slight improvement protection against Omicron clades. Regarding exhibited combination non-clade P2046L P2287S L829I (ORF1b), T95I Y145H R158- Q9L (N), was Discussion Vaccine coverage associations appear influenced harbored marketed vaccines. An analysis revealed primarily hydrophobic polar substitutions occurred. results suggest non-defining proteome could affect extent vaccine. In addition, alteration characteristics acids disrupt function both.

Язык: Английский

Процитировано

0