Clinically observed deletions in SARS‐CoV‐2 Nsp1 affect its stability and ability to inhibit translation

Kumar, Pravin; Schexnaydre, Erin; Rafie, Karim; Kurata, Tatsuaki; Terenin, Ilya M.; Hauryliuk, Vasili; Carlson, Lars A.

doi:10.1002/1873-3468.14354

Cited by 6 publications

(5 citation statements)

References 46 publications

(119 reference statements)

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“…The main function of NSP1 is to inhibit the host protein synthesis by inserting its C-terminus into the mRNA entry tunnel on the ribosome, and thereby “shutoff” the host protein translation process ( Schubert et al 2020 ; Thoms et al 2020 ). The N-terminal domain, nevertheless, has also been demonstrated to contribute to this process to some extent ( Mendez et al 2021 ; Kumar et al 2022 ). In particular, deletion mutations at this location have been shown to result in a lower level of mRNA translation inhibition ( Kumar et al 2022 ), and alter the host transcriptome profiles to be more like the negative control one, although still distinct ( Lin et al 2021 ), likely due to the protein structure destabilization ( Lin et al 2021 ; Kumar et al 2022 ).…”

Section: Resultsmentioning

confidence: 99%

“…The N-terminal domain, nevertheless, has also been demonstrated to contribute to this process to some extent ( Mendez et al 2021 ; Kumar et al 2022 ). In particular, deletion mutations at this location have been shown to result in a lower level of mRNA translation inhibition ( Kumar et al 2022 ), and alter the host transcriptome profiles to be more like the negative control one, although still distinct ( Lin et al 2021 ), likely due to the protein structure destabilization ( Lin et al 2021 ; Kumar et al 2022 ). Perhaps due to its potent negative effect on the host gene expression system, NSP1 has been shown to cause the most severe viability reduction in the human lung H1299 cells compared to other SARS-CoV-2 NSPs ( Yuan et al 2020 ).…”

Section: Resultsmentioning

confidence: 99%

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Systematic Exploration of SARS-CoV-2 Adaptation to Vero E6, Vero E6/TMPRSS2, and Calu-3 Cells

Aiewsakun

Phumiphanjarphak

Ludowyke

et al. 2023

Genome Biology and Evolution

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to spread globally, and scientists around the world are currently studying the virus intensively in order to fight against the on-going pandemic of the virus. To do so, SARS-CoV-2 is typically grown in the lab to generate viral stocks for various kinds of experimental investigations. However, accumulating evidence suggests that such viruses often undergo cell culture adaptation. Here, we systematically explored cell culture adaptation of two SARS-CoV-2 variants, namely the B.1.36.16 variant and the AY.30 variant, a sub lineage of the B.1.617.2 (Delta) variant, propagated in three different cell lines, including Vero E6, Vero E6/TMPRSS2, and Calu-3 cells. Our analyses detected numerous potential cell culture adaptation changes scattering across the entire virus genome, many of which could be found in naturally circulating isolates. Notable ones included mutations around the spike glycoprotein's multibasic cleavage site, and the Omicron-defining H655Y mutation on the spike glycoprotein, as well as mutations in the nucleocapsid protein's linker region, all of which were found to be Vero E6-specific. Our analyses also identified deletion mutations on the non-structural protein 1 and membrane glycoprotein as potential Calu-3-specific adaptation changes. S848C mutation on the non-structural protein 3, located to the protein's papain-like protease domain, was also identified as a potential adaptation change, found in viruses propagated in all three cell lines. Our results highlight SARS-CoV-2 high adaptability, emphasize the need to deep-sequence cultured viral samples when used in intricate and sensitive biological experiments, and illustrate the power of experimental evolutionary study in shedding lights on the virus evolutionary landscape.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Systematic Exploration of SARS-CoV-2 Adaptation to Vero E6, Vero E6/TMPRSS2, and Calu-3 Cells

Aiewsakun

Phumiphanjarphak

Ludowyke

et al. 2023

Genome Biology and Evolution

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“…HEK293F lysate was prepared as described in ( 67 ). 0.26 pmol of capped or uncapped Fluc mRNA (0.52 pmol for Vaccinia capped mRNA) wild-type (wt) or premature termination codon (PTC)-containing was incubated in 10 μl mixture containing 50% (v/v) HEK293F lysate, 20 mM HEPES–KOH pH 7.5, 2 mM DTT, 0.25 mM spermidine, 0.6 mM Mg (OAc) 2 , 16 mM creatine phosphate, 0.06 U/μl creatine kinase (SigmaAldrich), 1 mM ATP, 0.6 mM GTP, 60 mM KOAc, 0.05 mM of each proteinogenic amino acid (Promega), 0.2 U/μl RiboLock (Thermo Scientific), 5 mM d -luciferin.…”

Section: Methodsmentioning

confidence: 99%

The impact of mRNA poly(A) tail length on eukaryotic translation stages

Biziaev,

Shuvalov,

Salman

et al. 2024

Nucleic Acids Research

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The poly(A) tail plays an important role in maintaining mRNA stability and influences translation efficiency via binding with PABP. However, the impact of poly(A) tail length on mRNA translation remains incompletely understood. This study explores the effects of poly(A) tail length on human translation. We determined the translation rates in cell lysates using mRNAs with different poly(A) tails. Cap-dependent translation was stimulated by the poly(A) tail, however, it was largely independent of poly(A) tail length, with an exception observed in the case of the 75 nt poly(A) tail. Conversely, cap-independent translation displayed a positive correlation with poly(A) tail length. Examination of translation stages uncovered the dependence of initiation and termination on the presence of the poly(A) tail, but the efficiency of initiation remained unaffected by poly(A) tail extension. Further study unveiled that increased binding of eRFs to the ribosome with the poly(A) tail extension induced more efficient hydrolysis of peptidyl-tRNA. Building upon these findings, we propose a crucial role for the 75 nt poly(A) tail in orchestrating the formation of a double closed-loop mRNA structure within human cells which couples the initiation and termination phases of translation.

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“…Mutation of the full region in experiments with infected cells induced a lower IFN-I response, correlated with lower viral load and serum IFN-β [ 59 ]. Deleting this region reduced the translation inhibition efficiency of Nsp1 [ 60 ].…”

Section: Evolutionary Insights and Variantsmentioning

confidence: 99%

The art of hijacking: how Nsp1 impacts host gene expression during coronaviral infections

Karousis

2024

Biochemical Society Transactions

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Non-structural protein 1 (Nsp1) is one of the first proteins produced during coronaviral infections. It plays a pivotal role in hijacking and rendering the host gene expression under the service of the virus. With a focus on SARS-CoV-2, this review presents how Nsp1 selectively inhibits host protein synthesis and induces mRNA degradation of host but not viral mRNAs and blocks nuclear mRNA export. The clinical implications of this protein are highlighted by showcasing the pathogenic role of Nsp1 through the repression of interferon expression pathways and the features of viral variants with mutations in the Nsp1 coding sequence. The ability of SARS-CoV-2 Nsp1 to hinder host immune responses at an early step, the absence of homology to any human proteins, and the availability of structural information render this viral protein an ideal drug target with therapeutic potential.

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Clinically observed deletions in SARS‐CoV‐2 Nsp1 affect its stability and ability to inhibit translation

Cited by 6 publications

References 46 publications

Systematic Exploration of SARS-CoV-2 Adaptation to Vero E6, Vero E6/TMPRSS2, and Calu-3 Cells

Systematic Exploration of SARS-CoV-2 Adaptation to Vero E6, Vero E6/TMPRSS2, and Calu-3 Cells

The impact of mRNA poly(A) tail length on eukaryotic translation stages

The art of hijacking: how Nsp1 impacts host gene expression during coronaviral infections

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