Structure of Nonstructural Protein 1 from SARS-CoV-2

Abstract

The periodic emergence of novel coronaviruses (CoVs) represents an ongoing public health concern with significant health and financial burden worldwide. The most recent occurrence originated in the city of Wuhan, China where a novel coronavirus (SARS-CoV-2) emerged causing severe respiratory illness and pneumonia. The continual emergence of novel coronaviruses underscores the importance of developing effective vaccines as well as novel therapeutic options that target either viral functions or host factors recruited to support coronavirus replication. The CoV nonstructural protein 1 (nsp1) has been shown to promote cellular mRNA degradation, block host cell translation, and inhibit the innate immune response to virus infection. Interestingly, deletion of the nsp1-coding region in infectious clones prevented the virus from productively infecting cultured cells. Because of nsp1’s importance in the CoV life cycle, it has been highlighted as a viable target for both antiviral therapy and vaccine development. However, the fundamental molecular and structural mechanisms that underlie nsp1 function remain poorly understood, despite its critical role in the viral life cycle. Here we report the high-resolution crystal structure of the amino, globular portion of SARS-CoV-2 nsp1 (residues 10 – 127) at 1.77 Å resolution. A comparison of our structure with the SARS-CoV-1 nsp1 structure reveals how mutations alter the conformation of flexible loops, inducing the formation of novel secondary structural elements and new surface features. Paired with the recently published structure of the carboxyl end of nsp1 (residues 148 – 180), our results provide the groundwork for future studies focusing on SARS-CoV-2 nsp1 structure and function during the viral life cycle. IMPORTANCE The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the causative agent for the COVID-19 pandemic. One protein known to play a critical role in the coronavirus life cycle is nonstructural protein1 (nsp1). As such, it has been highlighted in numerous studies as a target for both the development of antivirals and for the design of live-attenuated vaccines. Here we report the high-resolution crystal structure of nsp1 derived from SARS-CoV-2 at 1.77 Å resolution. This structure will facilitate future studies focusing on understanding the relationship between structure and function for nsp1. In turn, understanding these structure-function relationships will allow nsp1 to be fully exploited as a target for both antiviral development and vaccine design.

SARS-CoV-2 NSP1 C-terminal (residues 131–180) is an intrinsically disordered region in isolation

“…Recently two crystal structure of SARS-CoV-2 NSP1 corresponding to residues 10–127 (PDB ID: 7K7P ) and 13–127 (PDB ID: 7K3N ) have been reported, which suggest that residue 1–10 and 130–180 are highly flexible and cannot be crystallized ( Fig. 1 ) ( Semper et al., 2021 ; Clark et al., 2021 ). Also, the cryo-EM structure of SARS-CoV-2 NSP1-CTR has been reported in the presence of a binding partner ( Thoms et al., 2020 ; Schubert et al., 2020 ).…”

The N-terminal and central domains of CoV-2 nsp1 play key functional roles in suppression of cellular gene expression and preservation of viral gene expression

“…We next sought to better define which residues within the N-terminal domain are required for suppressing gene expression. Guided by existing structural data for the N-terminus 27,28 , we mutated a series of conserved, surface exposed and charged residues (E36A/E37A, E55A/E57A/K58A, R99A and R119A/K120A) (Figure S3A). The mutants were then screened using our GFP reporter assay alongside the R124A/K125A and K164A/H165A controls to determine the effects on protein translation and mRNA decay.…”

“…Further, the identification of a double point mutant at the border of the N-terminal and central domains of SARS CoV nsp1 that disrupts mRNA cleavage but retains translational repression activity has led to the hypothesis that mRNA cleavage occurs subsequent to translational repression and is a functionally separable phenotype 21 . The structure of the N-terminal domain in isolation has been solved, but neither it nor the unstructured central region was resolved in the cryo-electron microscopy structures of CoV-2 nsp1 bound to the 40S ribosomal subunit and thus their role in host shutoff is unclear 28,29 .…”

Multi-Omics Approach in the Identification of Potential Therapeutic Biomolecule for COVID-19

“…Among them, β -CoV has become the utmost concern of the world due to its ability to cause serious illness in the human population, like the Middle East respiratory syndrome–related coronavirus (MERS-CoV), SARS-CoV, and SARS-CoV-2, which cause fatal respiratory tract infection in humans ( Lu et al, 2020 ). The structural and nonstructural information of SARS-CoV-2 has already been explained and explored by many studies available in the literature ( Hillen et al, 2020 ; Jin et al, 2020 ; Clark et al, 2021 ; Hasana et al, 2021 ; Semper et al, 2021 ).…”