SARS-CoV-2 Nsp14 mediates the effects of viral infection on the host cell transcriptome.

Michela Zaffagni,Nagarjuna Reddy Pamudurti,Sebastian Kadener,Jenna M Harris,Sinead Nguyen,Ines L Patop

doi:10.7554/elife.71945

Abstract

Viral infection involves complex set of events orchestrated by multiple viral proteins. To identify functions of SARS-CoV-2 proteins, we performed transcriptomic analyses of cells expressing individual viral proteins. Expression of Nsp14, a protein involved in viral RNA replication, provoked a dramatic remodeling of the transcriptome that strongly resembled that observed following SARS-CoV-2 infection. Moreover, Nsp14 expression altered the splicing of more than 1000 genes and resulted in a dramatic increase in the number of circRNAs, which are linked to innate immunity. These effects were independent of the Nsp14 exonuclease activity and required the N7-guanine-methyltransferase domain of the protein. Activation of the NFkB pathway and increased expression of CXCL8 occurred early upon Nsp14 expression. We identified IMPDH2, which catalyzes the rate-limiting step of guanine nucleotides biosynthesis, as a key mediator of these effects. Nsp14 expression caused an increase in GTP cellular levels, and the effect of Nsp14 was strongly decreased in the presence of IMPDH2 inhibitors. Together, our data demonstrate an unknown role for Nsp14 with implications for therapy.

Highlights

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus responsible for the COVID-19 pandemic that began in 2019
Non-structural proteins are required for viral genome replication and are generated by proteolytic cleavage of the polyprotein encoded by ORF1a and ORF1ab
To identify unknown functions of the individual SARS-CoV-2 proteins and to determine how much each protein contributes to the takeover of cellular systems, we determined how the transcriptome changed when we individually express each viral protein in a human cell line

Summary

Introduction

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus responsible for the COVID-19 pandemic that began in 2019. Coronaviruses are enveloped, relatively small (60-140 nm diameter), positive-stranded RNA viruses belonging to the Coronaviridae family. They derive their name from the crown-like appearance (corona means crown in Latin) that results from the spike glycoproteins in their envelope (V’kovski et al, 2021a). The SARS-CoV-2 RNA genome is 30-kb long and has 14 open reading frames (ORFs) that encode 29 proteins (16 non-structural proteins, 4 structural proteins, and 9 accessory factors, Kim et al, 2020). Non-structural proteins are required for viral genome replication and are generated by proteolytic cleavage of the polyprotein encoded by ORF1a and ORF1ab. New viral particles are incorporated into vesicles and secreted by the host cells (V’kovski et al, 2021a)

Results

Discussion

Conclusion