Dataset Information

Gene expression profiling of HBEpCs and Caco-2 cells during infection with WT SARS-CoV-2 or a recombinant SARS-CoV-2 deficient in PLpro deISGylation activity

ABSTRACT: Interferon-stimulated gene 15 (ISG15) regulates diverse cellular processes, including antiviral immunity, through its conjugation to proteins, a process known as ISGylation. Several pathogens, including SARS-CoV-2, subvert ISGylation by encoding deISGylating enzymes. However, the direct targets and physiological consequences of coronaviral deISGylation remain poorly defined. Here, we engineered a recombinant SARS-CoV-2 harboring a mutant Nsp3 (Nsp3mut) with impaired papain-like protease (PLpro) deISGylating activity. Caco-2 and human bronchial epithelial (HBEpC) cells were infected with either wild-type or Nsp3mut SARS-CoV-2. Comparative transcriptomic profiling revealed that Nsp3mut infection led to a stronger induction of IFN- and ISG-related gene signatures compared to wild-type virus infection in both cell types. These results show that loss of PLpro-mediated deISGylation restores efficient antiviral innate immune responses during SARS-CoV-2 infection.

ORGANISM(S): Homo sapiens

PROVIDER: GSE308448 | GEO | 2026/05/08

REPOSITORIES: GEO

ACCESS DATA

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description:Human coronaviruses have become an increasing threat to global health; three highly pathogenic strains have emerged since the early 2000s, including most recently SARS-CoV-2, the cause of COVID-19. A better understanding of the molecular mechanisms of coronavirus pathogenesis is needed, including how these highly virulent strains differ from those that cause milder, common-cold like disease. While significant progress has been made in understanding how SARS-CoV-2 proteins interact with the host cell, non-structural protein 3 (nsp3) has largely been omitted from the analyses. Nsp3 is a viral protease with important roles in viral protein biogenesis, replication complex formation, and modulation of host ubiquitinylation and ISGylation. Herein, we use affinity purification-mass spectrometry to study the host-viral protein-protein interactome of nsp3 from five coronavirus strains: pathogenic strains SARS-CoV-2, SARS-CoV, and MERS-CoV, and endemic common-cold strains hCoV-229E and hCoV-OC43. We divide each nsp3 into three fragments and use tandem mass tag technology to directly compare the interactors across the five strains for each fragment. We find that that few interactors are common across all variants for a particular fragment, but we identify shared patterns between select variants, such as ribosomal proteins enriched in the N-terminal fragment (nsp3.1) analysis for SARS-CoV-2 and SARS-CoV. We also identify unique biological processes enriched for individual homologs, for instance nuclear protein important for the middle fragment of hCoV-229E, as well as ribosome biogenesis of the MERS nsp3.1 homolog. Lastly, we further investigate the interaction of the SARS-CoV-2 nsp3.1 N-terminal fragment with ATF6, a regulator of the unfolded protein response. We show that SARS-CoV-2 nsp3.1 directly binds to ATF6 and can suppress the ATF6 stress response. Characterizing the host interactions of nsp3 widens our understanding of how coronaviruses co-opt cellular pathways and presents new avenues for host-targeted antiviral therapeutics.

Dataset Information

Gene expression profiling of HBEpCs and Caco-2 cells during infection with WT SARS-CoV-2 or a recombinant SARS-CoV-2 deficient in PLpro deISGylation activity

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets