High-sensitivity profiling of SARS-CoV-2 noncoding region–host protein interactome reveals the potential regulatory role of negative-sense viral RNA

Abstract

A deep understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)–host interactions is crucial to developing effective therapeutics and addressing the threat of emerging coronaviruses. The role of noncoding regions of viral RNA (ncrRNAs) has yet to be systematically scrutinized. We developed a method using MS2 affinity purification coupled with liquid chromatography-mass spectrometry and designed a diverse set of bait ncrRNAs to systematically map the interactome of SARS-CoV-2 ncrRNA in Calu-3, Huh7, and HEK293T cells. Integration of the results defined the core ncrRNA–host protein interactomes among cell lines. The 5′ UTR interactome is enriched with proteins in the small nuclear ribonucleoproteins family and is a target for the regulation of viral replication and transcription. The 3′ UTR interactome is enriched with proteins involved in the stress granules and heterogeneous nuclear ribonucleoproteins family. Intriguingly, compared with the positive-sense ncrRNAs, the negative-sense ncrRNAs, especially the negative-sense of 3′ UTR, interacted with a large array of host proteins across all cell lines. These proteins are involved in the regulation of the viral production process, host cell apoptosis, and immune response. Taken together, our study depicts the comprehensive landscape of the SARS-CoV-2 ncrRNA–host protein interactome and unveils the potential regulatory role of the negative-sense ncrRNAs, providing a new perspective on virus–host interactions and the design of future therapeutics. Given the highly conserved nature of UTRs in positive-strand viruses, the regulatory role of negative-sense ncrRNAs should not be exclusive to SARS-CoV-2. IMPORTANCE Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19, a pandemic affecting millions of lives. During replication and transcription, noncoding regions of the viral RNA (ncrRNAs) may play an important role in the virus–host interactions. Understanding which and how these ncrRNAs interact with host proteins is crucial for understanding the mechanism of SARS-CoV-2 pathogenesis. We developed the MS2 affinity purification coupled with liquid chromatography-mass spectrometry method and designed a diverse set of ncrRNAs to identify the SARS-CoV-2 ncrRNA interactome comprehensively in different cell lines and found that the 5′ UTR binds to proteins involved in U1 small nuclear ribonucleoprotein, while the 3′ UTR interacts with proteins involved in stress granules and the heterogeneous nuclear ribonucleoprotein family. Interestingly, negative-sense ncrRNAs showed interactions with a large number of diverse host proteins, indicating a crucial role in infection. The results demonstrate that ncrRNAs could serve diverse regulatory functions.

SARS-CoV-2 Nsp1 cooperates with initiation factors EIF1 and 1A to selectively enhance translation of viral RNA

“…For example, EIF3A regulates re-initiation after termination of uORF translation [ 53 , 54 ], and DDX3 facilitates translation of mRNAs with complex 5’UTR [ 55 ] and promotes CoV2 infection [ 56 ]. Many RNA helicases are also known to bind CoV2 RNA [ 12 , 57 ] and modulate infection [ 58 ]. Future work will need to determine how EIF1/1A depletion remodels polysome interactions during CoV2 infection, and whether additional factors contribute to initiation fidelity on CoV2 RNAs.…”

Integration of risk variants from GWAS with SARS-CoV-2 RNA interactome prioritizes FUBP1 and RAB2A as risk genes for COVID-19

“…Since FUBP1 binds to SARS-CoV-2, we propose that FUBP1 functions in an anti-viral way by suppressing transcription or protein translation. It has been validated that FUBP1 binds to the negative-sense of 29534-29870 in SARS-CoV-2 RNA (ORF10, 3’UTR, and poly(A)) in Calu-3 cells and might play a transcription role 62 . We speculate that FUBP1 functions in an anti-viral way by binding to ORF10 and 3’UTR of the negative strand in SARS-CoV-2 RNA and repressing the transcription of SARS-CoV-2.…”