The SARS-CoV-2 RNA–protein interactome in infected human cells

Abstract

Characterizing the interactions that SARS-CoV-2 viral RNAs make with host cell proteins during infection can improve our understanding of viral RNA functions and the host innate immune response. Using RNA antisense purification and mass spectrometry, we identified up to 104 human proteins that directly and specifically bind to SARS-CoV-2 RNAs in infected human cells. We integrated the SARS-CoV-2 RNA interactome with changes in proteome abundance induced by viral infection and linked interactome proteins to cellular pathways relevant to SARS-CoV-2 infections. We demonstrated by genetic perturbation that cellular nucleic acid-binding protein (CNBP) and La-related protein 1 (LARP1), two of the most strongly enriched viral RNA binders, restrict SARS-CoV-2 replication in infected cells and provide a global map of their direct RNA contact sites. Pharmacological inhibition of three other RNA interactome members, PPIA, ATP1A1, and the ARP2/3 complex, reduced viral replication in two human cell lines. The identification of host dependency factors and defence strategies as presented in this work will improve the design of targeted therapeutics against SARS-CoV-2.

Revealing the host antiviral protein ZAP-S as an inhibitor of SARS-CoV-2 programmed ribosomal frameshifting

“…1C, Supplementary Table 1). Proteins recently identified in genome-wide interactome studies as direct RNA interaction partners for SARS-CoV-2 were selected for downstream functional characterization 3,[20][21][22] . Several of these have been shown to play a role in RNA processing, including splicing (such as HNRNPs F, H1, and H2), RNA trimming (POP1) and RNA decay (ZAP) [23][24][25] .…”

“…Global analyses of RNA-and protein-interaction networks have increased our understanding of SARS-CoV-2 viral replication in a short time 2,3 . However, there is a lack of detailed mechanistic understanding of the interplay between RNA-protein complexes, which could inform the design of novel antivirals.…”

The mutation profile of SARS-CoV-2 is primarily shaped by the host antiviral defense

“…Target sequence preferences of APOBEC proteins are observed in our mutational profile, where the 5 out of 7 highest normalized mutational counts on C>U distributes along 5’-UC-3’ and 5’–CC–3’ motifs (Figure 2A) . It is also experimentally found that A1CF RNA editing cofactor, which is APOBEC1 complementation factor, is among the SARS-CoV-2 RNA binders (Schmidt et al, 2020) that strengthens the hypothesis of APOBEC proteins’ activity on the C>U substitutions.…”

SARS-CoV-2 Portrayed Against HIV: Contrary Viral Strategies in Similar Disguise

“…Proteomic studies further showed that SARS-CoV-2 reshapes cellular translation, splicing, carbon metabolism, protein homeostasis, and nucleic acid metabolism [143]. In addition to viral proteins, it was shown that SARS-CoV-2 RNA directly and specifically binds and/or modulates a broad network of human proteins in infected human cells [145], and host mitochondria serve as an organelle platform for anti-SARS-CoV-2 immunity [146].…”