A Comparative Analysis of Coronavirus Nucleocapsid (N) Proteins Reveals the SADS-CoV N Protein Antagonizes IFN-β Production by Inducing Ubiquitination of RIG-I

Abstract

Coronaviruses (CoVs) are a known global threat, and most recently the ongoing COVID-19 pandemic has claimed more than 2 million human lives. Delays and interference with IFN responses are closely associated with the severity of disease caused by CoV infection. As the most abundant viral protein in infected cells just after the entry step, the CoV nucleocapsid (N) protein likely plays a key role in IFN interruption. We have conducted a comprehensive comparative analysis and report herein that the N proteins of representative human and animal CoVs from four different genera [swine acute diarrhea syndrome CoV (SADS-CoV), porcine epidemic diarrhea virus (PEDV), severe acute respiratory syndrome CoV (SARS-CoV), SARS-CoV-2, Middle East respiratory syndrome CoV (MERS-CoV), infectious bronchitis virus (IBV) and porcine deltacoronavirus (PDCoV)] suppress IFN responses by multiple strategies. In particular, we found that the N protein of SADS-CoV interacted with RIG-I independent of its RNA binding activity, mediating K27-, K48- and K63-linked ubiquitination of RIG-I and its subsequent proteasome-dependent degradation, thus inhibiting the host IFN response. These data provide insight into the interaction between CoVs and host, and offer new clues for the development of therapies against these important viruses.

Time-Resolved Analysis of N-RNA Interactions during RVFV Infection Shows Qualitative and Quantitative Shifts in RNA Encapsidation and Packaging

“…It remains unknown whether the interactions between N and these antiviral protein-coding transcripts affect the protein levels, although this would constitute an intriguing strategy to evade host antiviral responses. It is notable that nucleocapsid proteins of other viruses have been shown to interfere with the host antiviral response [60][61][62][63].…”

Swine Enteric Coronavirus: Diverse Pathogen–Host Interactions

“…SADS-CoV N protein inhibits IFN-β production by targeting TBK1 to interfere with TIR domain-containing adaptor inducing interferon-beta (TRAF3) and TBK1 [ 177 ]. The SADS-CoV N protein also interacts with RIG-I and mediates the ubiquitination of K27-, K48-, and K63-connections of RIG-I to antagonize IFN-β production [ 178 ]. The PDCoV N protein inhibits IFN-β production by interfering with dsRNA binding and the protein activator of protein kinase R (PACT) to RIG-I to inhibit the K63 polyubiquitin of RIG-I [ 169 , 179 ].…”

Modulation of Innate Antiviral Immune Response by Porcine Enteric Coronavirus

“…Moreover, the N-terminal region (1-246aa) of PDCoV N protein is the key part of interacting with porcine RIG-I ( Likai et al, 2019 ). In addition, the N protein of PDCoV and SADS-CoV mediates K63-linked ubiquitination of porcine RIG-I, thereby, inhibit the host IFN-β production ( Likai et al, 2019 ; Liu et al, 2021 ). The expression of the TGEV N gene promotes the accumulation of p53 and p21 and suppresses the expression of cyclin B1, cdc2, and cdk2.…”