The Role of the Host Ubiquitin System in Promoting SARS-CoV-2 replication and Pathogenesis

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The Severe Acute Respiratory Syndrome Coronavirus 2 (CoV-2) belongs to a family of pathogenic enveloped RNA viruses of the family Coronaviridae. The ongoing pandemic has caused a public health emergency worldwide, accompanied by dire health and economic consequences. There is evidence suggesting that CoV-2 may have relatively higher infection rates compared to previous epidemic strains of SARS and higher affinity to the receptor ACE2 than SARS-1. In addition, new CoV-2 variants have appeared recently with mutations that correlate with higher infection rates and the ability to escape specific immunity, causing major concerns. A major gap in knowledge remains as to how CoV-2 may have acquired the ability to spread more efficiently, and how new mutations may affect virus infectivity. The overarching goal of this proposal is to better understand the molecular mechanisms that regulate CoV-2 cell entry and replication, and how the appearance of new variants could lead to immune escape. We will focus on the role of the host Ubiquitin (Ub) system in promoting CoV-2 infection. This information could help predict appearance of more transmissible variants of coronaviruses, and to develop antiviral approaches by targeting specific steps of the ubiquitination process. Our data recently published in Nature, show that the envelope protein of flaviviruses is K63-linked polyubiquitinated, which enhances virus attachment to host cell receptors. Therefore, we asked whether a similar mechanism applies to SARS-CoV-2. Our preliminary data indicate that CoV-2 structural proteins are ubiquitinated on multiple lysine residue, some of which are not conserved in the original epidemic CoV strain. In addition, new variants of CoV-2 have appeared with mutations on these ubiquitination sites. Our data also suggest that ubiquitination of Spike (S) protein may play a role in stabilizing the CoV-2 S-ACE2 interaction, potentially leading to enhanced entry and pathogenesis. It is currently unknown whether any member of the Coronaviridae family, including SARS-CoV-2, utilize ubiquitination of viral structural proteins as a mechanism of virus attachment and entry. We have also identified E3-Ub ligases of the Tripartite Motif (TRIM) family of proteins, which ubiquitinates viral structural proteins. Our general hypothesis is that the variants of CoV-2 that have gained specific lysine residues provide new Ub acceptor sites on structural proteins, which can enhance virus replication and immune escape. By using in vitro biochemical approaches, novel recombinant mutant viruses, and in vivo models, we will assess how ubiquitination of structural CoV-2 proteins contribute to CoV-2 infectivity. In Aim 1 we will determine the mechanistic role of ubiquitination of the CoV-2 S protein in virus replication and antibody escape, and in Aim 2 we will determine the mechanistic role of ubiquitination of the CoV-2 Membrane protein in virus replication and IFN antagonism. The outcome of these studies may help explain how new more infectious viruses may appear by gaining ubiquitination sites and will provide the basis for the development of an antiviral approach that could be applied to a broad range of enveloped viruses.