Proximity Proteomics Identifies IFI16 as a Host Factor of Human Coronavirus Infection 2258522

Abstract

Abstract Introduction Several proteomic approaches have been employed to determine the interacting partners of SARS-CoV-2 encoded proteins, with the goal of identifying protein targets for the design and evaluation of host-directed therapies against SARS-CoV-2. Proximity-dependent labelling followed by mass spectrometry (PDL-MS) is one such approach that has been employed in the study of interactions between SARS-CoV-2 proteins and the host cell. However, the proximity-dependent proteomic approaches employed in the study of SARS-CoV-2 so far have utilized either BioID or miniTurboID, a modified version of BioID. Methods We utilized split-TurboID, a versatile tool for probing the proximal partners of protein-protein interactions, to identify host proteins that are proximal partners of the non-structural proteins of SARS-CoV-2. We further carried out CRISPR-Ca9 knockout and CRISPRi knockdown assays to determine the role of the identified proximal partners of SARS-CoV-2 NSPs in human coronavirus infection. Results We identified IFI16, along with several RNA-binding proteins, as proximal partners of SARS-CoV-2 NSPs. Follow-up CRISPR-Cas9 knockout and CRISPRi knockdown of IFI16 in A549-ACE2 cells resulted in a decrease in human coronavirus infection. We further demonstrated reduced viral RNA replication and viral protein synthesis upon loss of IFI16. Interestingly, the loss of IFI16 results in reduced expression of type I IFNs and other interferon-stimulated genes. Conclusion Taken together, these data demonstrate that IFI16 promotes human coronavirus infection, and its role in coronavirus replication is independent of its role as a regulator of type I IFN gene expression. Funding Source VCIID COBRE (5P30GM118228-02) and TGIR COBRE (5P20GM125498-03) Topic Categories Viral Immunology (VIR)