Identification of RC3H1 as antiviral host factor binding to the non-structural protein 1 of Influenza A virus via a 3-stage computational pipeline and cell-based analysis

To complete its life-cycle in the infected host, Influenza A virus (IAV) hijacks host machineries by expressing multiple viral proteins to bind to specific host proteins. In the era of integrative genomics, there is an opportunity to develop computational techniques to accurately and quickly predict host-pathogen protein-protein interactions (HP-PPI). Our 3-stage computational pipeline shortlisted host proteins (of which stages (i) and (ii) have been previously reported) containing the C3H zinc finger domain as putative interactors of the non-structural protein (NS1) of A/PR8/34 (H1N1), which is a well-characterized laboratory strain. To assess the accuracy of this computational pipeline, the top 7 highest scoring C3H zinc finger proteins were examined in co-immunoprecipitation experiments to determine which pair(s) of interaction is detectable in mammalian cell lines. Interestingly, one of them is CPSF30 which is a known NS1 binder. For the other 6 C3H zinc finger proteins, they have not been reported to be involved in IAV replication and co-immunoprecipitation experiments reveals that 4 of them bind to NS1. As a proof-of-concept, one shortlisted C3H protein was studied using live IAV infection and the knockdown of RC3H1 slightly increased the production of progeny virion, suggesting that it acts as an antiviral host factor.