The RBPome of influenza A virus mRNA reveals a role for TDP-43 in viral replication

Recent technical advances, particularly in mass spectrometry-based proteomics, have significantly improved our understanding of the RNA-binding protein (RBP) repertoire present within eukaryotic cells, with particular emphasis on RBPs that interact with cellular polyadenylated mRNAs. However, recent studies using the same technologies have distinguished the RBP interactome of viral mRNAs, including SARS-CoV-2, revealing both similarities and differences between the RBP profiles of viral and cellular mRNAs.

In our study, we combined recent protein-RNA crosslinking, RNA interactome capture using a sequence-specific antisense RNA probe with recent quantitative proteomics approaches with high-resolution mass spectrometry, and dedicated bioinformatics and statistical analysis to identify the RBP proteins that are associated with the NP mRNA of an influenza A virus (IAV).

In our study, we combined recent methods of protein-RNA cross-linking, RNA interactome capture using a sequence-specific antisense RNA probe, and mass spectrometry to identify RBP proteins associated with NP mRNA from an influenza A virus (IAV). These technologies, combined with a robust quantitative proteomic approach and dedicated bioinformatics and statistical tools, allowed us to identify 51 RBP proteins in infected human cells that interact directly with the NP mRNA of an influenza A virus.

By combining our proteomic data with loss-of-function experiments, we discovered cellular factors important for productive viral infection, among which the host protein TDP-43 is recruited by the transcribing viral polymerase through an RNA-independent interaction between FluPol and TDP-43. Overall, our data provide the first insights into the composition and function of influenza mRNPs and reveal a critical role for viral transcriptase in the recruitment of cellular RBPs to viral mRNPs.