Phospholipid scramblase 1 interacts with influenza A virus NP, impairing its nuclear import and thereby suppressing virus replication

Transcription and replication of the influenza A virus (IAV) genome occur in the nucleus of infected cells and are carried out by the viral ribonucleoprotein complex (vRNP). As a major component of the vRNP complex, the viral nucleoprotein (NP) mediates the nuclear import of the vRNP complex via its nuclear localization signals (NLSs). Clearly, an effective way for the host to antagonize IAV infection would be by targeting vRNP nuclear import. Here, we identified phospholipid scramblase 1 (PLSCR1) as a binding partner of NP by using a yeast two-hybrid (Y2H) screen. The interaction between NP and PLSCR1 in mammalian cells was demonstrated by using co-immunoprecipitation and pull-down assays. We found that the stable overexpression of PLSCR1 suppressed the nuclear import of NP, hindered the virus life cycle, and significantly inhibited the replication of various influenza subtypes. In contrast, siRNA knockdown or CRISPR/Cas9 knockout of PLSCR1 increased virus propagation. Further analysis indicated that the inhibitory effect of PLSCR1 on the nuclear import of NP was not caused by affecting the phosphorylation status of NP or by stimulating the interferon (IFN) pathways. Instead, PLSCR1 was found to form a trimeric complex with NP and members of the importin α family, which inhibited the incorporation of importin β, a key mediator of the classical nuclear import pathway, into the complex, thus impairing the nuclear import of NP and suppressing virus replication. Our results demonstrate that PLSCR1 negatively regulates virus replication by interacting with NP in the cytoplasm and preventing its nuclear import.
Author summary Influenza viral RNA is encapsidated by three polymerase proteins and the NP protein to form the vRNP complex, which is transported to the nucleus of infected cells for viral transcription and replication. The active nuclear import of the vRNP complex is mediated by the interaction between NP and importin α through the nuclear import pathway. Because the interactions between NP and the components of the nuclear import pathway are indispensable in mediating the nuclear import of the vRNP complex, the host has evolved mechanisms to antagonize influenza virus infection that target this crucial step. In this study, we identified PLSCR1 as an interacting partner of the influenza NP protein. We found that PLSCR1 negatively regulates influenza virus replication by inhibiting the nuclear import of the NP/vRNP complex. Importantly, we found that PLSCR1 did not disrupt the interaction between NP and importin α. Instead, NP, PLSCR1, and importin α formed a stable complex that blocked the interaction between importin α and importin β, thereby inhibiting the import of NP/vRNP complex through the nuclear import pathway. Our findings provide an example of a host restriction factor binding simultaneously to a nuclear import adaptor and to a cargo protein to inhibit the import of that cargo into the nucleus.