Protein turnover dynamics of IAV-infected HeLa cells

The abundance of a protein is defined by its continuous synthesis and degradation, a process known as protein turnover. Here, we systematically profiled the turnover of proteins in influenza A virus (IAV) infected cells using a pulse-chase SILAC-based approach combined with downstream statistical modeling. We identified 1414 virus-affected proteins with turnover changes (tVAPs) out of 7739 detected proteins. In particular, the affected proteins were involved in RNA transcription, splicing and nuclear transport, protein translation and stability, and energy metabolism. Many tVAPs are known IAV-interacting proteins that regulate virus propagation, such as KPNA6, PPP6C and POLR2A. Notably, our analysis identified novel IAV host and restriction factors, such as the splicing factor GPKOW, that exhibit significant turnover rate changes, while their total abundance is not affected. Overall, we show that protein turnover is a critical factor both for virus replication and antiviral defense.