A new study published in Cell Systems looked at the ways influenza A virus (IAV) manipulates the dynamic process of protein turnover to infect host cells and evade the immune response.
Protein turnover, which involves the continuous synthesis and degradation of proteins, plays a pivotal role in maintaining cellular function. During IAV infection, however, this process becomes a site of intense competition. The virus manipulates the host’s protein synthesis machinery to favor viral protein production while evading immune defenses. Although previous studies have explored the regulation of protein synthesis and degradation during viral infections, comprehensive, system-wide insights into these processes have been limited.
The new study systematically profiled the turnover of thousands of proteins in IAV-infected cells using a technique called pulse-chase stable isotope labeling with amino acids in cell culture (pSILAC). This approach enabled precise tracking of protein synthesis and degradation over time, revealing how these processes change in response to viral infection.
Researchers examined HeLa cells infected with both a wild-type IAV strain and a mutant strain lacking the non-structural protein 1 (NS1), a key factor in IAV’s ability to suppress host immune responses. The team identified nearly 1,800 proteins, termed virus-affected proteins with turnover changes (tVAPs), out of 7,739 detected proteins that exhibited altered turnover rates during infection. These tVAPs spanned various biological processes, including RNA transcription, protein stability, energy metabolism, and nuclear transport.
Interestingly, many of the proteins with altered turnover, including KPNA6, PPP6C, and POLR2A, were previously known to interact with IAV proteins and play roles in viral propagation. The study also identified new proteins with significant turnover changes not previously linked to IAV infection, such as GPKOW, a splicing factor that was found to regulate antiviral immune responses.
The study revealed IAV significantly alters the degradation rates of various proteins involved in crucial cellular functions, including splicing, translation, and energy production. Notably, proteins forming large complexes, such as components of the eukaryotic translation initiation factor 3 (eIF3) and cytosolic ribosomal subunits, were found to be more degraded, potentially allowing the virus to selectively manipulate protein synthesis.
Conversely, mitochondrial ribosomal proteins, which are essential for cellular energy production, were stabilized during infection. This stabilization might help IAV maintain the activity of energy-producing pathways needed for efficient viral replication. These findings suggest that the virus actively reshapes the host's protein turnover landscape to support its life cycle.
By combining protein turnover data with published genome-wide screens, the study found many tVAPs were either pro- or antiviral factors. This suggests protein turnover changes can have a significant impact on IAV replication and host defense mechanisms. For instance, GPKOW was found to influence the induction of type I interferon, a critical component of the immune response to viral infections. Knockdown of GPKOW resulted in enhanced viral replication, indicating its role in restricting viral propagation.
The study emphasized the importance of understanding protein turnover as a dynamic and regulated process during viral infections. Identifying proteins whose turnover is manipulated by IAV could provide new targets for antiviral therapy.
By mapping the changes in protein synthesis and degradation during IAV infection, the study uncovered potential avenues for developing treatments that could disrupt these processes and enhance antiviral immunity.
