Caspase cleavage of Influenza A virus M2 disrupts M2-LC3 interaction and regulates virion production

Influenza A virus (IAV) Matrix 2 (M2) protein is an ion channel, required for efficient viral entry and egress. M2 interacts with the small ubiquitin-like LC3 protein through a cytoplasmic C-terminal LC3 interacting region (LIR). Here, we report that M2 is cleaved by caspases, abolishing the M2-LC3 interaction. A crystal structure of the M2 LIR in complex with LC3 indicates the caspase cleavage tetrapeptide motif (₈₂SAVD₈₅) is an unstructured linear motif that does not overlap with the LIR. Furthermore, an IAV mutant expressing a permanently truncated M2, mimicking caspase cleavage, is impaired in M2 plasma membrane transport and produces a significantly attenuated virus. Our results reveal a dynamic regulation of the M2-LC3 interaction by caspases. This highlights the role of host proteases in regulating IAV exit, relating virion production with host cell state.