Activation of the unfolded protein response and inhibition of translation initiation during coronavirus infection

Coronaviruses (CoV), such as severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV), are of medical importance with high mortality rates and significant zoonotic and pandemic potential. Here, we apply ribosome profiling and parallel RNASeq to globally analyse changes in the host cell translatome and transcriptome upon infection with mouse hepatitis virus, strain A59 (MHV-A59), a model murine coronavirus in the same genus as SARS-CoV and MERS-CoV. We observed translational upregulation of ATF4, ATF5 and Ddit3 and activation of the unfolded protein response (UPR). Phosphorylation of eIF2α led to the global inhibition of translation and a substantial increase in empty 80S ribosomes. A drug that inhibits the UPR attenuates virus growth suggesting that MHV may have evolved to subvert the UPR to its own advantage. We also investigated an artefact of cycloheximide pretreatment in ribosome profiling whereby ribosomes accumulate at the 5ʹ end of coding sequences in stressed cells but not in unstressed or untreated cells, thus extending earlier studies in yeast to mammalian cells. The study sheds light on the mechanisms of CoV translational shutoff and reveals a potential new therapeutic strategy.