LTO1/YAE1 inhibit PKR phosphorylation and translational shutdown through suppressing readthrough in NMD

Nonsense-mediated RNA decay (NMD) is a highly conserved RNA quality and quantity surveillance system targeting mRNAs containing premature termination codon (PTC) and ~10% unmutated mammalian mRNAs to maintain homeostasis. Aberrant NMD is involved in neurodevelopmental disorders and cancer. Using a genome wide CRISPR screening, we identified LTO1 and YAE1 as NMD factors to inhibit PTC readthrough. Moreover, our data demonstrated that defective NMD led to translational shutdown by activating PKR, a stress response gene and major regulator of viral infection and cellular processes, including mRNA translation, transcriptional control, apoptosis and cell proliferation. We also found that the highly conserved deca-GX3 motif of LTO1, involved in the cytosolic Fe-S protein assembly (CIA) machinery, plays a critical role in NMD and PKR activation. This finding also led us to uncover that low doses of iron chelators recapitulated the phenotypes of LTO1 deficiency and induced NMD. Our data demonstrated the connection among iron homeostasis, NMD and PKR-dependent stress response.