mA modification of plant virus enables host recognition by NMD factors in plants.

N-methyladenosine (mA) is the most abundant eukaryotic mRNA modification and is involved in various biological processes. Increasing evidence has implicated that mA modification is an important anti-viral defense mechanism in mammals and plants, but it is largely unknown how mA regulates viral infection in plants. Here we report the dynamic changes and functional anatomy of mA in Nicotiana benthamiana and Solanum lycopersicum during Pepino mosaic virus (PepMV) infection. mA modification in the PepMV RNA genome is conserved in these two species. Overexpression of the mA writers, mRNA adenosine methylase A (MTA), and HAKAI inhibit the PepMV RNA accumulation accompanied by increased viral mA modifications, whereas deficiency of these writers decreases the viral RNA mA levels but enhances virus infection. Further study reveals that the cytoplasmic YTH-domain family protein NbECT2A/2B/2C as mA readers are involved in anti-viral immunity. Protein-protein interactions indicate that NbECT2A/2B/2C interact with nonsense-mediated mRNA decay (NMD)-related proteins, including NbUPF3 and NbSMG7, but not with NbUPF1. mA modification-mediated restriction to PepMV infection is dependent on NMD-related factors. These findings provide new insights into the functionality of mA anti-viral activity and reveal a distinct immune response that NMD factors recognize the mA readers-viral mA RNA complex for viral RNA degradation to limit virus infection in plants.