An extensive survey of phytoviral RNA 3′ uridylation identifies extreme variations and virus-specific patterns

Viral RNAs can be uridylated in eukaryotic hosts. However, our knowledge of uridylation patterns and roles remains rudimentary for phytoviruses. Here, we report global 3 ' terminal RNA uridylation profiles for representatives of the main families of positive single-stranded RNA phytoviruses. We detected uridylation in all 47 viral RNAs investigated here, revealing its prevalence. Yet, uridylation levels of viral RNAs varied from 0.2% to 90%. Unexpectedly, most poly(A) tails of grapevine fanleaf virus (GFLV) RNAs, including encapsidated tails, were strictly monouridylated, which corresponds to an unidentified type of viral genomic RNA extremity. This monouridylation appears beneficial for GFLV because it became dominant when plants were infected with nonuridylated GFLV transcripts. We found that GFLV RNA monouridylation is independent of the known terminal uridylyltransferases (TUTases) HEN1 SUPPRESSOR 1 (HESO1) and UTP:RNA URIDYLYLTRANSFERASE 1 (URT1) in Arabidopsis (Arabidopsis thaliana). By contrast, both TUTases can uridylate other viral RNAs like turnip crinkle virus (TCV) and turnip mosaic virus (TuMV) RNAs. Interestingly, TCV and TuMV degradation intermediates were differentially uridylated by HESO1 and URT1. Although the lack of both TUTases did not prevent viral infection, we detected degradation intermediates of TCV RNA at higher levels in an Arabidopsis heso1 urt1 mutant, suggesting that uridylation participates in clearing viral RNA. Collectively, our work unveils an extreme diversity of uridylation patterns across phytoviruses and constitutes a valuable resource to further decipher pro- and antiviral roles of uridylation. Plant viral RNAs are uridylated to various levels, and virus-specific profiles indicate potential anti- and proviral functions.

Automated summary

Plant viral RNAs can undergo uridylation, which has diverse patterns and potential pro- and antiviral functions. In this study, the global 3' terminal RNA uridylation profiles of various phytoviruses were analyzed, revealing the prevalence of uridylation in viral RNAs. It was found that grapevine fanleaf virus (GFLV) RNAs have a unique monouridylation pattern, which becomes dominant during infection. The uridylation of viral RNAs was found to be independent of known terminal uridylyltransferases (TUTases), but these TUTases can uridylate other viral RNAs. Our findings highlight the importance of uridylation in plant-virus interactions and provide valuable insights into the diverse roles of uridylation.