RNA viruses can exploit self-cleaving ribozymes for translation initiation

Abstract

Small self-cleaving ribozymes are catalytic RNAs discovered in viroid-like agents, which are replicating circular RNAs (circRNAs) postulated as relics of a prebiotic RNA world. In the last decade, however, small ribozymes have also been detected across the tree of life, from bacterial to human genomes, and more recently, in unusual circRNA viruses. Here we report the conserved occurrence of diverse small ribozymes within the linear genomes of typical single- and double-stranded RNA viruses infecting fungi and plants. We identified type I hammerhead ribozymes in the 5′-UTRs of chrysovirids and fusarivirids, displaying self-cleaving activity in vitro and in vivo. Similar hammerhead, as well as hepatitis delta and twister ribozymes, occur in diverse megabirna-, hypo-, fusagra-, toti-, or tombus-like viruses. The ribozymes appear as isolated motifs within the UTRs or as tandem pairs that encompass small RNA segments (186–399 nt) resembling Zetavirus-like sequences. In vivo characterization of the 5′-UTR from a fungal chrysovirus revealed that its RNA self-cleaving activity is essential for protein translation initiation. Analogous experiments in plants with diverse ribozyme motifs confirmed that self-cleaving activity alone can induce cap-independent translation. We conclude that RNA self-cleaving activity, historically linked to the rolling circle replication of viroid-like circRNAs, appears to be co-opted by some linear RNA viruses for translational roles.