Cis- and trans-regulation of luteovirus gene expression by the 3′ end of the viral genome

Translation of the 5.7 kb luteovirus genome is controlled by the 3′ untranslated region (UTR). Base pairing between regions of the 3′ UTR and sequences kilobases upstream is required for cap-independent translation and ribosomal frameshifting needed to synthesize the viral replicase. Luteoviruses produce subgenomic RNAs, which can serve as mRNA, but one sgRNA also regulates translation initiation in trans. As on all viruses, the 3′ and 5′ ends contain structures that are presumed to facilitate RNA synthesis. This review describes the structures and interactions of barley yellow dwarf virus RNA that facilitate the complex interplay between the above events and result in a successful virus infection. We also present surprising results on the apparent lack of need for some subgenomic RNAs for the virus to infect cells or whole plants. In summary, the UTRs of luteoviruses are highly complex entities that control and fine-tune many key events of the virus replication cycle.