A secondary structure model for the 3'-untranslated region of ilarvirus RNAs

Alfamo-and ilarviruses are plant viruses with a positive strand tripartite RNA genome belonging to the family of Bromoviridae. Unlike the bromoviruses and cucumoviruses, the genomic RNAs of ilar-and alfamoviruses cannot be charged with an amino acid at their 3' end, although tRNA-like structures (TLS) have been proposed for Alfalfa mosaic virus (AMV) and Prunus necrotic ringspot virus (PNRSV) RNAs. Whether a TLS is also present in other ilarviruses has not been investigated in detail. Here we present secondary structure models for the 3' terminal 180 nucleotides of all sequenced alfamoand ilarvirus RNAs. On the basis of these structure models the ilarviruses can be divided into three distinct types. In all these types the 3' end can exist in two mutually exclusive conformations: one that consists of a "linear" array of hairpins and another "pseudoknotted" conformation that displays features of a TLS. One type, which includes PNRSV, shows remarkable structural resemblance with the AMV model. In one of the types, the pseudoknotted conformation shows low resemblance with tRNA and some viruses of this type have found an alternative solution. In most ilarvirus RNAs a hairpin that is similar to the AMV core promoter hairpin can be identified. The relationship with other members of the Bromoviridae is discussed on the basis of RNA structural features.