3′UTRs of carmoviruses

•Carmoviruses are plus-sense RNA viruses that serve as models for replication and translation.•Most of the 3′ UTR of TCV contains elements necessary for replication, translation or both.•Carmoviruses contain different 3′ cap-independent translation enhancers.•The TCV 3′ UTR is highly interactive, changing conformation upon RdRp binding.

Carmovirus is a genus of small, single-stranded, positive-strand RNA viruses in the Tombusviridae. One member of the carmoviruses, Turnip crinkle virus (TCV), has been used extensively as a model for examining the structure and function of RNA elements in 3′UTR as well as in other regions of the virus. Using a variety of genetic, biochemical and computational methods, a structure for the TCV 3′UTR has emerged where secondary structures and tertiary interactions combine to adopt higher order 3-D structures including an internal, ribosome-binding tRNA-shaped configuration that functions as a 3′ cap-independent translation enhancer (3′CITE). The TCV 3′CITE also serves as a scaffold for non-canonical interactions throughout the 3′UTR and extending into the upstream open reading frame, interactions that are significantly disrupted upon binding by the RNA-dependent RNA polymerase. Long-distance interactions that connect elements in the 3′UTR with both the 5′ end and the internal ribosome recoding site suggest that 3′UTR of carmoviruses are intimately involved in multiple functions in the virus life cycle. Although carmoviruses share very similar genome organizations, lengths of 5′ and 3′UTRs, and structural features at the 3′ end, the similarity rapidly breaks down the further removed from the 3′ terminus revealing different 3′CITEs and unique virus-specific structural features. This review summarizes 20 years of work dissecting the structure and function of the 3′UTR of TCV and other carmoviruses. The astonishing structural complexity of the 3′UTRs of these simple carmoviruses provides lessons that are likely applicable to many other plant and animal RNA viruses.