A newly discovered 5' translation-regulatory element with a unique three stem-loop structure in sweet potato feathery mottle virus.

Sweet potato feathery mottle virus (SPFMV), a member of the Potyviridae family and Potyvirus genus, severely affects the yield and quality of sweet potato. Internal ribosome entry site (IRES) elements were first identified in animal RNA viruses and have since been identified in plant RNA viruses and eukaryotic mRNAs. Herein, we show that the 5' untranslated region (UTR) of SPFMV possesses IRES activity and contains the complete IRES sequence. Furthermore, the 3'UTR can synergistically enhance the cap-independent translation efficiency of the 5'UTR. Within the 5'UTR of SPFMV, three stem-loop structures, H1, H2, and H3, play critical roles in cap-independent translation. The top loop of H1 interacts with the 3'UTR through RNA-RNA interaction between 10850GUG and 42CAC, thereby enhancing IRES activity of the 5'UTR. The top loops of H2 and H3 serve as binding sites for eukaryotic translation initiation factor 4E (eIF4E) or its complex, while their stem structures provide essential structural support. in conclusion, we discovered a unique three-stem-loop IRES element within the SPFMV 5'UTR, providing a potential target for the prevention and control of sweet potato virus disease caused by SPFMV.