A long-distance RNA–RNA interaction plays an important role in programmed − 1 ribosomal frameshifting in the translation of p88 replicase protein of Red clover necrotic mosaic virus

Programmed − 1 ribosomal frameshifting (− 1 PRF) is one viral translation strategy to express overlapping genes in positive-strand RNA viruses. Red clover necrotic mosaic virus (RCNMV) uses this strategy to express its replicase component protein p88. In this study, we used a cell-free translation system to map cis-acting RNA elements required for − 1 PRF. Our results show that a small stem-loop structure adjacent to the cap-independent translation element in the 3′ untranslated region (UTR) of RCNMV RNA1 is required for − 1 PRF. Site-directed mutagenesis experiments suggested that this stem-loop regulates − 1 PRF via base-pairing with complementary sequences in a bulged stem-loop adjacent to the shifty site. The existence of RNA elements responsible for − 1 PRF and the cap-independent translation of replicase proteins in the 3′ UTR of RNA1 might be important for switching translation to replication and for regulating the ratio of p88 to p27.