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. (C) 2011 Published by Elsevier