At the 5'-end of Rubella virus genomic RNA there are sequences that can form stem-loop structure (SL), which are stable under physiological conditions. The complementary minus-strand equivalent of the 5'(+) SL structure is thought to serve as a promoter for the initiation of plus- strand synthesis. We screened the minus-strand equivalent of the 5' (+) SL (64 nucleotides) and the adjacent region of the minus-strand RNA for their ability to bind to host cell proteins. Specific high-affinity binding to the 64nucleotide long SL structure of three cytosolic proteins with relative molecular masses of 97, 79 and 56kDa was observed by UV-induced covalent crosslinking. There was significant increase in the binding of 97kDa protein from cells upon infection. Altering the stem-loop structure by deleting either one of the two loops abolished the binding interaction. The 56kDa protein also appeared to bind specifically to a stem-loop derived from the 3'-end of plus-strand RNA. The 3'-terminal SL structure of Rubella virus minus-strand RNA shares the same protein binding activity with similar structures in alphaviruses, such as Sindbis and Eastern Equine Encephalitis Virus. Studies are in progress to isolate the proteins and analyze their function in replication process.
