RNA sequence and secondary structural determinants in a minimal viral promoter that directs replicase recognition and initiation of genomic plus-strand RNA synthesis

Viral RNA replication provides a useful system to study the structure and f unction of RNAs and the mechanism of RNA synthesis from RNA templates. Prev iously we demonstrated that a 27 nt RNA from brome mosaic virus (BMV) can d irect correct initiation of genomic plus-strand RNA synthesis by the BMV re plicase. In this study, using biochemical, nuclear magnetic resonance, and thermodynamic analyses, we determined that the secondary structure of this 27 nt RNA can be significantly altered and retain the ability to direct RNA synthesis. In contrast, we find that position-specific changes in the RNA sequence will affect replicase recognition, modulate the polymerization pro cess, and contribute to the differential accumulation of viral RNAs. These functional results are in agreement with the phylogenetic analysis of BMV a nd related viral sequences and suggest that a similar mechanism of RNA synt hesis takes place for members of the alphavirus superfamily. (C) 1999 Acade mic Press.