Sequences 5′ of the Conserved tRNA-like Promoter Modulate the Initiation of Minus-Strand Synthesis by the Brome Mosaic Virus RNA-Dependent RNA Polymerase

Abstract

Each of the brome mosaic virus (BMV) genomic RNAs contains a conserved tRNA-like structure that is sufficient to direct minus-strand RNA synthesisin vitro.The tRNA-like promoters, tB1 and tB3, direct approximately equal amounts of synthesisin vitro.However, 5′ sequences were found to affect the amount of minus-strand synthesis, suggesting that sequences beyond the tRNA-like structure are important in moderating minus-strand synthesis. Consistent with this, sequences upstream the tRNA-like structure are able to partially suppress mutations at or near the initiation site. This activity is observed in the 5′ sequences of both BMV and CMV (cucumber mosaic virus) templates. However, a chimeric RNA containing the CMV tRNA-like promoter fused to the 5′ sequences of BMV was not able to suppress mutations at the initiation site, suggesting that homologous 5′ and 3′ sequences are required to affect initiation. The ability to suppress mutations at the initiation site was correlated with a slight increase in the ability of the BMV RNA-dependent RNA polymerase to interact with the RNA.