Sequences at the 3 ' untranslated region of bamboo mosaic potexvirus RNA interact with the viral RNA-dependent RNA polymerase

The 3' untranslated region (UTR) of bamboo mosaic potexvirus (BaMV) genomic RNA was found to fold into a series of stem-loop structures including a ps eudoknot structure. These structures were demonstrated to be important for viral RNA replication and were believed to be recognized by the replicase ( C.-P. Cheng and C.-H. Tsai, J. Mel. Biol. 288:555-565, 1999). Electrophoret ic mobility shift and competition assays have now been used to demonstrate that the Escherichia coli-expressed RNA-dependent RNA polymerase domain (De lta 893) derived from BaMV open reading frame 1 could specifically bind to the 3' UTR of BaMV RNA. No competition was observed when bovine liver tRNAs or poly(I)(C) double-stranded homopolymers,were used as competitors, and t he cucumber mosaic virus 3' UTR was a less efficient competitor. Competitio n analysis with different regions of the BaMV 3' UTR shelved that Delta 893 binds to at least two independent RNA binding sites, stem-loop D and the p oly(A) tail. Footprinting analysis revealed that Delta 893 could protect th e sequences at Loop D containing the potexviral conserved hexamer motif and part of the stem of domain D from chemical cleavage.