Template requirement and initiation site selection by hepatitis C virus polymerase on a minimal viral RNA template

RNA-dependent RNA polymerase, NS5B protein, catalyzes replication of viral genomic RNA, which presumably initiates from the 3'-end, We have previously shown that NS5B can utilize the 3'-end 98-nucleotide (nt) X region of the hepatitis C virus (HCV) genome as a minimal authentic template. In this stu dy, we used this RNA to characterize the mechanism of RNA synthesis by the recombinant NS5B, We first showed that NS5B formed a complex with the 3'-en d of HCV RNA by binding to both the poly(U-U/C)-rich and X regions of the 3 '-untranslated region as well as part of the NS5B-coding sequences. Within the X region, NS5B bound stem II and the single-stranded region connecting stem-loops I and II. Truncation of 40 nt or more from the 3'-end of the X r egion abolished its template activity, whereas X RNA lacking 35 nt or less from the 3'-end retained template activity, consistent with the NS5B-bindin g site mapped. Furthermore, NS5B initiated RNA synthesis from a specific si te within the single-stranded loop I. All of the RNA templates that have a double-stranded stem at the 3'-end had the same RNA initiation site. Howeve r, the addition of single-stranded nucleotides to the 5'-end of X RNA or re moval of double-stranded structure in stem I generated RNA products of temp late size. These results indicate that HCV NS5B initiates RNA synthesis fro m a single-stranded region closest to the 3'-end of the X region. These res ults have implications for the mechanism of HCV RNA replication and the nat ure of HCV RNA templates in the infected cells.