A cis -Acting Replication Element in the Sequence Encoding the NS5B RNA-Dependent RNA Polymerase Is Required for Hepatitis C Virus RNA Replication

• DOI: 10.1128/jvi.78.3.1352-1366.2004
• Publication Date: 2004-01-13T21:28:00Z
• Authors: Shihyun You; Decherd D. Stump; Andrea D. Branch; Charles M. Rice
• Keywords: NS5B; Small nuclear RNA; Nucleic acid structure; Replicon

RNA structures play key roles in the replication of viruses. Sequence alignment software, thermodynamic folding programs, and classical comparative phylogenetic analysis were used to build models six elements coding region hepatitis C virus (HCV) RNA-dependent polymerase, NS5B. The importance five these was evaluated by site-directed mutagenesis a subgenomic HCV replicon. Mutations disrupting one predicted stem-loop structures, designated 5BSL3.2, blocked replication, implicating it as an essential cis-acting element (CRE). 5BSL3.2 is about 50 bases length part larger cruciform structure (5BSL3). As confirmed probing, consists 8-bp lower helix, 6-bp upper 12-base terminal loop, 8-base internal loop. Mutational probing explore features. Primary sequences loops shown be important for helix appears serve scaffold that helps maintain overall structure. Unlike certain picornavirus CREs, whose function position independent, context dependent. Understanding role determining how this new CRE functions previously identified at 5' 3' ends genome should provide insights into replication.