Previously, we described two RNA structural motifs in the hepatitis C viral (HCV) genome that can be processed in vitro by human ribonuclease P (RNase P) enzyme [J. Biol. Chem. 277 (2002) 30606]. One of these structures is located in the internal ribosome entry site and is conserved in the related animal pestiviruses [J. Biol. Chem. 278 (2003) 26844]. Here, we tested two prokaryotic RNase P ribozymes (P RNA) against this conserved structural motif. In vitro experiments indicated that P RNA from Synechocystis sp. can specifically process the viral transcript preparations in a position close to the human RNase P cleavage site. This provides additional support for the presence of an RNA structure similar to tRNA near the AUG start codon and suggests that Synechocystis P RNA may be an active agent for HCV antigenomic interventions.