The epsilon motif of hepatitis B virus RNA exhibits a potassium-dependent ribonucleolytic activity.

Fourteen different classes of ribozymes are known that catalyse a range of diverse chemical reactions. We report here a novel potassium-dependent nucleolytic activity present in hepatitis B virus (HBV) RNA. A short RNA region (53 nt) with enzymatic properties released itself from the viral sequence by cis cleavages and could subsequently act in trans. The released region encompassed the epsilon motif present in the HBV RNA. The 3' end of the liberated fragment was within the noncanonical polyadenylation signal (UAUAAA) of the viral RNA while cleavages at about 53 nt upstream sites released the fragment. Mutations of the primary scissile sites or annealing these sites with the antisense oligodeoxyribonucleotides blocked the release of this short fragment and annulled subsequent trans cleavage activity. An exogenously synthesized short transcript of only this 53 nt was active as a sequence-independent trans-acting nuclease and cleaved after pyrimidines in viral or other substrate transcripts under physiological potassium ion concentrations. Formation of a G-quadruplex within this region was suggested by circular dichroism and nondenaturing polyacrylamide gel analyses. Our results reveal a unique natural example of a trans-acting ribonuclease that cleaves at multiple sites in a sequence-independent fashion. The presence of this novel activity implores a dynamic structural behaviour in the ε region and raises new questions about HBV gene regulation.