A short cis-acting sequence is required for hepatitis B virus pregenome encapsidation and sufficient for packaging of foreign RNA

Abstract

The selective encapsidation of the hepadnaviral RNA pregenome from an excess of other viral and cellular mRNAs predicts specific protein-RNA interactions involving one or several sites on the pregenome. Using deletion analysis in a transient expression/packaging system in which all relevant viral proteins are provided in trans from a packaging-deficient helper genome, we identified near the 5'-end of the pregenome a 137 nucleotide sequence that is necessary and sufficient for RNA encapsidation; other parts of the 3 kb pregenome were found not to contribute to this process. The encapsidation sequence, which we call epsilon, possesses several interesting features with implications for the pregenome's function in RNA packaging, RNA translation and reverse transcription. (i) epsilon contains several indirect repeat sequences, suggesting a high degree of secondary structure, (ii) epsilon overlaps with the start signal for core gene translation, suggesting a mechanism to regulate the alternative use of the pregenome as core mRNA, (iii) epsilon does not contain the direct repeat sequences known to be involved in the initiation of viral DNA synthesis. Finally, our deletion analysis suggests that ribosomes translating the epsilon sequence from the precore start codon may interfere with genomic RNA packaging.