Few basepairing-independent motifs in the apical half of the avian HBV ε RNA stem-loop determine site-specific initiation of protein-priming

Sci Rep. 2017 Aug 2;7(1):7120. doi: 10.1038/s41598-017-07657-z.

Abstract

Hepadnaviruses, including human hepatitis B virus (HBV), replicate their tiny DNA genomes by protein-primed reverse transcription of a pregenomic (pg) RNA. Replication initiation as well as pgRNA encapsidation depend on the interaction of the viral polymerase, P protein, with the ε RNA element, featuring a lower and an upper stem, a central bulge, and an apical loop. The bulge, somehow assisted by the loop, acts as template for a P protein-linked DNA oligo that primes full-length minus-strand DNA synthesis. Phylogenetic conservation and earlier mutational studies suggested the highly based-paired ε structure as crucial for productive interaction with P protein. Using the tractable duck HBV (DHBV) model we here interrogated the entire apical DHBV ε (Dε) half for sequence- and structure-dependent determinants of in vitro priming activity, replication, and, in part, in vivo infectivity. This revealed single-strandedness of the bulge, a following G residue plus the loop subsequence GUUGU as the few key determinants for priming and initiation site selection; unexpectedly, they functioned independently of a specific structure context. These data provide new mechanistic insights into avihepadnaviral replication initiation, and they imply a new concept towards a feasible in vitro priming system for human HBV.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Aptamers, Nucleotide / genetics
  • Base Pairing*
  • Base Sequence
  • Binding Sites
  • Cell Line, Tumor
  • Chickens
  • Gene Expression Regulation, Viral
  • Hepatitis B Virus, Duck / genetics*
  • Inverted Repeat Sequences*
  • Mutation
  • Nucleic Acid Conformation
  • Nucleotide Motifs*
  • Protein Binding
  • RNA
  • RNA, Viral / chemistry*
  • RNA, Viral / genetics*
  • Transcription Initiation Site*
  • Virus Replication

Substances

  • Aptamers, Nucleotide
  • RNA, Viral
  • pgRNA
  • RNA