Relaxing the restricted structural dynamics in the human hepatitis B virus RNA encapsidation signal enables replication initiation in vitro

PLoS Pathog. 2022 Mar 8;18(3):e1010362. doi: 10.1371/journal.ppat.1010362. eCollection 2022 Mar.

Abstract

Hepadnaviruses, including hepatitis B virus (HBV) as a major human pathogen, replicate their tiny 3 kb DNA genomes by capsid-internal protein-primed reverse transcription of a pregenomic (pg) RNA. Initiation requires productive binding of the viral polymerase, P protein, to a 5´ proximal bipartite stem-loop, the RNA encapsidation signal ε. Then a residue in the central ε bulge directs the covalent linkage of a complementary dNMP to a Tyr sidechain in P protein´s Terminal Protein (TP) domain. After elongation by two or three nucleotides (nt) the TP-linked DNA oligo is transferred to a 3´ proximal acceptor, enabling full-length minus-strand DNA synthesis. No direct structural data are available on hepadnaviral initiation complexes but their cell-free reconstitution with P protein and ε RNA (Dε) from duck HBV (DHBV) provided crucial mechanistic insights, including on a major conformational rearrangement in the apical Dε part. Analogous cell-free systems for human HBV led at most to P-ε binding but no detectable priming. Here we demonstrate that local relaxation of the highly basepaired ε upper stem, by mutation or via synthetic split RNAs, enables ε-dependent in vitro priming with full-length P protein from eukaryotic translation extract yet also, and without additional macromolecules, with truncated HBV miniP proteins expressed in bacteria. Using selective 2-hydroxyl acylation analyzed by primer extension (SHAPE) we confirm that upper stem destabilization correlates with in vitro priming competence and show that the supposed bulge-closing basepairs are largely unpaired even in wild-type ε. We define the two 3´ proximal nt of this extended bulge as main initiation sites and provide evidence for a Dε-like opening of the apical ε part upon P protein binding. Beyond new HBV-specific basic aspects our novel in vitro priming systems should facilitate the development of high-throughput screens for priming inhibitors targeting this highly virus-specific process.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Hepatitis B Virus, Duck / genetics
  • Hepatitis B Virus, Duck / physiology
  • Hepatitis B virus* / genetics
  • Hepatitis B virus* / physiology
  • Nucleic Acid Conformation
  • RNA, Viral* / chemistry
  • RNA-Directed DNA Polymerase / chemistry
  • Virus Replication*

Substances

  • RNA, Viral
  • RNA-Directed DNA Polymerase

Grants and funding

This work was supported by the Deutsche Forschungsgemeinschaft (DFG) through grants Na154/7-3 and, in part, Na154/12 to MN. We acknowledge support by the Open Access Publication Fund of the University of Freiburg. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.