Conservation of the HBV RNA element epsilon in nackednaviruses reveals ancient origin of protein-primed reverse transcription

Proc Natl Acad Sci U S A. 2021 Mar 30;118(13):e2022373118. doi: 10.1073/pnas.2022373118.

Abstract

Hepadnaviruses, with the human hepatitis B virus as prototype, are small, enveloped hepatotropic DNA viruses which replicate by reverse transcription of an RNA intermediate. Replication is initiated by a unique protein-priming mechanism whereby a hydroxy amino acid side chain of the terminal protein (TP) domain of the viral polymerase (P) is extended into a short DNA oligonucleotide, which subsequently serves as primer for first-strand synthesis. A key component in the priming of reverse transcription is the viral RNA element epsilon, which contains the replication origin and serves as a template for DNA primer synthesis. Here, we show that recently discovered non-enveloped fish viruses, termed nackednaviruses [C. Lauber et al., Cell Host Microbe 22, 387-399 (2017)], employ a fundamentally similar replication mechanism despite their huge phylogenetic distance and major differences in genome organization and viral lifestyle. In vitro cross-priming studies revealed that few strategic nucleotide substitutions in epsilon enable site-specific protein priming by heterologous P proteins, demonstrating that epsilon is functionally conserved since the two virus families diverged more than 400 Mya. In addition, other cis elements crucial for the hepadnavirus-typical replication of pregenomic RNA into relaxed circular double-stranded DNA were identified at conserved positions in the nackednavirus genomes. Hence, the replication mode of both hepadnaviruses and nackednaviruses was already established in their Paleozoic common ancestor, making it a truly ancient and evolutionary robust principle of genome replication that is more widespread than previously thought.

Keywords: HBV long-term evolution; HBV replication mechanism; initiation of reverse transcription; paleovirology; protein priming.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Conserved Sequence
  • DNA Replication*
  • DNA, Viral / biosynthesis*
  • Evolution, Molecular*
  • Hepadnaviridae / classification
  • Hepadnaviridae / genetics
  • Hepadnaviridae / physiology*
  • Hepatitis B virus / classification
  • Hepatitis B virus / genetics
  • Phylogeny
  • RNA, Viral / genetics
  • Replication Origin
  • Reverse Transcription*
  • Viral Proteins / genetics
  • Viral Proteins / metabolism*
  • Virus Replication*

Substances

  • DNA, Viral
  • RNA, Viral
  • Viral Proteins