Conformational Dynamics of the Hepatitis B Virus Pre-genomic RNA on Multiple Time Scales: Implications for Viral Replication

Lukasz T Olenginski; Wojciech K Kasprzak; Christina Bergonzo; Bruce A Shapiro; Theodore K Dayie

doi:10.1016/j.jmb.2022.167633

Conformational Dynamics of the Hepatitis B Virus Pre-genomic RNA on Multiple Time Scales: Implications for Viral Replication

J Mol Biol. 2022 Sep 30;434(18):167633. doi: 10.1016/j.jmb.2022.167633. Epub 2022 May 17.

Authors

Lukasz T Olenginski¹, Wojciech K Kasprzak², Christina Bergonzo³, Bruce A Shapiro⁴, Theodore K Dayie⁵

Affiliations

¹ Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA.
² Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
³ Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and University of Maryland, Rockville, MD 20850, USA.
⁴ RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
⁵ Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA. Electronic address: dayie@umd.edu.

PMID: 35595167
DOI: 10.1016/j.jmb.2022.167633

Abstract

Human hepatitis B virus (HBV) replication is initiated by the binding of the viral polymerase (P) to epsilon (ε), an ≈85-nucleotide (nt) cis-acting regulatory stem-loop RNA located at the 5'-end of the pre-genomic RNA (pgRNA). This interaction triggers P and pgRNA packaging and protein-primed reverse transcription and is therefore an attractive therapeutic target. Our recent nuclear magnetic resonance (NMR) structure of ε provides a useful starting point toward a detailed understanding of HBV replication, and hints at the functional importance of ε dynamics. Here, we present a detailed description of ε motions on the ps to ns and μs to ms time scales by NMR spin relaxation and relaxation dispersion, respectively. We also carried out molecular dynamics simulations to provide additional insight into ε conformational dynamics. These data outline a series of complex motions on multiple time scales within ε. Moreover, these motions occur in mostly conserved nucleotides from structural regions (i.e., priming loop, pseudo-triloop, and U43 bulge) that biochemical and mutational studies have shown to be essential for P binding, P-pgRNA packaging, protein-priming, and DNA synthesis. Taken together, our work implicates RNA dynamics as an integral feature that governs HBV replication.

Keywords: NMR spectroscopy; conformational selection; dynamics; hepatitis B virus; viral replication.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.
Research Support, N.I.H., Extramural

MeSH terms

Genomics
Hepatitis B virus* / genetics
Hepatitis B virus* / physiology
Humans
Nucleic Acid Conformation*
RNA, Viral* / chemistry
Reverse Transcription
Virus Replication*

Substances

RNA, Viral