ArticleNucleic acids research2002
The apical stem-loop of the hepatitis B virus encapsidation signal folds into a stable tri-loop with two underlying pyrimidine bulges.
Article in Nucleic acids research, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Hepatitis B Virus Nucleocapsid Assembly.Journal of molecular biology · 2025Review
- Structural Analysis of the Hepatitis B Virus RNA Encapsidation Signal ε by Selective 2'-Hydroxyl Acylation Analyzed by Primer Extension (SHAPE).Methods in molecular biology (Clifton, N.J.) · 2024Article
- Hepatitis B Virus Epsilon (ε) RNA Element: Dynamic Regulator of Viral Replication and Attractive Therapeutic Target.Viruses · 2023Review
- ISG20: an enigmatic antiviral RNase targeting multiple viruses.FEBS open bio · 2022Review
- N6-methyladenosine modification of the 5' epsilon structure of the HBV pregenome RNA regulates its encapsidation by the viral core protein.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Review
- Structural phylogenetic analysis reveals lineage-specific RNA repetitive structural motifs in all coronaviruses and associated variations in SARS-CoV-2.Virus evolution · 2021Article
- Few basepairing-independent motifs in the apical half of the avian HBV ε RNA stem-loop determine site-specific initiation of protein-priming.Scientific reports · 2017Article
- Assembly and Release of Hepatitis B Virus.Cold Spring Harbor perspectives in medicine · 2015Review
- Structural and thermodynamic signatures that define pseudotriloop RNA hairpins.RNA (New York, N.Y.) · 2013Article
- Article
- Fast production of homogeneous recombinant RNA--towards large-scale production of RNA.Nucleic acids research · 2012Article
- The subgenomic promoter of brome mosaic virus folds into a stem-loop structure capped by a pseudo-triloop that is structurally similar to the triloop of the genomic promoter.RNA (New York, N.Y.) · 2012Article
- In vitro epsilon RNA-dependent protein priming activity of human hepatitis B virus polymerase.Journal of virology · 2012Article
- Distinct families of cis-acting RNA replication elements epsilon from hepatitis B viruses.RNA biology · 2012Article
- Ultra-deep pyrosequencing analysis of the hepatitis B virus preCore region and main catalytic motif of the viral polymerase in the same viral genome.Nucleic acids research · 2011Article
- A SELEX-screened aptamer of human hepatitis B virus RNA encapsidation signal suppresses viral replication.PloS one · 2011Article
- Preparation of selective and segmentally labeled single-stranded DNA for NMR by self-primed PCR and asymmetrical endonuclease double digestion.Nucleic acids research · 2009Article
- RNA-protein interactions in hepadnavirus reverse transcription.Frontiers in bioscience (Landmark edition) · 2009Review
- Regulation of pyrimidine biosynthetic gene expression in bacteria: repression without repressors.Microbiology and molecular biology reviews : MMBR · 2008Review
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Reverse transcription of hepatitis B virus (HBV) pregenomic RNA is essential for virus replication. In the first step of this process, HBV reverse transcriptase binds to the highly conserved encapsidation signal, epsilon (epsilon), situated near the 5' end of the pregenome. epsilon has been predicted to form a bulged stem-loop with the apical stem capped by a hexa- loop. After the initial binding to this apical stem- loop, the reverse transcriptase synthesizes a 4 nt primer using the bulge as a template. Here we present mutational and structural data from NMR on the apical stem-loop of epsilon. Application of new isotope-labeling techniques (13C/15N/2H-U-labeling) allowed resolution of many resonance overlaps and an extensive structural data set could be derived. The NMR data show that, instead of the predicted hexa-loop, the apical stem is capped by a stable UGU tri-loop closed by a C-G base pair, followed by a bulged out C. The apical stem contains therefore two unpaired pyrimidines (C1882 and U1889), rather than one as was predicted, spaced by 6 nt. C1882, the 3' neighbour to the G of the loop-closing C-G base pair, is completely bulged out, while U1889 is at least partially intercalated into the stem. Analysis of 205 of our own HBV sequences and 1026 strains from the literature, covering all genotypes, reveals a high degree of conservation of epsilon. In particular, the residues essential for this fold are either totally conserved or show rare non-disruptive mutations. These data strongly indicate that this fold is essential for recognition by the reverse transcriptase.
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