Complementarity between epsilon and phi sequences in pregenomic RNA influences hepatitis B virus replication efficiency

Oropeza, Claudia E.; McLachlan, Alan

doi:10.1016/j.virol.2006.08.036

Cited by 24 publications

(22 citation statements)

References 55 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…10B). Indeed, it has been reported recently that a sequence element designated phi is complementary to the RNA packaging signal epsilon, and such complementarity is required for efficient minus-strand DNA synthesis, probably related to the TP-protein primer translocation from epsilon to DR1 (55). Similarly, the chaperone activity could contribute to the plus-strand DNA synthesis by affecting the DNA-RNA base pairing at the step of RNA primer translocation to DR2 (Fig.…”

Section: Discussionmentioning

confidence: 98%

“…Nucleic acid chaperone activity has been detected in the nucleocapsid proteins of several other viruses (20,24,27,32,55). These earlier studies with different viruses on the nucleic acid chaperone hypothesis in the literature can perhaps be extended to hepatitis B virus, as was discussed in the study of the arginine clusters of the carboxy-terminal domain of HBc (63).…”

Section: Figmentioning

confidence: 90%

See 1 more Smart Citation

Nucleic Acid Chaperone Activity Associated with the Arginine-Rich Domain of Human Hepatitis B Virus Core Protein

Chu

Liou

et al. 2014

J Virol

View full text Add to dashboard Cite

Hepatitis B virus (HBV) DNA replication occurs within the HBV icosahedral core particles. HBV core protein (HBc) contains an arginine-rich domain (ARD) at its carboxyl terminus. This ARD domain of HBc 149-183 is known to be important for viral replication but not known to have a structure. Recently, nucleocapsid proteins of several viruses have been shown to contain nucleic acid chaperone activity, which can facilitate structural rearrangement of viral genome. Major features of nucleic acid chaperones include highly basic amino acid residues and flexible protein structure. To test the nucleic acid chaperone hypothesis for HBc ARD, we first used the disassembled full-length HBc from Escherichia coli to analyze the nucleic acid annealing and strand displacement activities. To exclude the potential contamination of chaperones from E. coli, we designed synthetic HBc ARD peptides with different lengths and serine phosphorylations. We demonstrated that HBc ARD peptide can behave like a bona fide nucleic acid chaperone and that the chaperone activity depends on basic residues of the ARD domain. The loss of chaperone activity by arginine-to-alanine substitutions in the ARD can be rescued by restoring basic residues in the ARD. Furthermore, the chaperone activity is subject to regulation by phosphorylation and dephosphorylation at the HBc ARD. Interestingly, the HBc ARD can enhance in vitro cleavage activity of RNA substrate by a hammerhead ribozyme. We discuss here the potential significance of the HBc ARD chaperone activity in the context of viral DNA replication, in particular, at the steps of primer translocations and circularization of linear replicative intermediates. IMPORTANCEHepatitis B virus is a major human pathogen. At present, no effective treatment can completely eradicate the virus from patients with chronic hepatitis B. We report here a novel chaperone activity associated with the viral core protein. Our discovery could lead to a new drug design for more effective treatment against hepatitis B virus in the future. Hepatitis B virus (HBV) is a human pathogen that chronically infects about 350 million people worldwide. Chronic HBV carriers have an increased risk of developing cirrhosis and hepatocellular carcinoma (1-4). As an enveloped DNA virus, HBV reverse transcribes an encapsidated pregenomic RNA (pgRNA) to generate a double-strand DNA genome with a relaxed circular (RC) conformation (rcDNA).The full-length HBV core protein (HBc) consists of 183 to 185 amino acid residues. It contains two distinct domains connected by a hinge region. The N terminus is an assembly domain of HBc 1-140, and the C terminus is the arginine-rich domain (ARD) of HBc 150-183 (5, 6) (see Fig. 2A). The ARD is dispensable for capsid assembly in Escherichia coli but is required for pgRNA packaging (5,7,8). The ARD can be phosphorylated predominantly at serines 155, 162, and 170. HBV RNA encapsidation, DNA synthesis, and virion secretion are known to be regulated by serine phosphorylation at the ARD domain (9-13).Proteins w...

show abstract

Section: Discussionmentioning

confidence: 98%

Section: Figmentioning

confidence: 90%

Nucleic Acid Chaperone Activity Associated with the Arginine-Rich Domain of Human Hepatitis B Virus Core Protein

Chu

Liou

et al. 2014

J Virol

View full text Add to dashboard Cite

show abstract

“…More recently, we (1) and others (13) demonstrated that the 5Ј half of the upper stem of ε base pairs with another sequence, , which is near the 3Ј end of pgRNA, to make an important contribution to the synthesis of minus-strand DNA.…”

mentioning

confidence: 92%

“…Previous studies showed that base pairing between the adjacent portion of and the 5Ј half of the upper stem of ε was important for function (1,13). Thus, appears to act as a scaffold by base pairing with two regions: and the 5Ј half of the upper stem of ε.…”

mentioning

confidence: 99%

See 1 more Smart Citation

The Topology of Hepatitis B Virus Pregenomic RNA Promotes Its Replication

Abraham

Loeb

2007

J Virol

View full text Add to dashboard Cite

Previous analysis of hepatitis B virus (HBV) indicated base pairing between two cis-acting sequences, the 5 half of the upper stem of and , contributes to the synthesis of minus-strand DNA. Our goal was to identify other cis-acting sequences on the pregenomic RNA (pgRNA) involved in the synthesis of minus-strand DNA. We found that large portions of the pgRNA could be deleted or substituted without an appreciable decrease in the level of minus-strand DNA synthesized, indicating that most of the pgRNA is dispensable and that a specific size of the pgRNA is not required for this process. Our results indicated that the cis-acting sequences for the synthesis of minus-strand DNA are present near the 5 and 3 ends of the pgRNA. In addition, we found that the first-strand template switch could be directed to a new location when a 72-nucleotide (nt) fragment, which contained the cis-acting sequences present near the 3 end of the pgRNA, was introduced at that location. Within this 72-nt region, we uncovered two new cis-acting sequences, which flank the acceptor site. We show that one of these sequences, named and located 3 of the acceptor site, base pairs with to contribute to the synthesis of minus-strand DNA. Thus, base pairing between three cis-acting elements (5 half of the upper stem of , , and ) are necessary for the synthesis of HBV minus-strand DNA. We propose that this topology of pgRNA facilitates first-strand template switch and/or the initiation of synthesis of minus-strand DNA.Hepatitis B virus (HBV), the prototype member of the Hepadnaviridae family, is a liver-tropic virus with a small, doublestranded DNA genome. HBV replicates by reverse transcription of an RNA intermediate termed pregenomic RNA (pgRNA) (17). The pgRNA has several roles during virus replication. It is the mRNA for the translation of two viral replication proteins: the polymerase (P) and the capsid subunit (C). In the cytoplasm of the hepatocyte, pgRNA is selectively encapsidated along with P protein into capsid particles (2,8). It is within these viral capsids that pgRNA serves as the template for reverse transcription.RNA encapsidation requires that P protein recognize and bind an encapsidation signal (ε), a stem-loop within the 5Ј end of pgRNA (2, 15). P protein acts as primer and reverse transcriptase to initiate the synthesis of minus-strand DNA, using a bulge within ε as a template (20,21). Synthesis of minus-strand DNA pauses after 4 nucleotides (nt). At this point, nascent minus-strand DNA, which is covalently bound to P protein (6,16,18,19), switches templates and anneals to a complementary 4-nt acceptor site (AS) within the 3Ј copy of DR1 (Fig. 1) (16,18,19). Synthesis of minus-strand DNA resumes from this location.ε plays a crucial role in at least two processes: pgRNA encapsidation and initiation of minus-strand DNA synthesis (2, 4, 15). More recently, we (1) and others (13) demonstrated that the 5Ј half of the upper stem of ε base pairs with another sequence, , which is near the 3Ј end of pgRNA, to make an important contribution...

show abstract

Hepatitis B Virus: Replication, Mutation, and Evolution

Sherman

Kottilil

2011

HIV and Liver Disease

View full text Add to dashboard Cite

Complementarity between epsilon and phi sequences in pregenomic RNA influences hepatitis B virus replication efficiency

Cited by 24 publications

References 55 publications

Nucleic Acid Chaperone Activity Associated with the Arginine-Rich Domain of Human Hepatitis B Virus Core Protein

Nucleic Acid Chaperone Activity Associated with the Arginine-Rich Domain of Human Hepatitis B Virus Core Protein

The Topology of Hepatitis B Virus Pregenomic RNA Promotes Its Replication

Hepatitis B Virus: Replication, Mutation, and Evolution

Contact Info

Product

Resources

About