Replication-defective missense mutations within the terminal protein and spacer/intron regions of the polymerase gene of human hepatitis B virus

Spacer Domain in Hepatitis B Virus Polymerase: Plugging a Hole or Performing a Role?

Hepatitis B virus (HBV) polymerase is divided into terminal protein, spacer, reverse transcriptase, and RNase domains. Spacer has previously been considered dispensable, merely acting as a tether between other domains or providing plasticity to accommodate deletions and mutations. We explore evidence for the role of spacer sequence, structure, and function in HBV evolution and lineage, consider its associations with escape from drugs, vaccines, and immune responses, and review its potential impacts on disease outcomes.

Isolation, characterization and biological significance of hepatitis B virus mutants from serum of a patient with immunologically negative HBV infection

BACKGROUND/AIM

A low-titered hepatitis B virus infection without immunological markers was identified in a prospective study in the serum of a kidney transplant recipient by PCR. The aim of this study was to analyze HBV genomes and their biological significance.

METHODS

The genome was amplified in two overlapping fragments A and B. Sequencing of 22 clones of the A- and 12 clones of the B-fragment revealed a heterogeneous virus population. A consensus and a mutant sequence were computed, representing the complete sequence of the virus population. The two sequences were compared with 41 published genomes of the different HBV geno- and serotypes.

RESULTS

Ninety-five point mutations and two deletions were identified. Two mutations were observed in all clones and 17 other mutations in three or more clones. The deletions were found in ten and seven of 22 clones. They were located in the C-gene and led to stop codons yielding truncated e- and/or core proteins. In vitro transfection of DNA constructs containing these deletions demonstrated a stop of HBV replication and of HBeAg expression. Cotransfection experiments demonstrated a dominant negative effect of the mutants containing the deletions. In addition, we describe new variants of naturally occurring HBsAg mutants that may cause HBV infection less detectable by standard HBsAg measurement assays. They were characterized by two point mutations which were observed in 9 of 12 and 13 of 22 clones of the S-gene. They significantly reduced the HBsAg expression in in vitro transfection experiments.

CONCLUSION

We found a patient with low-titered HBV infection, with mutations of the 'a' epitope of the Santigen as well as with mutations leading to truncated core proteins which may cause a dominant negative effect.

Active human hepatitis B viral polymerase expressed in rabbit reticulocyte lysate system

Human HBV polymerase has been expressed in reticulocyte lysate system. The expressed protein shows the DNA-dependent DNA polymerase activity. In vitro transcription and translation produces a major protein product with an apparent molecular weight of approximately 100 kD. The HBV DNA polymerase has been characterized biochemically in the condition that the contaminating cellular DNA polymerases were fairly suppressed by aphidicolin and NEM. The polymerization reaction is optimal at pH 7.5 and 37 degrees C and the polymerase requires either MnCl2 or MgCl2, with a preference for MnCl2. The protein represented an optimal activity in the presence of either 75 mM NaCl or 100 mM KCl, with a higher activity at 75 mM NaCl than 100 mM KCl. Study of the polymerizing activity of the deleted versions of the polymerase protein suggests that the terminal protein is essential for full polymerase function and the spacer region may decrease the stability of the P protein.

Detection of an RNase H activity associated with hepadnaviruses

Replication of the hepadnavirus DNA genome is accomplished via reverse transcription of an intermediate, pregenomic RNA molecule. This process is likely to be carried out by a virally encoded, multifunctional polymerase which possesses DNA- and RNA-dependent DNA polymerase and RNase H activities. However, the nature of the product(s) of the polymerase gene predicted to mediate these functions is unclear. Biochemical studies of the polymerase protein(s) have been limited by its apparent low abundance in virus particles and, until recently, the inability to express active polymerase protein(s) heterologously. We have used activity gel assays to detect DNA- and RNA-dependent DNA polymerase activities associated with highly purified duck hepatitis B virus (DHBV) core particles (S. M. Oberhaus and J. E. Newbold, J. Virol. 67:6558-6566, 1993). Now we report that the same approach identifies a 35-kDa RNase H activity in association with highly purified DHBV core particles and crude preparations of virions from DHBV-infected ducks and woodchuck hepatitis virus-infected woodchucks. This is the first report of the detection of an hepadnavirus-associated RNase H activity. Its apparent size is smaller than any of the DNA polymerase activities that we detected previously and significantly smaller than the full-length protein predicted from the polymerase open reading frame (p85 for DHBV). These data suggest that the viral polymerase and RNase H activities are separable and that these enzymes may coordinate their activities in vivo by forming a complex.

Release of the hepatitis B virus-associated DNA polymerase from the viral particle by the proteolytic cleavage

Previous efforts for biochemical study of the human hepatitis B virus (HBV) DNA polymerase have been limited by its tight association with viral nucleocapsids. We report here that the soluble DNA polymerase from HBV particles was obtained by low pH treatment of the viral particles followed by incubation with small amounts of subtilisin. By these treatments, the approximately 100-kDa band in the activity gel assay was gradually converted to approximately 70 kDa, which subsequently showed reverse transcriptase activity on several exogenous templates. The single approximately 70-kDa active band, which did not show any DNA polymerase activity in endogenous reaction, was eluted through DEAE-Sepharose chromatography. These results suggest that the approximately 100-kDa protein, most likely the product of HBV Pol open reading frame, is tightly associated with viral nucleocapsids, and the approximately 70-kDa protein, the proteolytic cleavage product of approximately 100-kDa enzyme, is solubilized from viral particles as an active enzyme on exogenous templates.

Detection of DNA polymerase activities associated with purified duck hepatitis B virus core particles by using an activity gel assay

Replication of hepadnaviruses involves reverse transcription of an intermediate RNA molecule. It is generally accepted that this replication scheme is carried out by a virally encoded, multifunctional polymerase which has DNA-dependent DNA polymerase, reverse transcriptase, and RNase H activities. Biochemical studies of the polymerase protein(s) have been limited by the inability to purify useful quantities of functional enzyme from virus particles and, until recently, to express enzymatically active polymerase proteins in heterologous systems. An activity gel assay which detects in situ catalytic activities of DNA polymerases after electrophoresis in partially denaturing polyacrylamide gels was used by M.R. Bavand and O. Laub (J. Virol. 62:626-628, 1988) to show the presence of DNA- and RNA-dependent DNA polymerase activities associated with hepatitis B virus particles produced in vitro. This assay has provided the only means by which hepadnavirus polymerase proteins have been detected in association with enzymatic activities. Since conventional methods have not allowed purification of useful quantities of enzymatically active polymerase protein(s), we have devised a protocol for purifying large quantities of duck hepatitis B virus (DHBV) core particles to near homogeneity. These immature virus particles contain DNA- and RNA-dependent DNA polymerase activities, as shown in the endogenous DNA polymerase assay. We have used the activity gel assay to detect multiple DNA- and RNA-dependent DNA polymerase proteins associated with these purified DHBV core particles. These enzymatically active proteins appear larger than, approximately the same size as, and smaller than an unmodified DHBV polymerase protein predicted from the polymerase open reading frame. This is the first report of the detection of active hepadnavirus core-associated DNA polymerase proteins derived from a natural host.

Sequence analysis of hepatitis B virus DNA in immunologically negative infection

It was previously demonstrated that the serum of some patients without immunological evidence of HBV infection contains the virus. Here we demonstrated by sequence analysis that the serum of such a patient contained a mixed HBV population. In comparison with HBV genomes of different genotypes twenty-two nucleotide variations were found in all clones sequenced in parallel. One nucleotide variation was identified within the enhancer I. Twelve of the twenty-two nucleotide variations caused altogether fifteen changes of amino acid sequence in known or predicted viral proteins. The proteins of the P open reading frame, which are most important for viral replication, were affected by nine amino acid substitutions. Three amino acid substitutions concerned the product of the X gene, a transcriptional transactivator of various viral and cellular promoters. Three mutations were only observed in some of the clones. One point mutation affected the direct repeats of the enhancer II. It occurred together with an 8 bp-deletion involving the C promoter region and the X gene. The third mutation was a single insertion, causing a fusion of the X and C gene. One or several of the identified mutations could be responsible for the diminished rate of replication and consequently for the low-titred, immunologically negative HBV infection.