Sequence of a replication competent hepatitis B virus genome with a preX open reading frame

Pre- and Post-Transcriptional Control of HBV Gene Expression: The Road Traveled towards the New Paradigm of HBx, Its Isoforms, and Their Diverse Functions

Hepatitis B virus (HBV) is an enveloped DNA human virus belonging to the Hepadnaviridae family. Perhaps its main distinguishable characteristic is the replication of its genome through a reverse transcription process. The HBV circular genome encodes only four overlapping reading frames, encoding for the main canonical proteins named core, P, surface, and X (or HBx protein). However, pre- and post-transcriptional gene regulation diversifies the full HBV proteome into diverse isoform proteins. In line with this, hepatitis B virus X protein (HBx) is a viral multifunctional and regulatory protein of 16.5 kDa, whose canonical reading frame presents two phylogenetically conserved internal in-frame translational initiation codons, and which results as well in the expression of two divergent N-terminal smaller isoforms of 8.6 and 5.8 kDa, during translation. The canonical HBx, as well as the smaller isoform proteins, displays different roles during viral replication and subcellular localizations. In this article, we reviewed the different mechanisms of pre- and post-transcriptional regulation of protein expression that take place during viral replication. We also investigated all the past and recent evidence about HBV HBx gene regulation and its divergent N-terminal isoform proteins. Evidence has been collected for over 30 years. The accumulated evidence simply strengthens the concept of a new paradigm of the canonical HBx, and its smaller divergent N-terminal isoform proteins, not only during viral replication, but also throughout cell pathogenesis.

Hepatitis B virus whole-X and X protein play distinct roles in HBV-related hepatocellular carcinoma progression

Background

The role of HBV X protein (HBx) in the development of hepatocellular carcinoma (HCC) has been well studied. However, little is known about the molecular functions of HBV whole-X protein (HBwx), a protein fused with HBx and upstream 56 amino acid, in HCC. In current study, the molecular functions of HBwx in HCC pathogenesis has been investigated, as well as comparison between HBwx and HBx.

Methods

Expression of HBwx and HBx in 50 HCC tissues was examined by immunohistochemistry. Their tumor-forming abilities were evaluated by an animal model and colony formation assay. Migration and invasion were detected by transwell assay and subcellular localization was tracked by GFP fluorescence. Cell proliferation, cell cycle and apoptosis were detected by CCK8 and FCM. Protein level was determined by Western blotting.

Results

HBwx was present in 72 % (36/50) of the liver tumor tissues and mainly expressed in the nucleus and deposited in the cytoplasm surrounding karyotheca. HBwx showed a promoting effect on tumorigenesis and growth in vivo and in vitro as well as cell migration and invasion, whilst such effect is compromised compared with that of HBx. Further analysis demonstrated differences in cell proliferation, cell cycle and cell apoptosis between cells expressing HBwx and those expressing HBx. Additionally, it was confirmed that RKIP-p-ERK pathway was involved in HBwx-related tumor formation.

Conclusion

HBwx, with the extra 56 amino acids, is closely related with hepatocarcinogenesis, while displays different biological functions from HBx.

Comparative study of the different activities of hepatitis B virus whole-X protein and HBx in hepatocarcinogenesis by proteomics and bioinformatics analysis

The hepatitis B virus (HBV) whole-X gene comprises the HBV X gene and the 168-bp region immediately upstream. Although the functions of HBx in hepatocarcinogenesis are well known, the activity of the HBV whole-X protein (HBwx), with 56 additional amino acids, has not yet been explored. In this study, proteomic and bioinformatic analysis was done to determine the protein interaction profiles of HBwx and HBx and to describe their functions in carcinogenesis. A total of 203 proteins were identified that interacted with HBwx, of which 149 were unique, the rest interacting also with HBx, and 73% (148/203) of these proteins are involved in carcinogenesis. Gene ontology (GO) analysis showed that HBwx- and HBx-interacting proteins are involved in different processes, the former mainly in biosynthetic processes (glycolysis, cell-cycle functions, and protein folding), and the latter mainly in localization, viral transcription, biological adhesion and angiogenesis. Pathway networks analysis revealed that proteins interacting with HBx participate mainly in oxidative phosphorylation, localization, the cytoskeleton, and cell adhesion. In contrast, more-specific functional analysis showed that proteins interacting with HBwx are involved in apoptosis and survival, cell-cycle functions, glycolysis, and gluconeogenesis (Pathway Maps); to cellular macromolecular complex assembly, protein folding and mRNA metabolic process (GO Processes); and to regulation of protein folding in the endoplasmic reticulum and cytoplasm, transcription, cell cycle G2-M and cytoskeleton rearrangement (Process Networks). In conclusion, this study shows that HBwx functions in carcinogenesis in a way that is different from that of HBx.

Effect of the HBV whole-X gene on the expression of hepatocellular carcinoma associated proteins

BACKGROUND

The hepatitis B virus (HBV) pre-X gene resides upstream of the HBV X gene, and together they form the HBV whole-X gene. Although it has been evident that the HBV whole-X protein is involved in the development of hepatocellular carcinoma, its biological role and molecular mechanism remain largely unknown.

METHODS

In this study, we subcloned the HBV whole-X gene and constructed a HBV whole-X expressing vector. After transfection of the HBV whole-X gene into HL-7702 cells, the profile of the differential cellular protein composition in the cells was analyzed by using two-dimensional electrophoresis coupled to matrix-assisted laser desorption/ionization-time of flight mass spectrometry.

RESULTS

The results showed that 18 major proteins were differentially expressed in the cells transfected with or without the HBV whole-X gene. The expression of these genes was further confirmed by reverse transcription-polymerase chain reaction and Western blot analysis.

CONCLUSION

Our findings provide a new insight into the investigation of the pathological role that the HBV whole-X gene plays in the development of hepatocellular carcinoma and may lead to the design of novel strategies for the treatment of this disease.

X gene/core promoter deletion mutation: a novel mechanism leading to hepatitis B 'e' antigen‑negative chronic hepatitis B

Mutations in the precore and core promoter regions of hepatitis B 'e' antigen (HBeAg) are implicated in HBeAg‑negative chronic hepatitis B virus (HBV) infection (CHB). The objective of the current study was to investigate novel mutant patterns that lead to HBeAg‑negative CHB. The . PreX-X genomic region from the sera of HBV‑infected patients was amplified, and analysis of the sequences displayed a unique deletion region, 234 nucleotides in length, which was observed in 54 clones and named core promoter deletion (CPD). CPD may have an important role in the cause of HBeAg‑negative CHB. In addition, a novel deletion mutation in the X gene was observed in patients with CHB. This deletion mutant codes a 76‑amino‑acid X factor instead of the X protein. In the present study, a new mutation pattern was discovered that may contribute to the cause of HBeAg-negative CHB, and therefore it is worthy of future studies.

A new mutation pattern of hepatitis B virus X gene

AIM: To identify a novel X gene mutation pattern of hepatitis B virus (HBV) in patients with chronic HBV infection.

METHODS: A pair of primers was designed on the basis of nucleotide sequences of X gene. Polymerase chain reaction (PCR) was used to amplify the target region from HBV DNA samples extracted from chronic hepatitis B patients in Xiamen city. After electrophoresis of the PCR products in 9 g/L agarose gel, the target regions were cut, re-purified and TA-cloned into pMD19 T vector. The inserted regions in positive clones were sequenced. Sequence comparison with HBV genome submitted in GenBank was made to find the mutation sites.

RESULTS: Totally 74 strains from 21 patients with chronic HBV infection were sequenced, and the results showed that there was a characteristic deletion region, with a length of 234 nt (nt 1601-1834) in 54 clones, and a length of 245 nt in 1 clone. There were 3 replacement mutations bounding to deletion mutation: G/A1515C, G1518C and A1585T, which caused substitutions in the 44th and 45th amino acid site to LL. These mutant strains only coded 76 aa of up-stream HBx.

CONCLUSION: A novel deletion mutation in HBV X gene is observed in patients with chronic HBV infection. The deletion mutants encode 76-aa X factor instead of X protein.

Circulating hepatitis B virus RNA in newborns from carrier mothers

OBJECTIVE

Despite intermittent flares, progression of chronic infection with hepatitis B virus has generally been related to a decrease in replication levels. In our laboratory, this decrease has been found to be associated with a decline in circulating full-length transcripts (fRNA) and to a shift to truncated transcripts (trRNA). Monitoring fRNA and trRNA as markers allows a more detailed analysis of high or low or non-replicative HBV infection stages.

METHODS

Here, we determined circulating HBV RNA in newborns from a total of 69 HBsAg-positive carrier mothers with and without immunotherapy administered during the last 3 months of pregnancy.

RESULTS

In line with previous observations, serum HBV DNA in newborns was only found when their mothers had not been treated (7/23). HBV RNA measured as trRNA was detected both in the presence and in apparent absence of serum HBV DNA. fRNA (coexisting with HBV DNA and HBeAg) was detected only in newborns from untreated mothers (8/23) and was always combined with trRNA. In contrast, trRNA was found in newborns from both untreated (20/23) and treated mothers (26/46).

CONCLUSIONS

Our data strongly suggest a direct intrauterine transmission of a low-replicative (unapparent) HBV infection stage. However, a feto-maternal transfer of trRNA (transfer of a marker) rather than transmission of the infectious virus cannot be excluded.

Impact of the hepatitis B virus genotype and genotype mixtures on the course of liver disease in Vietnam

Eight genotypes (A-H) of hepatitis B virus (HBV) have been identified. However, the impact of different genotypes on the clinical course of hepatitis B infection remains controversial. We investigated the frequency and clinical outcome of HBV genotypes and genotype mixtures in HBV-infected patients from Vietnam, Europe, and Africa. In addition, we analyzed the effects of genotype mixtures on alterations in in vitro viral replication. In Asian patients, seven genotypes (A-G) were detected, with A, C, and D predominating. In European and African patients, only genotypes A, C, D, and G were identified. Genotype mixtures were more frequently encountered in African than in Asian (P = .01) and European patients (P = .06). In Asian patients, the predominant genotype mixtures included A/C and C/D, compared to C/D in European and A/D in African patients. Genotype A was more frequent in asymptomatic compared with symptomatic patients (P < .0001). Genotype C was more frequent in patients with hepatocellular carcinoma (HCC; P = .02). Genotype mixtures were more frequently encountered in patients with chronic hepatitis in comparison to patients with acute hepatitis B (P = .015), liver cirrhosis (P = .013), and HCC (P = .002). Viral loads in patients infected with genotype mixtures were significantly higher in comparison to patients with a single genotype (P = .019). Genotype mixtures were also associated with increased in vitro HBV replication. In conclusion, infection with mixtures of HBV genotypes is frequent in Asia, Africa, and Europe. Differences in the replication-phenotype of single genotypes compared to genotype-mixtures suggest that co-infection with different HBV-genotypes is associated with altered pathogenesis and clinical outcome.

Alternative peptide-fusion proteins generated by out-of-frame mutations, just upstream ORFs or elongations in mutants of human hepatitis B viruses

By various means including out-of-frame mutations, just upstream ORFs and elongations, additional peptide fusions could be generated by mutants of Human Hepatitis B Virus (HBV). Numerous frameshift mutations inducing long alternative open reading frames have been evidenced in all HBV genes. Interestingly, these mutants are frequently detected in severe liver diseases, but seldom in asymptomatic carriers. The high level of conservation of some of these sequences in spite of the fact that they could be generated by different types of mutations, as their presence in mutants found on various continents, suggest that these mutations could play a role. These mutants could combine two advantages, that related to the loss of a part of a wild-type protein and that related to the putative advantage conferred by the additional sequences. In addition, in numerous Asian genomes (more than 300 to date) pre-X or pre-pre-S regions were found just upstream to, respectively, the X and the pre-S1 genes. These two regions are translated with their respective genes in frame and recent studies have evidenced the transactivating role of the corresponding proteins. With some exceptions, these regions are genotype- and serotype-specific (C/adr). In addition, these mutants have been found principally in patients with severe hepatitis diseases, for example, hepatocarcinoma in more than one third of the cases. As additional sequences generated by HBV variants may be relevant for viral life cycle, persistence and pathogenesis, further investigations are necessary to give a clearer picture of the subject.

Molecular epidemiological study on pre-X region of hepatitis B virus and identification of hepatocyte proteins interacting with whole-X protein by yeast two-hybrid

AIM: To identify the pre-X region in hepatitis B virus (HBV) genome and to study the relationship between the genotype and the pre-X region. To investigate the biological function of whole-X (pre-X plus X) protein, we performed yeast two-hybrid to screen proteins in liver interacting with whole-X protein.

METHODS: The pre-X region of HBV was amplified by polymerase chain reaction (PCR) method, and was cloned to pGEM Teasy vector. After the target region was sequenced, Vector 8.0 software was used to analyze the sequences. The whole-X bait plasmid was constructed by using yeast two-hybrid system 3. Yeast strain AH109 was transformed. After expression of the whole-X protein in AH109 yeast strains was proved, yeast two-hybrid screening was performed by mating AH109 with Y187 containing liver cDNA library plasmid. The mated yeast was plated on quadruple dropout medium and assayed for α-gal activity. The interaction between whole-X protein and the protein obtained from positive colonies was further confirmed by repeating yeast two-hybrid. After extracting and sequencing of plasmid from blue colonies, we carried out analysis by bioinformatics.

RESULTS: After sequencing, 27 of 45 clones (60%) were found encoding the pre-X peptide. Eighteen of twenty-seven clones (66.7%) of pre-X coding sequences were found from genotype C. Five positive colonies that interacted with whole-X protein were obtained and sequenced; namely, fetuin B, UDP glycosyltransferase 1 family-polypeptide A9, mannose-P-dolichol utilization defect 1, fibrinogen-B beta polypeptide, transmembrane 4 superfamily member 4-CD81 (TM4SF4).

CONCLUSION: The pre-X gene exists in HBV genome. Genes of proteins interacting with whole-X protein in hepatocytes were successfully cloned. These results brought some new clues for studying the biological functions of whole-X protein.

HBV core sequence: definition of genotype-specific variability and correlation with geographical origin

There are eight genotypes and nine subtypes of HBV. Small differences in geographical origin are associated with sequence changes in the surface gene. Here, we compared core gene sequences from different genotypes and geographical regions. Specific combinations of 24 amino acid substitutions at nine residues allowed allocation of a sequence to a subtype. Six of these nine residues were located in different T cell epitopes depending on HBV geographical area and/or genotype. Thirty-seven nucleotide changes were associated uniquely with specific genotypes and subtypes. Unique amino acid and nucleotide variants were found in a majority of sequences from specific countries as well as within subtype ayw2 and adr. Specific nucleotide motifs were defined for Korean, Indian, Chinese, Italian and Pacific region isolates. Finally, we observed amino acid motifs that were common to either South-east Asian or Western populations, irrespective of subtype. We believe that HBV strains spread within constrained ethnic groups, result in selection pressures that define sequence variability within each subtype. It suggests that particular T cell epitopes are specific for geographical regions, and thus ethnic groups; this may affect the design of immunomodulatory therapies.

Patterns of circulating hepatitis B virus serum nucleic acids during lamivudine therapy

Lamivudine treatment of individuals with chronic HBV infection leads to a rapid decline of hepatitis B virus (HBV) serum DNA. Because HBV replication quickly reaches pretreatment values following cessation of the drug, we addressed the question of whether changes during therapy in composition and amount of discernible circulating viral DNA and RNA might provide an explanation for this phenomenon. Nucleic acids were extracted from serial serum samples of two chronically infected patients. The first patient was treated with lamivudine for 14 weeks, whereas the second one, who displayed an HBV virus with a core gene mutation, received lamivudine for 10 weeks. Three sequence segments of the HBV genome synthesized successively during replication, namely, X, C, and X-preC, were analyzed via competitive polymerase chain reaction (PCR) and reverse transcriptase (RT)/PCR. HBV transcripts were also analyzed for differential polyadenylation. At the start of treatment, identical DNA copy numbers (10(9)/mL) were found for all three segments in the first patient. C segment DNA displayed the expected rapid decline. X-preC, a target contiguous only on plus-strand DNA, behaved similarly. In contrast, the X segment DNA copy numbers showed a less pronounced decrease, remaining at higher values (10(7)/mL) than the C and X-preC segments (both about 2 x 10(5)/mL) at the end of therapy. X segment RNA displayed a persisting copy number of about 10(7)/mL, whereas C and X-preC RNA decreased to about 10(5) copies/mL. Polyadenylated HBV RNA, both full-length and truncated, initially persisted at 10(5) but decreased to 10(4) to 10(3) copies/mL at the end of treatment. As expected, C segment DNA and RNA were not detected in the second patient, whereas X and X-preC segments showed essentially the same pattern as the first patient, although at a slightly lower level. We conclude that: (1) actual numbers of HBV genome equivalents during lamivudine therapy can be assessed only via X segment DNA, because it is reverse transcribed first; (2) lamivudine induces coexistence of DNA and RNA for the C and X segments at similar levels, indicating drug-arrested intermediates of reverse-transcribed HBV DNA minus-strand; and (3) packaged HBV RNA lacks a poly(A) tail, whereas polyadenylated RNA is likely not packaged.

Molecular epidemiological features of pre-X region in hepatitis B virus genome

AIM: To identify pre-X region in hepatitis B virus (HBV) genome and to study the relationship between the genotype and the existence of pre-X region.

METHODS: HBV genomic DNA was extracted from the sera of patients with HBV infection. Multiple-primers polymerase chain reaction (PCR) method was used to identify the genotype of HBV strains. Pre-X region was amplified by PCR method, and TA cloning technique was used to clone the DNA fragment into pGEM Teasy vector. After sequencing of the target region, Vector 8.0 software was used to analysis the sequences.

RESULTS: Seventeen samples were collected in this study. One genotype A, 3 genotype B, 10 genotype C and 3 B/C genotype mixture were identified. After sequencing, 27 clones from 45 clones (60%) were found encoding the pre-X peptide. Eighteen from 27 clones (66.7%) pre-X coding sequences were found from C genotype. Three types of replacement mutation led to pre-mature coding of pre-X gene. The mutation in pre-X peptide had feature of individually mutation.

CONCLUSION: Coding of the pre-X gene is popular in HBV genome.

Screening and identification of interacting proteins with pre-X protein of hepatitis B virus in hepatocytes by yeast-two hybrid technique

AIM: To investigate the biological function of pre-X protein encoded by hepatitis B virus (HBV) genome, and to screen proteins in hepatocytes interacting with pre-X protein by yeast-two hybrid technique.

METHODS: The pre-X gene was amplified by polymerase chain reaction (PCR) and pre-X bait plasmid was constructed by using yeast-two hybrid system 3, then the constructed vector was transformed into yeast AH109. The transformed yeast mated with yeast Y187 containing hepatocytes cDNA library plasmid in 2×YPDA medium. Diploid yeast was plated on synthetic dropout nutrient medium (SD/-Trp-Leu-His-Ade) and synthetic dropout nutrient medium (SD/-Trp-Leu-His-Ade) containing x--gal for selecting two times and screening. After extracting and sequencing of plasmid from blue colonies, the results were analyzed by bioinformatics.

RESULTS: Nineteen colonies were sequenced, in which five colonies were homo sapiens ferritin, one colonies was homo sapiens insulin-like growth factor binding protein 3 (IGFBP3), one homo sapiens aldolase B, one homo sapiens gene for glycosylphosphatidylinositol anchor attachment 1 (GAA1), one homo sapiens hemopexin, one homo sapiens C1 esterase inhibitor (C1-INH), one homo sapiens vitronectin, one homo sapiens voltage-dependent anion channel 1 (VDAC1), one hepsin (transmembrane protease, serine 1), one homo sapiens spindling, one homo sapiens plasminogen (PLG), three hypothetical proteins, and one homo sapiens chromosome 16 clone RP11-542M13.

CONCLUSION: Genes of pre-X interacting proteins in hepatocytes are successfully cloned and the results bring some new clues for studying the biological functions of pre-X and associated proteins.

N/A

N/A

Identification and characterization of high variable regions in hepatitis B virus genome of adr and adw serotypes

AIM: To identify a hypervariable region or a hyperconservative region in hepatitis B virus (HBV) genome and to study the pre-X region and the pre-pre-S region.

METHODS: Full-length of HBV genomes deposited in GenBank were searched and compared for their identity and homology. According to their sequences, the HBV genomes of adr or adw serotypes were selected. The Vector 6.0 software was used to compare the identity and difference among the strains of HBV genomes.

RESULTS: Twenty-eight strains of HBV genome in GenBank belong to adr serotype HBV genome, and 22 strains belong to adw serotype. After being compared, the total identity rates were 76.6% and 73.9%, respectively. There might be a hypervariable region and a hyperconservative region in adr serotype HBV genome, with the regional identity rate of 54.5% and 92.1%, respectively. There might be a hyperconservative region in adw serotype HBV genome, with the regional identity rate of 85.0%. Region coding pre-pre-S gene was popular in the strains. Pre-X region might be a serotype-specific gene. A²⁶⁰⁸ C/T and/or C/A²⁷³³ T replacement mutation resulted in disability of coding pre-X gene.

CONCLUSION: There may be a hyperconservative region in HBV genome. Pre-pre-S gene and pre-X gene are worthy of further study.

Patterns of circulating hepatitis B virus serum nucleic acids during lamivudine therapy

We examined whether lamivudine treatment, in addition to the rapid decline of HBV serum DNA described in a large number of laboratories, causes changes in composition and amount of discernable circulating viral DNA and RNA. Nucleic acids were extracted from serial serum samples of a patient infected chronically and treated with lamivudine for 14 weeks. Three sequence segments of the HBV genome synthesized successively during replication, X, C, and X-preC, were analyzed by competitive PCR and RT/PCR. In addition, RNA was examined for differential polyadenylation. Before treatment, identical DNA copy numbers (10(9)/ml) were found in all three segments. C segment DNA displayed the expected rapid decline. X-preC, a target contiguous only on plus-strand DNA behaved similarly. In contrast, the X segment DNA copy numbers showed a less pronounced decrease remaining at higher values (10(7)/ml) than the C and X-preC segment (both about 2 x 10(5)/ml) at the end of therapy. X segment RNA displayed a persisting copy number of about 10(7)/ml, while C and X-preC RNA decreased to about 10(5) copies/ml. Polyadenylated HBV RNA, full-length and truncated, persisted initially at 10(5) but decreased to 10(4) to 10(3) copies/ml at the end of treatment. The major conclusions are the actual numbers of virus particles during lamivudine therapy can only be assessed via X segment DNA, since it is reverse transcribed first, and Lamivudine induced coexistence of DNA and RNA for the C and X segment at similar levels indicates drug-arrested intermediates of reverse transcribed HBV DNA minus-strand. Packaged RNA lacks a poly(A) tail whereas polyadenylated RNA is likely not packaged.

N/A

N/A

Study on definition of pre-x region in hepatitis B virus genome

AIM

To identify the pre-X gene in HBV strains of Chinese patients.

METHODS

The whole HBV genome was amplified by long-distance and accurate polymerase chain reaction (LA-PCR) method from the serum of 2 patients with chronic HBV infection, and then the PCR products were cloned into pGEM Teasy vectors. Five clones of HBV genome were sequenced. Sequences of our finding were compared with other HBV genome sequence deposited in GenBank.

RESULTS

Pre-X region was found in the HBV genome of these 5 clones, just upstream to the X gene. The pre-X gene is 168 bp long, and can be translated with X gene in frame. The amino acids sequence of pre-X gene was as the following: MGLGYWPSPPAWNLCGSSADPYCGTPSSLFCS QPVWSETYRNRQLCCPLSQIHLLS.

CONCLUSION

Pre-X region may be a serotype-specific coding gene.

Study on definition of pre-pre-S region in hepatitis B virus genome

AIM

To investigate the new open reading frame (ORF) in hepatitis B virus (HBV) genome.

METHODS

The whole HBV genome was amplified by long-distance and accurate polymerase chain reaction (LA-PCR) method from the serum of 2 patients with chronic HBV infection, and then the PCR products were ligased into pGEM Teasy vectors. Five clones of HBV genome were sequenced. Sequences of our finding were compared with other HBV genome sequence deposited in GenBank.

RESULTS

A new ORF was found in HBV genome, just before Pre-S1 region. It was defined as pre-pre-S region. The pre-pre-S ORF was deduced to be translated with Pre-S1, Pre-S2 and S gene in frame. Its amino acids sequence was as the following: MQLIITSKLGIIYILCGRLVFYIREKLHAV PHFVGHHILGNKSYS. There was a TA-rich region before the ATG of pre-pre-S ORF, indicating a possible promoter for its transcription.

CONCLUSION

There is a new ORF pre-pre-S located upstream to pre-S1 region.

Structural organization of the hepatitis B virus minichromosome

The replicative intermediate of hepatitis B virus (HBV), the covalently closed, circular DNA, is organized into minichromosomes in the nucleus of the infected cell by histone and non-histone proteins. In this study we investigated the architecture of the HBV minichromosome in more detail. In contrast to cellular chromatin the nucleosomal spacing of the HBV minichromosome has been shown to be unusually reduced by approximately 10 %. A potential candidate responsible for an alteration in the chromatin structure of the HBV minichromosome is the HBV core protein. The HBV core protein has been implicated in the nuclear targeting process of the viral genome. The association of the HBV core protein with nuclear HBV replicative intermediates could strengthen this role. Our findings, confirmed by in vivo and in vitro experiments indicate that HBV core protein is a component of the HBV minichromosome, binds preferentially to HBV double-stranded DNA, and its binding results in a reduction of the nucleosomal spacing of the HBV nucleoprotein complexes by 10 %. From this model of the HBV minichromosome we propose that the HBV core protein may have an impact on the nuclear targeting of the HBV genome and be involved in viral transcription by regulating the nucleosomal arrangement of the HBV regulatory elements, probably in a positive manner.

Molecular bases for the development of hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC)

Hepatocellular carcinoma (HCC) is the most common histological form of primary liver cancer; the tumor cells having retained features of hepatocytic differentiation. It is important to emphasize the heterogeneity of the histological background on which the tumor develops. Most HCCs complicate the evolution of an active or inactive cirrhosis. However, some tumors occur on livers with minimal histological changes; the prevalence of such cases varies from one geographical region to the other; being much higher in the southern half of Africa (around 40% of HCCs) than in Asia, America and Europe, where at least 90% of HCCs are associated in the cirrhosis. This heterogeneity is probably a reflection of different environmental and genetic factors. A large number of epidemiological and molecular studies have indeed clearly demonstrated the prime importance of environmental factors to the development of primary liver cancers in humans. Chronic hepatitis B (HBV) and C (HCV) infections are major risk factors. This review will mainly analyse the impact of chronic HBV infection but it is important to emphasize the potential synergistic effects between HBV and HCV, as well as between viral infections and other environmental factors, such as alcohol, chemical carcinogens (see review by Dr Wogan) and other, still poorly defined, hormonal factors which may account for the higher incidence of the tumor in man. Finally the review by Dr Buendia highlights the emerging issue of liver-cancer genetics.

Full-genome sequence analyses of hepatitis B virus (HBV) strains recovered from chimpanzees infected in the wild: implications for an origin of HBV

Hepatitis B virus (HBV) belongs to the genus Orthohepadnavirus of the family Hepadnaviridae. Having been found in various animals (duck, heron, woodchuck, ground squirrel, and primates), hepadnaviruses must have undergone a long history of evolution and may comprise more members than currently recognized. Chimpanzees may also have their own hepadnavirus, even if it might be very close to HBV. We analyzed HBV-like sequences from three chimpanzees (Pan troglodytes) that were most likely infected during their life in Africa in the wild. Two chimpanzees (Ch256 and Ch258) possessed a viral genome of 3182 nt in length with a 33-nt deletion in the preS1 region, which could not be classified into any of the six genotypes (A-F) of human HBV but was very homologous to a previously reported isolate from a London Zoo chimpanzee. Phylogenetically distinct from the HBV-like sequences from gibbons, orangutans, and a gorilla so far reported, the Ch256 and Ch258 isolates would represent an indigenous chimpanzee HBV (tentatively ChHBV). A third chimpanzee (Ch195) had a 3212-nt genome, classifiable into the genotype E of HBV. Because HBV-E has been found mostly in Africans, Ch195 may have been infected from a human source in Africa. However, an inverse scenario is also possible: a spread of HBV-E might have occurred from chimpanzees to humans a long time ago in Africa. Analysis of the arginine-rich C-terminal region of the core protein, which is well conserved among mammalian hepadnaviruses, indicated that HBV-E/F and nonhuman primate hepadnaviruses are much closer than HBV-A/B/C/D to the hepadnaviruses of woodchuck and ground squirrel. Our results support an "ex-nonhuman primate" hypothesis for the origin of HBV.

Characterization of the reactivity pattern of murine monoclonal antibodies against wild-type hepatitis B surface antigen to G145R and other naturally occurring "a" loop escape mutations

The hepatitis B surface antigen (HBsAg) "a" domain harbors major B-cell epitopes. Viruses with mutations in this region emerge after vaccination or during hepatitis B immune globulin (HBIg) prophylaxis. A strain with G145R replacement has been almost invariably isolated as a major escape mutant. We investigated mutant antigen-antibody interactions with direct binding assays. G145R and 16 other naturally occurring recombinant HBsAg mutants were expressed in mammalian Cos-1 cells. The reactivity of a panel of 28 murine anti-hepatitis B surface antigen (anti-HBs) monoclonal antibodies to mutant antigens was measured with enzyme immunoassay and expressed as percentage compared with the wild-type (wt) HBsAg signal for each antibody. All point-mutated proteins displayed diffuse intracellular immunofluorescent labeling corresponding to a secretory pathway. Monoclonal antibodies (mAbs) were classified according to different binding patterns. The effect of mutations on antibody binding differs depending on the amino acid involved and on the location within the "a" loop. As expected, most antibodies had absent or negligible binding (<40%), notably with residue 145 replacements. However, we identified antibodies that reacted with conformational epitopes but nevertheless had adequate reactivity (>40%) with all mutant antigens, including G145R. The effect of G145R was more pronounced than that of G145A. A subgroup of antibodies had substantially increased recognition (>120%) of antigens with mutations in the first loop. We demonstrated that antibodies can be selected or combined that react with all mutants investigated, including G145R. These data offer perspectives for improving anti-HBs-based protection against hepatitis B.

Localization of a unique hepatitis B virus epitope sheds new light on the structure of hepatitis B virus surface antigen

In a search for monoclonal antibodies (MAbs) that can bind hepatitis B virus surface antigen (HBsAg) with amino acid substitutions in the immune dominant 'a' region (escape mutants) we investigated the epitope recognition site of the human MAb 4-7B. Pepscan analysis and experiments with alanine substitution as well as substitutions known from nature pointed to residues 178-186 in the small S protein with the amino acid sequence PFVQWFVGL (key amino acids in bold) as the minimal epitope. Single amino acid substitutions at positions 122(R/K)(d/y), 134(Y/F), 145(G/R), 148(T/A) and 160(K/R)(w/r), representing 'a' region variants in recombinant HBsAg COS-I cells, did not influence binding of MAb 4-7B. Synthetic peptides (residues 175-189) including the 4-7B epitope sequence were able to evoke an anti-HBs response in rabbits. According to established polypeptide models, the 4-7B epitope region is located in the lipid layer of 20 nm HBsAg particles. The present results, however, suggest that residues 178-186 are exposed on the surface of the 20 nm particle. This may change our view of the structure of HBsAg.

Hepatitis viruses: genetic variants and clinical significance

Variants of hepatitis B, C, and delta virus have been identified in patients both with acute and chronic infections. In the hepatitis B virus genome, naturally occurring mutations have been found in all viral genes, most notably in the genes coding for the structural envelope and nucleocapsid proteins. In the hepatitis C virus genome, the regions coding for the structural envelope proteins E1 and E2, as well as the 3'-contiguous non-structural region NS1, were found to be hypervariable. Viral variants may be associated with a specific clinical course of the infection, e.g., acute, fulminant or chronic hepatitis. Specific mutations may reduce viral clearance by immune mechanisms ('vaccine escape' and 'immune escape'), response to antiviral therapy ('therapy escape'), as well as detection ('diagnosis escape'). The exact contribution, however, of specific mutations to the pathogenesis and natural course of hepatitis B, C, or delta virus infection, including hepatocellular carcinoma development, and the response to antiviral treatment remains to be established.

Sequential changes in full-length genomes of hepatitis B virus accompanying acute exacerbation of chronic hepatitis B

BACKGROUND/AIM

During the course of persistent hepatitis B virus infection, viral replication markedly decreases after acute exacerbation of liver inflammation accompanied by emergence of antihepatitis B e antibody (anti-HBe) and/or anti-hepatitis B surface antibody (anti-HBs). In some cases, however, persistent viral replication continues even after such exacerbation with or without HBeAg/anti-HBe seroconversion. The aim of the present study was to investigate the extent of genetic variations of HBV in this phenomenon.

METHODS

Full-length HBV genomes were amplified by polymerase chain reaction from sera of three patients before and after acute exacerbation and were directly sequenced.

RESULTS

In the whole genomes of 3215 nucleotides, only six nucleotide mutations for six amino acid substitutions (2 in the surface gene, 2 in the X gene, 1 in the core gene and 1 in the polymerase gene) were observed in patient 1, 15 mutations for 14 amino acid substitutions (1 in the pre-core codon 28, 4 in the surface gene, 4 in the core gene and 5 in the polymerase gene) were observed in patient 2, and 5 mutations for 6 amino acid substitutions (2 in the surface gene, 2 in the X gene, pre-core stop codon mutation and 1 in the polymerase gene) were observed in patient 3. Substitution in the a determinant of the surface gene, which encodes target epitopes for neutralizing antibodies, as well as those in the pre-core/core gene, which encodes epitopes for cytotoxic T cells, were mainly found.

CONCLUSION

HBV that remained after the emergence of anti-HBe and anti-HBs are considered to possess mutations in epitopes for both humoral and cellular immunity. These mutant HBV may be involved in the pathogenesis of persistent hepatic injury after acute exacerbation.

Hepatitis B and C viruses and primary liver cancer

The data presented indicate that viral agents (namely, HBV and HCV) are major environmental aetiological factors for human primary liver cancer. It is important to elucidate the molecular mechanisms further because HCC is one of the few examples of virus-related human cancers. In addition, the available evidence points to the possibility of at least partial prevention of the tumour by large-scale vaccination.

Mutations in the core promoter region of hepatitis B virus in patients with chronic hepatitis B

The core promoter region of hepatitis B virus genomes regulates transcription of the precore and pregenomic mRNAs encoding hepatitis B e antigen (HBeAg) and core antigen that contain target epitopes for cytotoxic T lymphocytes. The prevalence and clinical significance of mutations in this region were investigated. DNA was extracted from six asymptomatic carriers positive for HBeAg, eight asymptomatic carriers positive for an anti-HBe antibody, and 24 patients with chronic liver disease. The core promoter and precore regions of hepatitis B virus genomes were amplified by polymerase chain reaction, and predominant sequences were determined by direct sequencing. Mutations were found in none of the HBeAg-positive asymptomatic carriers but in all of the anti-HBe-positive asymptomatic carriers and the patients with chronic liver disease. Especially, A to T mutations at nucleotide 1762 and G to A mutations at nucleotide 1764 were found in five anti-HBe-positive asymptomatic carriers, and 22 patients with chronic liver disease. These two mutation hot spots were located within binding sites of the nuclear factors, and nucleotide 1762 was also involved in the A, T rich sequence that is located 28 base pairs upstream of the precore mRNA initiation site. Serum HBeAg and DNA polymerase levels were significantly lower in patients with these mutations than those without these mutations, and five individuals with these mutations were positive for anti-HBe despite the absence of the precore stop codon mutation. These mutants may be selected by host immune response to HBeAg and/or core antigen.

Complete nucleotide sequences of hepatitis B virus genomes associated with epidemic fulminant hepatitis

Pre-core/core mutants are frequently observed in patients with fulminant hepatitis. To investigate the extent of molecular characteristics of hepatitis B virus (HBV) genomes implicated in the development of fulminant hepatitis, full-length HBV genomes were sequenced directly from sera of two patients with epidemic fatal fulminant hepatitis, after amplification by the polymerase chain reaction. These two genomes, of 3215 nucleotides, were 99.6% identical, indicating that a common source of HBV potentially caused fulminant hepatitis. Thirty unique nucleotide mutations were commonly found in the two entire HBV genomes. Three were located in the stem-loop structure, changing this element to a more stable structure. Twenty-five unique amino acid substitutions were found in each open reading frame, except for the X and pre-surface 2 genes. One was located in the pre-surface 1 gene; two were in the surface gene; three were in the pre-core gene, including codons 28 (tryptophan to stop codon) and 29 (glycine to aspartic acid); eight were in the core gene; and 11 were in the polymerase gene. The pre-core mutations at codons 28 and 29 were common to the two HBV strains reported previously in patients with epidemic fulminant hepatitis. Thus, HBV genomes associated with epidemic fatal fulminant hepatitis have numerous unique mutations, located mainly in the polymerase gene, as well as the pre-core/core gene, including mutations in the stem-loop structure of the pregenome encapsidation signal sequence. These mutations may be associated with the development of fulminant hepatitis.

Localization of hepatitis B virus core protein and viral DNA at the nuclear membrane

An early step in the replication of the hepatitis B virus (HBV) genome is the transport of the viral DNA into the nucleus of the infected cell. So far only little is known about the events and mechanisms at the nuclear membrane required for entry of the viral genome into the nucleus. Using a hepatoblastoma cell line that constitutively produces hepatitis B virions and in so doing displays intracellular viral amplification, we showed that nonparticulated HBV core protein is associated with nuclear membrane pore complexes. Additionally, viral DNA has been detected firmly attached to the nuclear membrane. Small amounts of viral core protein, as well as viral DNA, were detectable within the cell nucleus. However, core particles could not be shown at the nuclear membrane or within the nuclei of these cells. Our observations on localization of HBV DNA and core protein at the nuclear membrane thus provide a suggestion for further examinations of the transfer of the viral genome from the cytoplasm into the nucleus of the infected cell.

Mutations in the pre-core region of hepatitis B virus serve to enhance the stability of the secondary structure of the pre-genome encapsidation signal

We conducted a large-scale survey to determine the frequency and clinical significance of mutations in the pre-core region of hepatitis B virus (HBV). Sera from 263 patients with chronic HBV infection were analyzed by direct sequencing of PCR-amplified HBV DNA. Four major missense/nonsense mutations (M) were found: (M1) C-->T at nucleotide position 1856, Pro-->Ser at codon 15; (M2) G-->A at position 1896, Trp-->stop at codon 28; (M3) G-->A at position 1898, Gly-->Ser at codon 29; and (M4) G-->A at position 1899, Gly-->Asp at codon 29. The commonest conserved mutation was M0: T-->C at position 1858, Pro-->Pro at codon 15. We found that M1 and M2 were mutually exclusive, M3 was only found in association with M1, and M4 was predominantly found in association with M2. All patients with M1 but none of those with M2 had M0. The invariable coexistence of certain mutations in codon 15 and codons 28 and 29 and the mutual exclusion of other mutations in these two noncontiguous regions is related to the stem-loop structure of the pre-genome encapsidation sequence located in the precore/core region. M2 and M4 enhance the stability of the stem by providing two additional paired sites. M1 destroys an existing base pair. However, M1 only occurred in the presence of M0, which provides an extra paired site, and 50% of patients with M1 had M3, a compensatory mutation that restores base pairing at this site. Our data support the proposed secondary structure of the pre-genome encapsidation sequence. The primary function of the mutations in the pre-core region is to enhance stability of this secondary structure to ensure perpetuation of viral replication.

Hepatitis B virus genotype A rarely circulates as an HBe-minus mutant: possible contribution of a single nucleotide in the precore region

The emergence of HBe-minus hepatitis B virus (HBV) mutants, usually through a UAG nonsense mutation at codon 28 of the precore region, helps the virus to survive the anti-HBe immune response of the host. Host and viral factors that predispose to the emergence of such mutants are not well characterized. The fact that the precore region forms a hairpin structure essential for the packaging of viral pregenomic RNA may explain the extremely high prevalence of the UAG mutation at codon 28. It converts a wobble U-G pair in the packaging signal between nucleotide 3 of codon 15 (CCU) and nucleotide 2 of codon 28 (UGG) into a U-A pair. Since genotype A of HBV has a CCC sequence at codon 15, the UAG mutation would, instead, disrupt a C-G pair present in the wild-type virus. This alteration was shown by transfection experiments to greatly compromise the packaging of pregenomic RNA. The implication of this finding was elucidated by molecular epidemiological studies. Genotype A was found to be the most prevalent genotype in the wild-type virus populations in France but was found in only 1 of the 46 isolates of HBe-minus mutants found there. These mutants were contributed chiefly by genotype D, the second most prevalent genotype in France, which is characterized by a CCU sequence at codon 15. The role of the single nucleotide at codon 15 was confirmed by the finding of the single genotype A isolate in which both wild-type and mutant viruses were present. Interestingly, nearly all of the mutants had a codon 15 sequence of CCU instead of the CCC present in the wild-type viruses. Our results suggest that genotype A of HBV rarely circulates as HBe-minus mutants, probably because of a requirement for a simultaneous sequence change at codon 15. These data, together with the virtual absence of genotype A in the Chinese samples examined, may provide some insights into the uneven prevalence of HBe-minus mutants in the world.

Precore-mediated inhibition of hepatitis B virus progeny DNA synthesis

The capacities to induce the synthesis of hepatitis B virus (HBV) unit-length DNA were compared for two HBV DNAs with an overall sequence diversity of about 10%. They had been cloned from serum (DNA2) and from a hepatocellular carcinoma (DNA4), respectively. As a major difference, DNA4 carries a translational stop signal preventing the synthesis of precore protein. Progeny DNA yields obtained after transfection with respective pregenome transcription units allocated DNA2 to a low-replicator and DNA4 to a high-replicator phenotype. Cotransfection of DNA2 interfered with progeny DNA synthesis induced by DNA4. By mutual exchange of restriction fragments, the region on the viral genome responsible for the differing replicator phenotypes was confined to a sequence comprising the 3'-terminal part of the X gene, core promoter, encapsidation signal epsilon, precore/core gene, and 5'-terminal part of the pol gene. Point mutations in DNA2 abolishing proper expression of the precore gene strongly enhanced the yield of progeny DNA, whereas cotransfection of a precore expression plasmid with DNA4 or with the mutated DNA2 substantially lowered the amount of progeny DNA. Hence, precore expression acts as an inhibitory principle for HBV replication. The same stop mutation as in DNA4 has been found to arise frequently in virus carriers. Loss of precore expression and concomitant conversion to a more severe hepatitis, as observed in the course of a chronic infection, thus can be explained by a relaxation of replication-level control.

Diversity of hepatitis B virus X gene-related transcripts in hepatocellular carcinoma: a novel polyadenylation site on viral DNA

RNA was isolated from tissue of two patients with hepatocellular carcinoma developed on the background of a chronic hepatitis B virus infection. For identification and characterization of 3' ends of X gene open reading frame (ORF)-related transcripts, RNA was reverse transcribed into cDNA and subjected to polymerase chain reaction. Cloned amplification products from tumor tissue of one patient represented an approximately even distribution of transcripts terminating at the established poly(A) signal (standard transcripts) and of truncated transcripts terminating at a CATAAA poly(A) signal within the 3' end region of X gene ORF (truncated transcripts). Amplified cDNA from tumor tissue of the second patient could be attributed mainly to the standard type of transcripts, whereas cDNA from the nontumor tissue of the same patient could be assigned to four groups of transcripts: (i) standard transcripts, (ii) transcripts with internal deletions affecting the 3' end of the X gene, (iii) truncated transcripts, and (iv) hybrid transcripts displaying 5' sequences from the X gene ORF fused to cellular sequences.

Expression of the X protein of hepatitis B virus in insect cells using recombinant baculoviruses

The baculovirus system was used to express the X protein of human hepatitis B virus (HBV). The X open reading frames (X ORFs) from cloned viral DNA of the HBV subtypes ayw and adr were introduced into the genome of Autographa californica nuclear polyhedrosis virus (AcNPV). The HBV-DNA of subtype adr derived from a hepatocellular carcinoma contains an X ORF and a 5' extended preX/X ORF, which were both used to construct X recombinant baculoviruses. Infection of Sf9 insect cells with these recombinant viruses yielded large amounts of the respective X proteins. They were identified by a set of mouse monoclonal antibodies directed against different epitopes of the ayw X protein using immunoblotting techniques. A subpopulation of the X protein expressed is modified, thus raising the molecular weight from the expected size of 17 kD to 21 kD. Indirect immunofluorescence and immunoelectron microscopy was performed to characterize the subcellular distribution of the X protein expressed in Sf9 cells. Data are presented that it accumulates as large globular structures within the cytoplasm and the nucleus of the infected cells.