Complete nucleotide sequence of hepatitis B virus DNA of subtype adr and its conserved gene organization

The complete nucleotide sequence of hepatitis B virus (HBV) DNA from Dane particles of subtype adr was determined. The 3215-bp sequence showed the presence of genes for the surface antigen (226 amino acids) and core antigen (183 amino acids), in addition to two (long and small) open reading frames (ORFs) capable of coding the 843 and 154 amino acids. These ORFs differed from those of the other adr clones so far reported [Ono et al., Nucl. Acids Res. 11 (1983) 1747–1757; Fujiyama et al., Nucl. Acids Res. 11 (1983) 4601–4610]. The gene organization of HBV DNA was found to be well conserved irrespective of subtype. The direct repeat of the undecanucleotide sequence near the 5′ ends of the short (S) and long (L) strands of HBV DNA and the two small direct repeats between both 5′ ends were found to be characteristic structures.     

Cloning and structural analyses of hepatitis B virus DNAs, subtype adr.

Entire genomes of hepatitis B virus (subtype adr) have been cloned. The nucleotide sequence data were compared with other sequences of HBV genome including: adw [Valenzuela et al. (1981) in Animal Virus Genetics. Fields et al. eds. Academic Press, Inc., NY. pp. 57-70], ayw [Galibert et al. (1979) Nature, 281, 646-650], and adyw [Pasek et al. (1979) Nature 282, 575-579]. Four open coding frames for polypeptides larger than 6,000 dalton were found to be conserved and were highly compressed by overlapping with each other in one strand (L-strand). Sites of initiation of the S gene and termination of the P gene were not conserved. No conserved coding frame was found on the opposite strand (S strand). Amino acid sequences of six surface antigen (HBsAg) peptides, including subtypes adr, adw, and ayw, are deduced from the DNA sequences, and the substitution of amino acid residues which are consistent with the change of subtypes are demonstrated.     

The comparative mapping of virion and cloned DNA of the hepatitis B virus

The entire hepatitis B virus (HBV) genome and its fragments have been cloned into the BamHI site of the plasmid pBR322 vector. The identity of physical maps of cloned and authentic virion DNAs was demonstrated by restriction enzyme analysis. The location of restriction sites is suggestive of a certain similarity between the studied HBV DNA and HBV DNA, subtype ayw (Galibert et al., 1979). From the restriction enzyme analysis of virion DNA repaired and 32P-labeled by the endogenous DNA-polymerase reaction, the new information concerning the location and maximal length (approximately 1500 nucleotides) of the single-stranded region of HBV DNA has been established.     

人乙型肝炎病毒(HBV)adr亚型基因组的多态性

由乙型肝炎adr亚型病毒(HBVadr)携带者26人的混合血清,得到了HBVadr基因组克隆株(PADR)158株,对这些克隆株进行四种限制性内切酶(BglⅡ,HindⅢ,PstⅠ,XhoⅠ)切点测定,并对其中S株的13种限制性内切酶图谱进行比较研究,发现同为adr亚型病毒,其基因组的限制性酶切图谱存在差异。另外,通过HindⅢ)切点得到的12个克隆株(PADR-H),也进行了酶切图谱分析。在这170个克隆株中,已经发现了5种类型的HBVadr基因组限制性酶切图谱,其中有6种酶(AvaⅠ,EglⅠ,BglⅡ,HincⅡ,HindⅢ,HpaⅠ)的7个变异点。本文报道了HBVadr基因组的多态性现象。     

The nucleotide sequence of cloned wheat dwarf virus DNA

Restriction analysis and cloning of virus-specific double-stranded DNA isolated from plants infected with wheat dwarf virus (WDV) indicated that the virus genome, like that of maize streak virus (MSV), consists of a single DNA circle. The complete nucleotide sequence of cloned WDV DNA (2749 nucleotides) has been determined. Comparison of the potential coding regions in WDV DNA with those in the DNA of two strains of MSV suggests that these viruses encode at least two functional proteins, the coat protein read in the virion (+) DNA sense and a composite protein, formed from two open reading regions, in the complementary (-) DNA sense. Although WDV and MSV are serologically unrelated their coat proteins showed 35% direct amino acid sequence and their DNAs showed 46% nucleotide sequence homology. There was too little homology between the DNAs of WDV and those of two geminiviruses with bipartite genomes, cassava latent virus (CLV) and tomato golden mosaic virus (TGMV), to align the sequences. However comparison of the amino acid sequences of predicted proteins of WDV, MSV, TGMV and CLV revealed clear relationships between these viruses and suggested that the monopartite and the bipartite geminiviruses have a common ancestral origin. Four inverted repeat sequences which have the potential to form hairpin structures of deltaG >/= -14 kcal/mol were detected in WDV DNA. The sequence TAATATTAC present in the loop of one of these hairpins is conserved in similar putative structures in MSV DNA and in both DNA components of CLV and TGMV and may function as a recognition sequence for a protein involved in virus DNA replication.     

Overexpression and purification of PreS region of hepatitis B virus antigenic surface protein adr subtype in Escherichia coli

PreS domain of Hepatitis B virus (HBV) surface antigen is a good candidate for an effective vaccine as it activates both B and T cells besides binding to hepatocytes. This report deals with overexpression and purification of adr subtype of surface antigen that is more prevalent in Pakistan. PreS region, comprising 119 aa preS1 region plus a 55 aa preS2 region plus 11 aa from the N-terminal S region, was inserted in pET21a+ vector, cloned in E. coli DH5alpha cells and expressed in E. coli BL21 codon+ cells. The conditions for over expression were optimized using different concentrations of IPTG (0.01-5 mM), and incubating the cells at different temperatures (23-41 degrees C) for different durations (0-6 h). The cells were grown under the given optimized conditions (0.5 mM IPTG concentration at 37 degrees C for 4 h), lysed by sonication and the protein was purified by ion exchange chromatography. On the average, 24.5 mg of recombinant protein was purified per liter of culture. The purified protein was later lyophilized and stored at -80 degrees.     

Organization and expression of hepatitis B sequences cloned from hepatocellular carcinoma tissue DNA

We have constructed a phage lambda library of liver DNA fragments from West African patient who died of liver failure due to advanced hepatocellular carcinoma. Four hepatitis B virus (HBV) DNA-carrying recombinants have been isolated, one clone (lambda IA22) being analyzed in greatest detail. It contains approximately 3.8 kb of HBV DNA without detectable deletions or rearrangements. One site of integration lies close to the nick in free viral DNA. The restriction map of the HBV sequences is close to those published for the ay subtype. Coconvection of mouse Ltk- cells with lambda IA22 and cloned thymidine kinase gene results in the expression of gene S and the excretion of hepatitis B surface antigen (HBsAg) particles into the culture supernatant.     

Data mining on DNA sequences of hepatitis B virus

Extraction of meaningful information from large experimental data sets is a key element in bioinformatics research. One of the challenges is to identify genomic markers in Hepatitis B Virus (HBV) that are associated with HCC (liver cancer) development by comparing the complete genomic sequences of HBV among patients with HCC and those without HCC. In this study, a data mining framework, which includes molecular evolution analysis, clustering, feature selection, classifier learning, and classification, is introduced. Our research group has collected HBV DNA sequences, either genotype B or C, from over 200 patients specifically for this project. In the molecular evolution analysis and clustering, three subgroups have been identified in genotype C and a clustering method has been developed to separate the subgroups. In the feature selection process, potential markers are selected based on Information Gain for further classifier learning. Then, meaningful rules are learned by our algorithm called the Rule Learning, which is based on Evolutionary Algorithm. Also, a new classification method by Nonlinear Integral has been developed. Good performance of this method comes from the use of the fuzzy measure and the relevant nonlinear integral. The nonadditivity of the fuzzy measure reflects the importance of the feature attributes as well as their interactions. These two classifiers give explicit information on the importance of the individual mutated sites and their interactions toward the classification (potential causes of liver cancer in our case). A thorough comparison study of these two methods with existing methods is detailed. For genotype B, genotype C subgroups C1, C2, and C3, important mutation markers (sites) have been found, respectively. These two classification methods have been applied to classify never-seen-before examples for validation. The results show that the classification methods have more than 70 percent accuracy and 80 percent sensitivity for most data sets, which are considered high as an initial scanning method for liver cancer diagnosis.     

Agroinfection and nucleotide sequence of cloned wheat dwarf virus DNA

Cloned DNA of the geminivirus wheat dwarf virus (WDV) was successfully used to infect seedling wheat plants. The clone was derived from circular double-stranded viral DNA isolated from naturally infected tissue. The initiation of infection was mediated by Agrobacterium tumefaciens using cloned dimeric WDV genomes in a binary Agrobacterium vector. The WDV DNA which comprised the infectious clone was sequenced and is compared with the published sequence of a Swedish isolate of the same virus. The results confirm that the single WDV genome component of 2.75 kb carries all the information necessary for production of viral symptoms, virus particles and viral double- and single-stranded DNA forms.     

Restriction map of the hepatitis B virus DNA cloned in Escherichia coli

A plasmid carrying the complete genome of hepatitis B virus (HBV) inserted into the BamHI site of the pBR322 plasmid vector has been constructed. The physical map of HBV DNA established for 13 restriction endonucleases allows to conclude that the cloned DNA is similar, but not identical to the HBV DNA of ayw subtype.     

Integration of hepatitis B virus DNA in chromosome-specific satellite sequences.

We previously reported the cloning and detailed analysis of the integrated hepatitis B virus sequences in a human hepatoma cell line. We report here the integration of at least one of hepatitis B virus at human satellite DNA sequences. The majority of the cellular sequences identified by this satellite DNA were organized as a multimeric composition of a 0.6-kilobase EcoRI fragment. This clone hybridized in situ almost exclusively to the centromeric heterochromatin of chromosomes 1 and 16 and to a lower extent to chromosome 2 and to the heterochromatic region of the Y chromosome. The immediate flanking host sequence appeared as a hierarchy of repeating units which were almost identical to a previously reported human satellite III DNA sequence.     

Total nucleotide sequences of the infectious cloned DNAs of bean golden mosaic virus

Complete nucleotide sequences of the infectious cloned DNA components (DNA A and B) of bean bolden mosaic virus were determined. The DNA A (2585 nucleotides) and DNA B (2647 nucleotides) have little sequence homology with each other, but both A and B contain a common region of 205 nucleotides. A possible large hairpin structure is detected in the common region. Nucleotide sequences of DNAs A and B revealed the presence of 8 potential coding regions for proteins (m.w. greater than 10,000). Among them, four open reading frames (ORFs 1-4) encode proteins of m.w. 30,000 or greater, and are individually coded in virion DNA A and B senses (+) and their complementary senses (-), respectively. The other four ORFs 5-8 are in virion DNA B(+) and its complementary sense (-). All of the ORFs 1-4 have regulatory signals for RNA synthesis (TATAA/T) in the region 5' upstream from a potential start codon ATG.     

Biophysical characterization of the adr subtype of hepatitis B antigen and preparation of anti-r sera in rabbits.

The biophysical properties of the adr subtype of HBSAg were determined and found to be identical to those of the adw and ayw phenotypes. These properties were used to purify the 22 nm spherical form of HBSAg/adr from the serum of a chronic antigen carrier by using zonal centrifuge techniques. The purified antigen was injected into 15 rabbits which were bled weekly to follow the development of antibodies to HBSAg by hemagglutination, and to the subtype determinants of HBSAg by counterelectrophoresis and agar gel diffusion (AGD) assays. From these data and two pilot studies to produce anti-w using an adw and an ayw antigen the relative immunogenicities of the various HBSAg determinants could be ranked as a greater than r greater than d greater than y greater than w. A selected pool of the sera from the rabbits immunized with HBSAg/adr was prepared as an interim reference reagent; when diluted 1:4 in saline and tested by AGD, it contains anti-a and anti-r without demonstrable anti-d or anti-normal human serum activity.