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Biomedical subjects

D Ganem

Publications and source records attributed to D Ganem.

At least 91 records · Page 5Linked to original sources
PubMed1993

Inhibition of duck hepatitis B virus replication by interferon-gamma.

Interferons have been evaluated extensively as candidate antiviral agents in hepadnaviral infection. We examined the effect of recombinant human interferon-gamma on duck hepatitis B virus replication in human hepatoma cells (Huh 7) transiently transfected with cloned duck hepatitis B virus DNA. Cells transfected in the presence of interferon-gamma display a dose-dependent reduction in the levels of encapsidated replicative intermediates in the cytoplasm, as judged by Southern blotting of purified viral core DNA. The effect is observed at interferon-gamma concentrations that do not affect growth rate or viability of Huh 7 cells or their transfection efficiency. Northern analysis of duck hepatitis B virus transcripts in transfected cells demonstrated markedly diminished levels of pre- and subgenomic RNA in interferon-gamma-treated cells. Nuclear run-on analysis was performed to determine whether these transcripts were diminished due to decreased rates of transcription initiation or increased rates of RNA degradation. Levels of transcription initiation were unaffected by interferon-gamma, implying that duck hepatitis B virus transcripts in interferon-gamma-treated cells are degraded more rapidly than in untreated cells.

Animals↗
PubMed1993

Cloning and characterization of the RNA polymerase alpha-subunit operon of Chlamydia trachomatis.

We have cloned the chlamydial operon that encodes the initiation factor IF1, the ribosomal proteins L36, S13, and S11, and the alpha subunit of RNA polymerase. The genes for S11 and alpha are closely linked in Escherichia coli, Bacillus subtilis, and plant chloroplast genomes, and this arrangement is conserved in Chlamydia spp. The S11 ribosomal protein gene potentially encodes a protein of 125 amino acids with 41 to 42% identity over its entire length to its E. coli and B. subtilis homologs; the gene encoding the alpha subunit specifies a protein of 322 amino acids with 25 to 30% identity over its entire length to its E. coli and B. subtilis homologs. In a T7-based expression system in E. coli, the chlamydial alpha gene directed the synthesis of a 36-kDa protein. Mapping of the chlamydial mRNA transcript by RNase protection studies and by a combination of reverse transcription and the polymerase chain reaction demonstrates that IF1, L36, S13, S11, and alpha are transcribed as a polycistronic transcript.

Amino Acid Sequence↗
PubMed1993

An RNA stem-loop structure directs hepatitis B virus genomic RNA encapsidation.

Selective encapsidation of hepatitis B virus (HBV) genomic RNA within cytoplasmic core particles requires recognition of the cis-encapsidation signal, (termed epsilon) located at the 5' end of genomic RNA. By transfecting plasmids expressing chimeric RNAs bearing HBV sequences fused to lacZ, we have mapped the minimal region of epsilon to the 5' 94 nucleotides (nt) of genomic RNA. Enzymatic probing of the RNA secondary structure in this region (by using either in vitro transcripts or RNA extracted from HBV core particles) reveals a stem-loop structure containing a lower stem, a 6-nt bulge, an upper stem with a single unpaired U residue, and a 6-nt loop. The functional role of this structure in encapsidation was explored by examining the effects of mutations in epsilon on encapsidation of RNA in vivo. These studies reveal that (i) in the lower stem, base pairing but not specific primary sequence is required for function; (ii) there is no requirement for base pairing in the lower portion of the upper stem, but base pairing elsewhere in this stem contributes to packaging efficiency; (iii) the presence of the 6-nt bulge, but not its primary sequence, is important for function; and (iv) specific nucleotide sequences in the loop and in regions of the upper stem are critical for RNA encapsidation.

Base Sequence↗
PubMed1993

Differential activation of myc gene family members in hepatic carcinogenesis by closely related hepatitis B viruses.

Woodchucks infected with woodchuck hepatitis virus (WHV) and ground squirrels infected with ground squirrel hepatitis virus (GSHV) both develop hepatocellular carcinoma (HCC), but WHV-associated tumors arise more frequently and much earlier in life. These differences are preserved when the oncogenic potentials of the two viruses are examined in the same host (woodchucks). We examined RNA and genomic DNA from tumors arising from WHV- and GSHV-infected woodchucks to determine whether these viruses use the same oncogenic pathway. N-myc RNA was not expressed in normal liver but was expressed in 10 of 13 WHV-associated HCCs examined. Southern blot analysis showed that 7 of 17 WHV-induced tumors (41%) contained rearrangements at N-myc loci due to viral genomic integration. Six of these seven inserts affected N-myc2, and most of these were at the 5' end of the gene. In contrast, only two of seven GSHV-induced woodchuck HCCs expressed N-myc RNA, and only 1 of the 16 tumors (6%) contained a rearranged N-myc allele. The GSHV-associated HCCs all contained numerous viral insertions, so the low frequency of integration into N-myc loci by GSHV was not due to a general block to integration. Four of sixteen GSHV-induced tumors harbored amplified c-myc alleles, and five of seven GSHV tumors tested contained elevated c-myc RNA levels. By contrast, enhanced c-myc RNA levels were observed in only 2 of 13 WHV-induced HCC. We conclude that N-myc overexpression is a regular feature of WHV- but not GSHV-associated hepatocarcinogenesis in a common host. In contrast, c-myc transcriptional deregulation is rarely encountered in WHV-induced HCC but is frequent in GSHV-induced HCC.

Animals↗
PubMed1992

A developmentally regulated chlamydial gene with apparent homology to eukaryotic histone H1.

We have developed a method for the isolation of genes whose expression is developmentally regulated from the murine strain of Chlamydia trachomatis. Here we describe the identification of two developmental stage-specific genes, one of which is predicted to encode a 26-kDa lysine- and alanine-rich protein that appears to be homologous to several eukaryotic histone H1 proteins. A substantial proportion of this homology relates to its distinctive amino acid composition. No sequence homology was observed between this protein and other bacterial "histone-like" chromosomal proteins, but homology does exist with two other recently described prokaryotic proteins. The protein is expressed late in chlamydial development, during the transition from reticulate bodies to elementary bodies. The basic nature of the protein predicts that it could bind DNA, and Southwestern blotting experiments confirm this finding. These properties are consistent with a role either in the regulation of late gene expression or in the compaction of the chlamydial genome.

Amino Acid Sequence↗
PubMed1992

Regulation of polyadenylation in human immunodeficiency virus (HIV): contributions of promoter proximity and upstream sequences.

Retroviruses synthesize a terminally redundant genomic RNA that contains canonical polyadenylation signals at both ends. Production of this RNA requires that the 5' copy of these signals be ignored, while the 3' copy must be utilized. Two models have been presented for how this occurs in the human immunodeficiency virus, HIV: (i) the core HIV poly(A) signals (AAUAAA and a downstream GU-rich element) might be inefficient and require supplementation by activating sequences found only at the 3' end of the RNA; or (ii) cap site proximity might actively suppress polyadenylation at the 5' site. We have examined both possibilities in HIV-infected cells and in cells transfected with a variety of model constructs. We find that infected cells harbor few or no detectable products of 5' polyadenylation; however, the core HIV processing signals can mediate processing fairly efficiently (65%) when positioned at the 3' end of heterologous transcripts. While this efficiency can be further increased to greater than 95% by inclusion of upstream sequences from the viral U3 region, the absence of these U3 signals is insufficient by itself to account for 5' signal bypass. By contrast, the efficiency of these core elements is greatly suppressed when they are positioned within approximately 450 nucleotides of the cap site. This distance-related suppression can be modestly diminished by insertion of U3 sequences between the cap site and HIV poly(A) signal. We suggest that the primary determinant of 5' poly(A) site bypass is cap site proximity; the absence of U3 sequences at this position contributes secondarily to the bypass by enhancing the sensitivity of the pA signal to the suppressive effects of promoter proximity.

Base Sequence↗
PubMed1992

Upstream sequences and cap proximity in the regulation of polyadenylation in ground squirrel hepatitis virus.

The polyadenylation signal of mammalian hepadnaviruses is unusual in that its hexanucleotide element is the variant UAUAAA rather than AAUAAA. This signal functions inefficiently and must be augmented by multiple activator elements located in the upstream 400 nucleotides (nt) to promote efficient processing. Here we characterize one of these upstream elements, termed PS2, in the ground squirrel hepatitis virus. PS2 is located within the 107 nt 5' to the UAUAAA and raises the efficiency of polyadenylation by this signal from < 10% to 50 to 60%. It can function independently of the more 5' activator elements and conversely is not required for their function. Its action is orientation dependent, and a predicted stem-loop structure within the element is not necessary for its activity. PS2 is the sole upstream element that maps within the terminal redundancy of viral genomic RNA. Thus, it is present, together with the UAUAAA, at both the 5' and 3' ends of this RNA. During genomic RNA synthesis, the poly(A) signals in the 5' repeat are bypassed, while those in the 3' copy are used. The ability of PS2 to function independently of the other, more upstream activators suggests that the absence of the latter elements from the 5' redundancy is insufficient to account for bypass of the 5' poly(A) site, as we had earlier proposed. Rather, the short distance from the cap site to the UAUAAA at the 5' end of genomic RNA actively suppresses its use, as this suppression can be experimentally relieved by increasing this distance to 230 to 400 nt.

Animals↗
PubMed1991

The role of envelope proteins in hepatitis B virus assembly.

Hepatitis B virus (HBV) particles are generated by budding of preformed cytoplasmic nucleocapsids into endoplasmic reticulum (ER) membranes containing the three viral envelope proteins (L, M, and S). We have examined the contributions of the envelope proteins to virion assembly by using cultured hepatoma cells transfected with mutant HBV genomes bearing lesions in the envelope coding regions. We show here that HBV nucleocapsids are not released from cells without expression of envelope proteins, implying an active role for these proteins in viral morphogenesis. S and L but not M proteins are necessary for virion production. L protein over-expression inhibits virion release, just as it inhibits the release of subviral hepatitis B surface antigen (HBsAg) particles. Mutant L proteins that are no longer capable of retaining HBsAg particles in the ER still allow virion formation, indicating that this ER retention reaction is not required for viral budding. Myristoylation of L protein is also dispensable for virion formation. A chimeric protein bearing foreign epitopes fused to the S protein can be incorporated into virions when coexpressed with the wild-type envelope proteins. Models for the dependence of virion formation on both L and S proteins are discussed.

Animals↗
PubMed1991

Sequence-independent RNA cleavages generate the primers for plus strand DNA synthesis in hepatitis B viruses: implications for other reverse transcribing elements.

Reverse transcription of RNA into duplex DNA requires accurate initiation of both minus and plus strand DNA synthesis; this in turn requires the generation of specific primer molecules. We have examined plus strand primer generation in the hepatitis B viruses, small DNA viruses that replicate via reverse transcription. The plus strand primer in these viruses is a short capped RNA derived from the 5' end of the RNA template by cleavage at a specific set of sites. To elucidate the cleavage mechanism we constructed a series of viral mutants bearing alterations in and around the cleavage sites. Our results reveal that the cleavage reaction is sequence-independent and indicate that the cleavage sites are positioned by measurement of the distance from the 5' end of the RNA. Comparison of these findings with what is known about RNase H-mediated primer generation in retroviruses and other retroid elements suggests that, despite many divergent features, some common molecular features are preserved.

Base Sequence↗
PubMed1991

Persistent hepatitis B virus following interferon alfa therapy and liver transplantation.

A 44-year-old man with chronic hepatitis B virus infection and cirrhosis was treated with recombinant human interferon alfa for 67 days immediately before orthotopic liver transplantation and immunoprophylaxis with hyperimmune globulin to hepatitis B virus in the peritransplant period. Dot blots for hepatitis B virus DNA demonstrated marked reduction in viremia after 41 days of interferon alfa treatment. Southern analysis for hepatitis B virus in liver showed a pronounced decrement in actively replicating forms in the explant, although hepatic infection was still detectable. After liver transplantation, tests for serum hepatitis B virus DNA and hepatitis B surface antigen remained negative. The patient died 32 days after transplantation of causes unrelated to hepatitis B virus. DNA isolated from liver and other visceral organs at autopsy showed infection of the engrafted liver and the persistence of monomeric relaxed circular forms of hepatitis B virus DNA in pancreas, kidney, and spleen. Thus, graft reinfection occurred despite aggressive antiviral therapy and immunoprophylaxis combined with liver transplantation. Existing viral serological markers appear insufficiently sensitive to assess residual infectivity.

Adult↗
PubMed1991

Myristylation of a duck hepatitis B virus envelope protein is essential for infectivity but not for virus assembly.

In addition to the major surface (S) protein, the envelope of the duck hepatitis B virus (DHBV) contains a related presurface (preS) protein whose N-terminus bears a covalently attached myristate group. We have explored the functional significance of this modification by examining the replicative potential of a mutant viral genome whose myristylation signal has been inactivated. Following transfection into permissive hepatoma cells, the mutant expresses an unmyristylated preS protein of normal size, immunoreactivity and stability. Cytoplasmic cores containing viral DNA are synthesized, and Dane particles are assembled and exported into the medium. However, the mutant is noninfectious when inoculated into susceptible ducklings. We conclude that myristylation of preS proteins is essential for hepadnaviral infectivity but not for viral assembly; myristylation is most likely required for an early step of the life cycle involving the entry or uncoating of virus particles.

Amino Acid Sequence↗
PubMed1991

Mutations affecting hepadnavirus plus-strand DNA synthesis dissociate primer cleavage from translocation and reveal the origin of linear viral DNA.

Hepadnaviruses replicate their circular DNA genomes via reverse transcription of an RNA intermediate. The initial product of reverse transcription, minus-strand DNA, contains two copies of a short direct repeat (DR) sequence, termed DR1 and DR2. Plus-strand DNA synthesis initiates at DR2 on minus-strand DNA, using as a primer a short, DR1-containing oligoribonucleotide derived by cleavage and translocation from the 5' end of pregenomic RNA. To clarify the sequence requirements for plus-strand primer cleavage and translocation, we have constructed mutants of the duck hepatitis B virus bearing base changes in or around the DR1 sequence in the primer. A point mutation at the terminal nucleotide of DR1 has a striking phenotype: normal levels of duplex viral DNA are produced, but nearly all of the DNA is linear rather than circular. Mapping of the 5' end of plus-strand DNA reveals that primer cleavage occurs with normal efficiency and accuracy, but the primer is not translocated to DR2; rather, it is extended in situ to generate duplex linear DNA. Other mutations just 3' to DR1 similarly affect primer translocation, although with differing efficiencies. Linear DNA found in wild-type virus preparations has the same fine structure as the mutant linears described above. These results indicate that (i) plus-strand primer cleavage and translocation are distinct steps that can be dissociated by mutation, (ii) lesions in sequences not included in the primer can severely inhibit primer translocation, and (iii) elongation of such untranslocated primers is responsible for the variable quantities of linear DNA that are found in all hepadnaviral stocks.

Animals↗
PubMed1991

Woodchuck hepatitis virus is a more efficient oncogenic agent than ground squirrel hepatitis virus in a common host.

Chronic infection with hepatitis B viruses (hepadnaviruses) is a major cause of hepatocellular carcinoma (HCC), but the incubation time varies from 1 to 2 years to several decades in different host species infected with indigenous viruses. To discern the influence of viral and host factors on the kinetics of induction of HCC, we exploited the recent observation that ground squirrel hepatitis virus (GSHV) is infectious in woodchucks (C. Seeger, P. L. Marion, D. Ganem, and H. E. Varmus, J. Virol. 61:3241-3247, 1987) to compare the pathogenic potential of GSHV and woodchuck hepatitis virus (WHV) in chronically infected woodchucks. Chronic GSHV infection in woodchucks produces mild to moderate portal hepatitis, similar to that observed in woodchucks chronically infected with WHV. However, HCC developed in GSHV carriers about 18 months later than in WHV carriers. Thus, although both viruses are oncogenic in woodchucks, GSHV and WHV differ in oncogenic determinants that can affect the kinetics of appearance of HCC in chronically infected animals.

Animals↗
PubMed1991

cis-acting sequences required for encapsidation of duck hepatitis B virus pregenomic RNA.

Hepadnavirus reverse transcription requires that pregenomic RNA first be selectively packaged into a cytoplasmic core particle. This process presumably requires the presence of specific recognition sequences on the pregenomic RNA. To define the cis-acting sequences required for pregenome encapsidation in the duck hepatitis B virus (DHBV), we assayed the packaging efficiency of a series of pregenomic RNA deletion mutants and hybrid DHBV/lacZ fusion transcripts. The 5' boundary of the packaging signal lies within the precore region, starting approximately 35 nucleotides from the cap site of pregenomic RNA; thus, the DR1 sequence required for proper viral DNA synthesis is not included in this signal. To define the 3' boundary of the encapsidation signal, fusion transcripts bearing foreign (lacZ) sequences fused to DHBV at different sites 3' to the pregenomic RNA start site were examined. A surprisingly large region of the DHBV genome proved to be required for packaging of such chimeras, which are efficiently encapsidated only when they contain the first 1,200 to 1,400 nucleotides of DHBV pregenomic RNA. However, mutant genomes bearing insertions within this region are packaged efficiently, making it likely that the actual recognition elements for encapsidation are smaller discontinuous sequences located within this region.

Animals↗
PubMed1991

Mutational analysis of hepatitis B surface antigen particle assembly and secretion.

Cells infected with hepatitis B virus produce both virions and 20-nm subviral (surface antigen or HBsAg) particles; the latter are composed of viral envelope proteins and host-derived lipid. Although hepatitis B virus encodes three envelope proteins (L, M, and S), all of the information required to produce an HBsAg particle resides within the S protein. This polypeptide spans the bilayer at least twice and contains three hydrophobic regions, two of which are known to harbor topogenic signal sequences that direct this transmembrane orientation. We have examined the effects of mutations in these and other regions of the S protein on particle assembly and export. Lesions in the N terminal signal sequence (signal I) can still insert into the endoplasmic reticulum bilayer but do not participate in any of the subsequent steps in assembly. Deletion of the major internal signal (signal II) completely destabilizes the chain. Deletion of the C-terminal hydrophobic domain results in a stable, glycosylated, but nonsecreted chain. However, when coexpressed with wild-type S protein this mutant polypeptide can be incorporated into particles and secreted, indicating that the chain is still competent for some of the distal steps in particle assembly. The correct transmembrane disposition of the N terminus of the molecule is important for particle formation: addition of a heterologous (globin) domain to this region impairs secretion, but the defect can be corrected by provision of an N-terminal signal sequence that restores the proper topology of this region. The resulting chimeric chain is assembled into subviral particles that are secreted with normal efficiency.

Animals↗
PubMed1990

Polymerase gene products of hepatitis B viruses are required for genomic RNA packaging as wel as for reverse transcription.

All reactions involving reverse transcription of RNA are segregated from the cytosol within a subviral particle or capsid composed of the major capsid protein, the polymerase and the RNA template. A key step in the formation of these particles is the selective encapsidation of the RNA template. Although an important general feature of the reverse transcription pathway, encapsidation has been carefully studied only for retroviruses. We have now examined the encapsidation reaction in a family of enveloped DNA viruses that replicate by reverse transcription--the hepatitis B viruses (hepadnaviruses). Our results indicate that the hepadnaviral polymerase (P) gene product is required for RNA packaging, and that the encapsidation function of the enzyme can be separated from its DNA polymerase activity. To our knowledge, this is the first description of a role for polymerase gene products in this step of the reverse transcription pathway.

Amino Acid Sequence↗