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B G Barrell

Publications and source records attributed to B G Barrell.

At least 55 records · Page 3Linked to original sources
PubMed1990

Human herpesvirus 6 is closely related to human cytomegalovirus.

A sequence of 21,858 base pairs from the genome of human herpesvirus 6 (HHV-6) strain U1102 is presented. The sequence has a mean composition of 41% G + C, and the observed frequency of CpG dinucleotides is close to that predicted from this mononucleotide composition. The sequence contains 17 complete open reading frames (ORFs) and part of another at the 5' end of the sequence. The predicted protein products of two of these ORFs have no recognizable homologs in the genomes of other sequenced human herpesviruses (i.e., Epstein-Barr virus [EBV], human cytomegalovirus [HCMV], herpes simplex virus [HSV], and varicella-zoster virus [VZV]). However, the products of nine other ORFs are clearly homologous to a set of genes that is conserved in all other sequenced herpesviruses, including homologs of the alkaline exonuclease, the phosphotransferase, the spliced ORF, and the major capsid protein genes. Measurements of similarity between these homologous sequences showed that HHV-6 is clearly most closely related to HCMV. The degree of relatedness between HHV-6 and HCMV was commensurate with that observed in comparisons between HSV and VZV or EBV and herpesvirus saimiri and significantly greater than its relatedness to EBV, HSV, or VZV. In addition, the gene for the major capsid protein and its 5' neighbor are reoriented with respect to the spliced ORFs in the genomes of both HHV-6 and HCMV relative to the organization observed in EBV, HSV, and VZV. Three ORFs in HHV-6 have recognizable homologs only in the genome of HCMV. Despite differences in gross composition and size, we conclude that the genomes of HHV-6 and HCMV are closely related.

Amino Acid Sequence↗
PubMed1990

Identification, cloning, and expression of the major capsid protein gene of human herpesvirus 6.

DNA sequence analysis of part of the human herpesvirus 6 (HHV-6) genome led to the identification of an open reading frame with amino acid sequence homology to the major capsid proteins (MCP) of other HHVs. DIAGON analysis showed that the closest homology was with human cytomegalovirus. Plasmids were constructed which were shown to express the HHV-6 MCP as either the entire open reading frame or as portions of it, and the recombinant-produced proteins were used to raise antisera. The antisera were shown by immunofluorescence to react with HHV-6-infected lymphoblastoid cells and in Western blots with a 135-kilodalton protein specific to HHV-6-infected cells. The recombinant protein expressed from the entire HHV-6 MCP gene was detected only weakly in Western blot assays with normal HHV-6-positive human sera as a probe.

Amino Acid Sequence↗
PubMed1990

Semiautomated preparation of DNA templates for large-scale sequencing projects.

The rate limiting step in a large-scale sequencing project is the generation of single-stranded DNA templates. We describe a fast, semiautomated procedure, using 96-well microtitre plates, in which 192 templates can be readily prepared in 1 day. The technique can be carried out manually or can be semiautomated using a robot pipetting device. We also provide evidence for the reliability and applicability of this method to a large-scale sequencing project.

Bacteriophages↗
PubMed1989

Deviations from expected frequencies of CpG dinucleotides in herpesvirus DNAs may be diagnostic of differences in the states of their latent genomes.

The DNA sequences of genomes from G + C-rich and A + T-rich lymphotropic herpesviruses [i.e. gammaherpesviruses; Epstein-Barr virus and herpesvirus saimiri (HVS)] are deficient in CpG dinucleotides and contain an excess of TpG and CpA dinucleotides relative to frequencies predicted from their mononucleotide compositions. In contrast, for sequences from genomes of G + C-rich and A + T-rich neurotropic herpesviruses (i.e. alphaherpesviruses; herpes simplex virus and varicellazoster virus) and human cytomegalovirus (HCMV; a betaherpesvirus) the mean observed frequencies of these dinucleotides are close to those expected from their mononucleotide compositions. Comparisons between DNA sequences that encode proteins conserved in all these viruses also show that sequences of these lymphotropic viruses are CpG-deficient whereas the homologous genes from the neurotropic viruses and the HCMV are not. Analyses of local variations in dinucleotide frequencies reveal some occurrences of clustered CpG dinucleotides in generally deficient genomes (e.g. upstream of the thymidylate synthase gene of HVS) and locally CpG-deficient regions within some generally non-deficient genomes (e.g. the major immediate early genes of human, simian and murine CMVs). A relative deficiency in CpG and an excess of TpG and CpA dinucleotides is a diagnostic feature of higher eukaryotic DNA sequences that have been subjected to methylation of cytosine residues in CpG doublets with the resulting increase in mutations to give TpG (and thereby its complement, CpA). The available evidence implicates the latent genome as the site of methylation of these herpesviruses. We conclude that in the neurotropic herpesviruses the normal latent precursors to infectious progeny are not methylated whereas there is local methylation of the immediate early locus in the latent genomes of CMVs, and the latent genomes of these lymphotropic herpesviruses are extensively methylated.

Base Sequence↗
PubMed1989

Alpha-, beta- and gammaherpesviruses encode a putative phosphotransferase.

We have sequenced a gene in human cytomegalovirus and a homologous gene in human herpesvirus 6 which could specify a product related to protein kinases. This gene appears to be generic in the herpesvirus family as homologues were found in three other human herpesviruses. The five sequences were aligned and found to be quite divergent. Some of the differences occur at amino acid positions which are functionally important and highly conserved in known protein kinases. Hence these genes may represent a significant departure from known protein kinases in terms of structure and/or function.

Amino Acid Sequence↗
PubMed1988

Human cytomegalovirus encodes a glycoprotein homologous to MHC class-I antigens.

Primary infection with human cytomegalovirus (HCMV) is persistent and widespread, with symptoms that are mostly subclinical but can cause serious illness or death, particularly in immunosuppressed patients. Recently, proteins from HCMV were shown to bind beta 2-microglobulin (beta 2-m) a protein that is normally found associated with the class-I major histocompatibility complex (MHC) antigens, which are essential for self-non-self recognition in the immune response. These findings led to the proposal that the virus may use beta 2-m binding as an infection mechanism. Here we present evidence from DNA sequence analysis that HCMV encodes a molecule similar to the MHC class-I antigens of higher eucaryotes, and propose that this protein is responsible for the observed beta 2-m binding. The deduced amino-acid sequence of the HCMV class-I-like protein reveals conservation of typical features of class-I structure, but we predict that the gene is not spliced, in contrast to the cellular genes.

Amino Acid Sequence↗
PubMed1988

Sequence analysis of Raji Epstein-Barr virus DNA.

The DNA sequence of the EcoRI Dhet and part of the BamHI E fragments of Raji EBV has been determined. Precise locations of two deletions in Raji DNA have been identified and their consequences for gene structure evaluated. The deletion in Raji of reading frames BALF1, BARF1, and BZLF2 and truncation of BALF2 and BERF5 probably account for the replication defect in this strain. The degree of sequence variation between B95-8 and Raji has been examined and shows considerable variation between genes. The latent membrane protein gene is exceptionally polymorphic and the initiator methionine for the late productive cycle protein overlapping the latent membrane protein is absent in Raji.

Amino Acid Sequence↗
PubMed1988

An immediate early gene of human cytomegalovirus encodes a potential membrane glycoprotein.

The sequence of a region of the HCMV genome transcribed during the immediate early (IE) transcriptional phase has been determined. Transcription analysis of this region at the junction between fragments HindIII Z and J has identified three moderately abundant mRNAs of 3.4, 1.7, and 1.65 kb. The 3.4-kb RNA is expressed only under IE conditions of infection. It is composed of four exons and its predicted translation product has features characteristic of a membrane-bound glycoprotein. The 1.7-kb RNA is transcribed at both IE and late times postinfection. It is expressed from the same promoter as the 3.4-kb RNA and does not appear to be spliced. The 1.65-kb RNA is present at the IE phase, but is more abundantly transcribed at late times. It is composed of two exons and is 3' coterminal to the 3.4-kb RNA. Within the predicted translation product of the 1.65-kb RNA there are three regions which show homology to a family of related open reading frames found within the short unique region of HCMV.

Amino Acid Sequence↗
PubMed1988

Identification and expression of a human cytomegalovirus glycoprotein with homology to the Epstein-Barr virus BXLF2 product, varicella-zoster virus gpIII, and herpes simplex virus type 1 glycoprotein H.

An open reading frame with the characteristics of a glycoprotein-coding sequence was identified by nucleotide sequencing of human cytomegalovirus (HCMV) genomic DNA. The predicted amino acid sequence was homologous with glycoprotein H of herpes simplex virus type 1 and the homologous protein of Epstein-Barr virus (BXLF2 gene product) and varicella-zoster virus (gpIII). Recombinant vaccinia viruses that expressed this gene were constructed. A glycoprotein of approximately 86 kilodaltons was immunoprecipitated from cells infected with the recombinant viruses and from HCMV-infected cells with a monoclonal antibody that efficiently neutralized HCMV infectivity. In HCMV-infected MRC5 cells, this glycoprotein was present on nuclear and cytoplasmic membranes, but in recombinant vaccinia virus-infected cells it accumulated predominantly on the nuclear membrane.

Amino Acid Sequence↗
PubMed1988

Identification and procaryotic expression of the gene coding for the highly immunogenic 28-kilodalton structural phosphoprotein (pp28) of human cytomegalovirus.

Human cytomegalovirus contains a structural polypeptide that is 28 kilodaltons in apparent molecular size and is reactive in Western blot (immunoblot) analysis with the majority of human sera. The gene coding for this polypeptide was mapped on the genome of human cytomegalovirus strain AD169. A monoclonal antibody specific for the 28-kilodalton polypeptide was used to screen a cDNA library constructed from poly(A)+ RNA of human cytomegalovirus-infected cells in the procaryotic expression vector lambda gt11. Hybridization of cDNA with cosmid and plasmid clones mapped the gene to the HindIII R fragment. The gene was transcribed into a late 1.3-kilobase RNA. The nucleotide sequence of the coding region was determined. Parts of the 28-kilodalton polypeptide were expressed in Escherichia coli as hybrid proteins fused to beta-galactosidase. In Western blots these proteins were recognized by human sera. Antibodies raised against the hybrid proteins reacted specifically with the viral antigen in immunoprecipitations and Western blots. In vitro phosphorylation of HCMV virions and immunoprecipitation showed that the 28-kilodalton polypeptide was phosphorylated.

Amino Acid Sequence↗
PubMed1987

Large-scale rearrangement of homologous regions in the genomes of HCMV and EBV.

The 20,349-bp sequence of the human cytomegalovirus (HCMV) HindIII F fragment has revealed eight open reading frames with homology to herpes simplex virus (HSV) and/or Epstein-Barr virus (EBV). With respect to EBV, these homologous genes can be divided into two blocks: one block contains three genes, including the DNA polymerase and glycoprotein B, and the other block contains five genes of unknown function. Although the relative organisation of genes within each block is identical in HCMV and EBV, the relative position of each block within the two genomes differs: in HCMV the two blocks are present directly adjacent to each other, whereas in EBV they are found 92 kb apart. This suggests that a genetic rearrangement has occurred in this region. Transcription analysis of the glycoprotein B gene is presented and the evolutionary relationship between the genomes of HCMV, EBV, and HSV is discussed.

Amino Acid Sequence↗
PubMed1987

Sequence and transcription analysis of the human cytomegalovirus DNA polymerase gene.

DNA sequence analysis has revealed that the gene coding for the human cytomegalovirus (HCMV) DNA polymerase is present within the long unique region of the virus genome. Identification is based on extensive amino acid homology between the predicted HCMV open reading frame HFLF2 and the DNA polymerase of herpes simplex virus type 1. We present here a 5280-base-pair DNA sequence containing the HCMV pol gene, along with the analysis of transcripts encoded within this region. Since HCMV pol also shows homology to the predicted Epstein-Barr virus pol, we were able to analyze the extent of homology between the DNA polymerases of three distantly related herpesviruses, HCMV, Epstein-Barr virus, and herpes simplex virus. The comparison shows that these DNA polymerases exhibit considerable amino acid homology and highlights a number of highly conserved regions; two such regions show homology to sequences within the adenovirus type 2 DNA polymerase. The HCMV pol gene is flanked by open reading frames with homology to those of other herpesviruses; upstream, there is a reading frame homologous to the glycoprotein B gene of herpes simplex virus type 1 and Epstein-Barr virus, and downstream there is a reading frame homologous to BFLF2 of Epstein-Barr virus.

Amino Acid Sequence↗
PubMed1987

Map position and nucleotide sequence of the gene for the large structural phosphoprotein of human cytomegalovirus.

Human cytomegalovirus particles contain a phosphoprotein of 150,000 (pp150) apparent molecular weight in their matrix; the protein appears particularly reactive in Western blot analyses with human antisera. The gene for pp150 was mapped by screening a bacteriophage lambda gt11 cDNA expression library with monospecific rabbit antisera. Subsequent hybridization of cDNA with cosmid and plasmid clones containing the human cytomegalovirus strain AD169 genome mapped the gene to HindIII fragments J and N. The gene is transcribed into a late 6.2-kilobase RNA. The nucleotide sequence of this region was determined, and a transcription initiation site and two polyadenylation sites of an abundant transcript were located by primer extension and nuclease protection experiments. The reading frame for pp150, deduced from computer analyses, gives rise to a polypeptide of 1,048 amino acids in length; protein secondary structure analysis revealed multiple beta-pleated sheets in hydrophilic clusters, providing a possible explanation for the immunogenic properties of the polypeptide.

Amino Acid Sequence↗
PubMed1986

Sequence of the short unique region, short repeats, and part of the long repeats of human cytomegalovirus.

We have determined the DNA sequence (46 kilobases) of the short unique region, the short repeat, and part of the long repeat of human cytomegalovirus strain AD169. Analysis of the sequence has revealed at least 38 possible regions that may code for protein. Many of these open reading frames show homology to each other, and five groups of homologous reading frames are identified. Half of the predicted translation products appear to be membrane proteins, and fall into two distinct classes; those that have potential signal and anchor sequences, and those that have seven potential membrane-spanning regions and appear to be integral membrane proteins. A number of the former class contain sites for N-linked glycosylation and may therefore be glycoproteins. None of the 38 open reading frames shows homology to other known herpesvirus proteins.

Amino Acid Sequence↗
PubMed1986

Coding content and expression of the EBV B95-8 genome in the region from base 62,248 to base 82,920.

The DNA sequence of a 20,672-base region of the EBV B95-8 genome from the BamHI site separating fragments BamHI-F and BamHI-Q to the EcoRI site separating fragments EcoRI-G2 and EcoR1-F has been determined. S1 mapping and northern blotting with probes from M13 recombinants have been used to search for RNAs from this region. Five mRNAs have been identified and correlated with five open reading frames in the DNA sequence. Two of these open reading frames encode ribonucleotide reductase subunits. A further two open reading frames are present including one for a predicted protein of 340 kDa for which no transcript has yet been detected.

Base Sequence↗
PubMed1985

The short unique region of the B95-8 Epstein-Barr virus genome.

The 12-kbp short unique region of the B95-8 Epstein-Barr virus (EBV) genome has been sequenced and analysed for latent and lytic cycle transcripts. Two latent and three late mRNAs have been detected, the largest of the late transcripts potentially encoding a 143-kDa protein. The region containing oriP, the putative origin of replication of the genome as a plasmid in latently infected B lymphocytes, is shown to contain 21 direct repeats of a 30-bp A+T-rich sequence and a related large inverted repeat.

Base Sequence↗
PubMed1985

The BamHI F region of the B95-8 Epstein-Barr virus genome.

The BamHI F region of the B95-8 Epstein-Barr virus (EBV) genome has been sequenced and analysed for transcription signals and open reading frames. S1 mapping and northern blotting with probes from M13 recombinants have been used to search for mRNAs. Four rightward-reading frames encoding basic proteins appear to be expressed by 3'-coterminal early mRNAs. Two leftward-reading frames appear to be expressed by 3'-coterminal early mRNAs.

Base Sequence↗