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P Beard

Publications and source records attributed to P Beard.

At least 37 records · Page 2Linked to original sources
PubMed1990

Nonstructural protein of parvoviruses B19 and minute virus of mice controls transcription.

The genome of the human parvovirus B19 contains a transcriptional promoter (BP06) at map position 6, upstream from the nonstructural protein genes. By cotransfecting HeLa cells with this promoter cloned before the chloramphenicol acetyltransferase (CAT) gene together with a plasmid containing almost the whole B19 genome, we showed that BP06 is transactivated by a B19 gene product. The transactivating viral protein was identified as the nonstructural protein NS-1. NS-1 synthesized in a wheat germ extract specifically stimulates transcription from BP06 in vitro. NS-1 of the minute virus of mice (MVM) activates the analogous MVM promoter, MP04. NS-1, therefore, has a positive feedback effect on the activity of its own promoter. Moreover, NS-1 of MVM activates the human BP06. We have identified, in the genome of B19, a second transcriptional promoter activity at map position 44, before the capsid protein genes. This promoter, BP44, was identified by cloning fragments of B19 DNA upstream of the CAT gene, transfecting the DNA into HeLa cells, and measuring CAT expression. The strength of the BP44 promoter is similar to that of the capsid gene promoter, MP39, of MVM. In (nonpermissive) HeLa cells, the BP44 promoter is not activated by NS-1. Thus, the BP06 promoter apparently does not determine the tissue specificity of B19 virus but BP44 could do so.

Base Sequence↗
PubMed1990

A member of the activator protein 1 family found in keratinocytes but not in fibroblasts required for transcription from a human papillomavirus type 18 promoter.

Papillomaviruses are tissue specific and replicate in differentiating keratinocytes. We are interested in the question of tissue specificity at the level of transcription. We used extracts from human keratinocytes and human fibroblasts at low passage number and from HeLa cells to look for factors binding to the E6 promoter of human papillomavirus type 18 (HPV-18) DNA by footprint and gel mobility shift experiments. We found a factor present in HeLa and keratinocyte extracts but not in fibroblast extracts which bound about 160 base pairs upstream from the start of E6. The binding site included the sequence TGACTAAG, which resembles the consensus binding site for the AP-1 family of proteins. Synthetic oligonucleotides containing this binding site specifically competed with factor binding to HPV-18 DNA, as did the AP-1 sequence of simian virus 40. They also inhibited transcription from the E6 promoter in vitro in extracts from HeLa cells. Thus, the presence of this keratinocyte-specific factor seems to be important for HPV-18 transcription.

Base Sequence↗
PubMed1989

Cytosine methylation in CTF and Sp1 recognition sites of an HSV tk promoter: effects on transcription in vivo and on factor binding in vitro.

We methylated specific cytosine residues within or immediately around the CTF and Sp1 binding sites of the Herpes simplex virus thymidine kinase promoter. The efficiency of transcription in vivo was reduced at least 50-fold compared with transcription from the unmethylated promoter. However, methylation within the CTF recognition site had no effect on the affinity of CTF for this site in vitro. Methylation of the Sp1 site resulted in only a small decrease in the affinity of this factor for its recognition site. In vivo studies showed that the same gene inserted in different vector DNAs was regulated differently by methylation in the promoter. These results show that cytosine methylation can inhibit transcription by a mechanism other than directly blocking the binding of transcription factors.

Animals↗
PubMed1989

ICP4-binding sites in the promoter and coding regions of the herpes simplex virus gD gene contribute to activation of in vitro transcription by ICP4.

The herpes simplex virus immediate-early gene product ICP4 activates the transcription of viral early and late genes. We characterized the DNA sequence elements of the early glycoprotein D (gD) gene that play a role in the response to ICP4 in vitro. Using gel mobility shift assays and DNase I footprinting, we identified three ICP4-binding sites, two 5' to the mRNA start site and a third within the coding region. Site II, which gave a footprint between nucleotides -75 and -111 relative to the RNA start site, was previously identified by Faber and Wilcox and contained the reported consensus ICP4-binding site. Site III, which was located between nucleotides +122 and +163, was very similar to the site II sequence, including a core consensus binding sequence, TCGTC. The site I sequence (nucleotides -308 to -282), however, did not share significant homology with either site II or site III. In vitro transcription experiments from mutant constructs of the gD promoter indicated that all three ICP4-binding sites contribute to the stimulation of transcription by ICP4. DNase I footprinting of the gD promoter with uninfected nuclear extracts of HeLa cells showed protection of two very G-rich sequences between nucleotides -33 and -75. We propose that optimal transcription of the gD gene depends on the interaction of ICP4 with multiple binding sites across the gene and cellular factors that recognize specific sequence elements in the promoter.

Animals↗
PubMed1988

Minute virus of mice non-structural protein NS-1 is necessary and sufficient for trans-activation of the viral P39 promoter.

The genome of the autonomous parvovirus minute virus of mice (MVM) is organized in two overlapping transcription units: the genes coding for the two non-structural proteins (NS-1 ad NS-2) are transcribed from a promoter (P04) located at map unit 4, whereas the promoter controlling the capsid protein genes (P39) lies at map unit 39. We studied the effect of viral proteins on the activity of the P39 promoter in vivo. By site-directed mutagenesis we constructed clones encoding only one of the two NS proteins. The activity of the P39 promoter was measured in HeLa or EL-4 cells transfected with these clones, either by an RNase protection assay or by following the expression of a reporter gene, CAT (which codes for chloramphenicol acetyltransferase), placed under the control of this promoter. We found that the P39 promoter of strain MVMi is activated in trans by a viral gene product, and evidence to suggest that NS-1 is the only viral gene product responsible for this trans-activation. We also determined that the mechanism of trans-activation is very rapid, since all species of viral mRNAs appear together in non-synchronized infected EL-4 cells within a 2 h interval.

Amino Acid Sequence↗
PubMed1988

A transcription factor from simian virus 40 chromosomes which activates the viral late promoter in vitro.

We have characterized a transcription factor, obtained from simian virus 40 (SV40) chromosomes, which activates transcription from the SV40 late promoter in vitro. The late promoter-activating factor was distinct from SV40 T antigen as judged by its behavior on chromatography on hydroxylapatite; it was not recognized by anti-T antibodies, while T antigen itself was recognized. T antigen from SV40 chromosomes, on the other hand, abolished transcription in vitro from the early promoter. In DNase I footprinting experiments, a partially purified late promoter-activating factor preparation protected a region of DNA centered on SV40 nucleotide 270, which is between the repeated 72-base-pair enhancer and the major late RNA start site. Proteins from HeLa cells did not give the same footprint at this position. Gel mobility shift assays showed that proteins from SV40-infected CV-1 cells form a complex with DNA containing this binding site. The complex has a different rate of gel migration and a higher stability than complexes formed with proteins from uninfected cells.

Antigens, Viral, Tumor↗
PubMed1988

Characterization of the cell type-specific determinant in the genome of minute virus of mice.

Two strains of minute virus of mice (MVM) show different host cell specificities. The prototype strain MVM(p) grows in fibroblasts, whereas the immunosuppressive variant MVM(i) grows in T lymphocytes. In this study, we have mapped on the viral genome a cell type-specific determinant: it is located between 69 and 85 map units in a region coding for the viral capsid proteins. The DNA of MVM(p) does not replicate in lymphocytes. MVM(i) cannot help MVM(p) grow in lymphocytes; thus the determinant acts in a cis fashion. We did not detect viral mRNA during a restrictive infection of lymphocytes with MVM(p). However, when the same cells were transfected with cloned DNA, both MVM(p) and MVM(i) DNAs were transcribed with the same efficiency from both promoters and the RNA was processed normally. Therefore, the specificity determinant is not a cell type-specific enhancer.

Cell Line↗
PubMed1987

Preferential repair of N-acetoxy-acetylaminofluorene lesions in the nuclease-hypersensitive region of simian virus 40.

We exposed simian virus 40-infected CV-1 monkey cells to the carcinogen N-acetoxy-acetylaminofluorene and monitored the removal of lesions from cellular DNA and from various regions of viral DNA. Exposure to 5.5 microM 3H-labeled carcinogen produced 20-80 adducts per 10(6) bases in cellular DNA in different experiments. The initial adduct concentration in viral DNA was always approximately half that in cellular DNA. At various times after treatment, cellular and viral DNA, and restriction fragments of viral DNA, were purified and examined for adduct density. Independent of the initial adduct concentration three rates of repair were observed. Cellular DNA was repaired at the lowest rate. Viral DNA was repaired about 50% more rapidly than was cellular DNA isolated from the same carcinogen-treated monolayers. Within the viral DNA a 366-base pair region containing the major nuclease-hypersensitive site was repaired at twice the rate of the rest of the viral genome. This region contains regulatory sequences that govern the initiation of DNA replication and viral gene expression. As reported previously this region was initially modified 1.71 +/- 0.20-fold higher than expected from its guanine content. Selective repair diminished the extent of hypermodification of this region by 6.0 +/- 2.1% per hour, partly compensating for the higher initial level of adducts.

2-Acetylaminofluorene↗
PubMed1987

A transcriptional promoter of the human parvovirus B19 active in vitro and in vivo.

The human parvovirus B19 causes aplastic crises in sickle cell anemia patients and the disease erythema infectiosum. So far, it has not been possible to grow B19 virus in cultured cells. Here we report the use of in vitro transcription in HeLa cell extracts and transient expression of cloned DNA transfected into HeLa cells to detect and map a strong transcriptional promoter on the B19 genome. The promoter is located near the left end of the B19 genome, at position 6 map units in the clone pYT103 (approximately 280 bp upstream of the first HindIII site), and directs transcription to the right. These results suggest that the strictly limited host range of B19 does not operate at the level of transcription from the promoter at the left end of the genome.

DNA, Viral↗
PubMed1986

Herpes simplex virus immediate early infected-cell polypeptide 4 binds to DNA and promotes transcription.

In herpes simplex virus (HSV)-infected cells, there is a sequential expression of viral genes. In vivo experiments have implicated the Mr 175,000 immediate early protein ICP4 (infected-cell polypeptide 4) in the regulation of viral RNA synthesis, but the mechanism whereby ICP4 regulates transcription of viral genes is at present unknown. In this report we describe experiments with an in vitro transcription system and a purified preparation of ICP4 (estimated 5% of total protein). Using DNA from the HSV glycoprotein D gene (gD) as the template, we have observed that specific binding occurs between ICP4 and DNA sequences adjacent to the gD gene promoter and ICP4 stimulates initiation of transcription from the gD gene. The degree of stimulation depends on the amount of ICP4 present in the incubation. The kinetics of RNA synthesis demonstrate that the protein acts at the initiation step of transcription. These results identify ICP4 as a viral transcription factor whose presence on DNA facilitates the formation of transcription complexes.

Animals↗
PubMed1986

Nucleoprotein complexes of minute virus of mice have a distinct structure different from that of chromatin.

We studied the structure of viral nucleoprotein complexes extracted from the nuclei of mouse cells infected with the immunosuppressive strain of the minute virus of mice (MVMi). Two types of complex were detected, with sedimentation coefficients of about 110 and 40S. The complexes sedimenting at 110S contained single-stranded MVMi DNA as well as a second form of viral DNA which apparently had a heat-sensitive secondary structure. The 110S peak also contained proteins which coelectrophoresed with the MVMi capsid proteins. Complexes sedimenting at 40S contained the double-stranded replicative form of MVMi DNA. These complexes sedimented faster than did the pure replicative form DNA (15S), but more slowly than cellular chromatin fragments containing DNA of the same length. They incorporated labeled deoxynucleoside triphosphate in vitro into the replicative form DNA. We investigated the structure of MVMi nucleoprotein complexes in the following ways. Nuclei of MVMi-infected cells were digested with staphylococcal nuclease, and the resulting DNA fragments were electrophoresed, transferred to nitrocellulose, and hybridized first with labeled MVMi DNA and then with cellular DNA. A nucleosomal repeat pattern was seen with the cellular DNA probe but not with the MVMi DNA probe. The DNA in MVMi nucleoprotein complexes was cross-linked with psoralen, purified, denatured, and examined with an electron microscope. Bubbles, indicating the presence of proteins, were seen in the MVMi DNA. The length of the DNA in the bubbles was 90 +/- 29 nucleotides. On the other hand, nucleosomes protected 160 base pairs from cross-linking by psoralen. The MVMi nucleoprotein complexes thus have a distinct structure which is different from that of chromatin.

Animals↗
PubMed1986

Regulation of transcription in vitro from herpes simplex virus genes.

In vitro transcription assays were carried out by using as templates DNAs cut from the herpes simplex virus early glycoprotein D gene, the late glycoprotein C gene, the late VP5 gene, and the immediate-early ICP22 gene. Nuclear extracts from suspension cultures of uninfected HeLa cells effectively synthesized RNAs from genes of the immediate-early and delayed-early classes. To a lesser extent, the extracts also used DNAs cut from the late genes as templates. Transcription from the immediate-early gene was inhibited in extracts prepared from infected cells. Analysis of the proteins in infected-cell extracts by gel electrophoresis, transfer to nitrocellulose, and probing with specific antibody demonstrated the presence of the viral regulatory protein ICP4. Chromatographic fractionation of nuclear extract from infected cells yielded a mixture of proteins (fraction VIII) enriched in ICP4 (S.W. Faber and K.W. Wilcox, Nucleic Acids Res., 14:6067-6083, 1986). Addition of fraction VIII to the in vitro assay affected transcription. Depending on the DNA in the assay, an inhibitory or stimulatory effect was observed. Inhibition of RNA synthesis was found when DNA from the immediate-early gene was used as a template, and stimulation was found when DNA from the early or late gene was used.

Capsid↗
PubMed1985

Both trans-acting factors and chromatin structure are involved in the regulation of transcription from the early and late promoters in simian virus 40 chromosomes.

We isolated simian virus 40 (SV40) chromosomes from lytically infected CV-1 cells at various times during the late phase and transcribed them in vitro with either whole-cell or nuclear extracts of HeLa cells. The late promoter was 3- to 10-fold more active than the early promoter. With bare SV40 DNA templates, the early promoter was up to 10-fold stronger than the late promoter. The relative strengths of the early and late promoters on SV40 chromosomes were essentially independent of template concentration or length of the replicative phase of the infection. When monoclonal antibodies or antisera against T antigen (T Ag) were added to SV40 chromosomes or when T Ag, both free and chromatin bound, was removed by immunoprecipitation with anti-T, the activity of the late promoter remained essentially unchanged. Washing with 0.4 M NaCl removed T Ag from more than 90% of the mature chromosomes associated with T Ag. Transcription from the late promoter still predominated in the salt-washed T Ag-depleted chromosomes, even though there was a marked increase in early promoter activity. The depression of the early promoter could be reversed by adding the T Ag-containing extract back to the depleted chromosomes. Extraction of SV40 chromosomes with 1.5 M NaCl resulted in a decrease in the activity of the late promoter and a further increase in the activity of the early promoter so that the relative amounts of early and late RNA synthesized were similar to those for bare SV40 DNA templates. Late RNA synthesis from bare SV40 DNA templates was stimulated by high-speed supernatants prepared from nuclear extracts of SV40-infected cells but not from those of uninfected cells. Pretreatment of the supernatants with anti-T did not alter the result. Our findings indicate that the activity of the early and late SV40 promoters is regulated by at least two different mechanisms at the chromosomal level. One is mediated by a subclass of T Ag bound to SV40 chromosomes which represses early SV40 transcription but has no effect on late transcription. A second level of regulation, involving a tightly bound trans-acting chromosomal factor and a stable nucleoprotein structure, favors the late promoter over the early promoter by up to 10-fold.

Animals↗
PubMed1984

Unwinding of the DNA helix in simian virus 40 chromosome templates by RNA polymerase.

We measured the distortion of the DNA helix by RNA polymerase transcribing simian virus 40 (SV40) chromosome templates and compared it with the distortion caused by the enzymes as it transcribes naked SV40 DNA, using RNA polymerase from Escherichia coli. Purified DNA topoisomerase I was added to the transcription reactions and the number of supercoil turns in DNA, after deproteinising and removal of RNA, was determined by gel electrophoresis and band-counting. The number of polymerase molecules bound per naked DNA molecule was determined by electron microscopy. Each bound RNA polymerase distorted the template in such a way as to lead to on apparent average of 0.6-0.7 negative superhelical turn in the extracted DNA. Thus only few base-pairs are melted per RNA polymerase molecule. When SV40 chromosomes were transcribed the extracted DNA had a higher number of supercoil turns than DNA extracted from the initial chromosomes. We conclude that the polymerase deforms the DNA in chromatin in the same way as it deforms pure DNA. From control experiments with inhibitors of initiation we estimated that on average 9-10 RNA polymerase molecules were bound per SV40 chromosome. This suggests that transcription can proceed while the majority or all the nucleosomal structures are intact on an SV40 DNA molecule. We discuss the implications of these findings for the mechanism of transcription of chromatin.

DNA Topoisomerases, Type I↗