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PubMed1989

Isolation and characterization of the tax protein of HTLV-I.

The transactivator protein tax of the human T-cell leukemia virus type I, HTLV-I, is responsible for transactivation of gene expression of viral and cellular genes and is involved in the onset of adult T-cell leukemia, ATL. Genetic deletion studies have implicated a region of the HTLV-I LTR designated as tax-acceptor region, TAR, which is the target of the tax protein. Using antibodies against a tax carboxyterminal synthetic decapeptide the tax protein was purified from an HTLV-I immortalized human T-lymphocyte cell line by immunoaffinity chromatography. The tax protein, purified to apparent homogeneity binds to double-stranded DNA irrespective of its origin from either a nuclear or cytoplasmic fraction of the HTLV-I immortalized cell-line - both of which harbor similar quantities of tax protein. The tax protein binds less to single-stranded DNA and not to single-stranded RNA in vitro. It also binds to DNA-cellulose and heparin-Sepharose. Nuclease treatment of isolated nuclei does not release the tax protein under conditions which release known DNA-binding proteins, such as the myb protein. Transactivation by the tax protein presumably involves host-cell factors, since it does not recognize specific DNA sequences.

DNA↗

PubMed1978

[Use of the MUF-5 microspectrophotometer for enzymatic and chromatographic research on a microscale].

The use of MUV-5 as a recording microspectrophotometer for enzymatic and chromatographic analysis on miscroscale is proposed. The tuning of MUV-5 for working with a thermostated microcuvette is described. A microspectrophotometric method of the assay of lactate dehydrogenase activity in a single ovum of the mouse according to the kinetics of enzyme reaction is described. The proposed method allows to analyse the enzyme quantity 470 times as small as that which can be measured with SPh-16. A method for chromatographic separation of RNA with poly-U-sepharose column is described. The use of MUV-5 for the procedure of chromatographic separation of poly-RNA permits to reduce the amount of RNA in the assayed sample to 50 ng.

Animals↗

PubMed1994

Enzymatic synthesis of milligram quantities of ribozymes in small volumes.

Milligram quantities of ribozymes (Rzs) can be synthesized in vitro in reaction volumes of 1 mL or less using AmpliScribe T7 RNA polymerase kits to transcribe either linear plasmids or oligodeoxynucleotide templates. Model hammerhead Rzs were synthesized that specifically cleave RNA-encoding chloramphenicol acetyl transferase sequences. Methods are presented for the transcription of Rzs of virtually any length and sequence composition at a fraction of the cost of chemical synthesis.

Base Sequence↗

PubMed1969

Composition of Pseudomonas aeruginosa slime.

1. The slime produced by eight strains of Pseudomonas aeruginosa on a number of different media was demonstrated to be qualitatively the same. Small quantitative differences may be occasioned by differences in the extraction procedure, the growth medium or the strain of organism used. 2. The slime was shown to be predominantly polysaccharide with some nucleic acid material and a small amount of protein. 3. The hydrolysed polysaccharide fraction consists mainly of glucose with smaller amounts of mannose. This accounts for some 50-60% of the total slime. In addition, there is some 5% of hyaluronic acid. The nucleic acid material represents approx. 20% of the total weight, and is composed of both RNA and DNA. 4. Minor components are protein, rhamnose and glucosamine, the protein being less than 5% of the total. 5. Hyaluronic acid is produced in greater quantities from nutrient broth than from chemically defined media, and is more firmly attached to the cells than the other components.

Bacterial Proteins↗

PubMed1996

A method for the quantitative assessment of malaria parasite development in organs of the mammalian host.

A non-radioactive PCR method was developed to quantify the development of malaria parasites in the infected host. This was achieved by using Plasmodium genus-specific primers corresponding to the parasite's small subunit ribosomal RNA genes. The quantification of the PCR product was performed by high performance liquid chromatography, and calibration curves were obtained by amplification from defined quantities of purified Plasmodium genomic DNA. Using this method, it was possible to quantify development of P. berghei and P. yoelii blood-stage parasites from blood and brain samples of infected mice, and of hepatic stage parasites, from liver samples of mice infected with different numbers of sporozoites.

Animals↗

PubMedDate not supplied

[Display of 8-hydroxy-GTP substrate properties of UTP in the reaction of polynucleotide synthesis catalyzed by RNA-polymerase from Escherichia coli in the presence of poly[d(AT).d(AT)] template].

8-oxy-GTP was obtained via reaction of GTP with ascorbic acid and addition of hydrogen peroxide. 8-oxy-GTP is recognized and displays substrate properties of UTP on substitution of 8-oxy-GTP for UTP in polynucleotide synthesis catalyzed by E. coli RNA polymerase on a poly[d(A-T)].poly[d(A-T)] template. Such incorporation does not take place at equimolar quantities of GTP and 8-Br-GTP. The incorporation of 8-oxy-GTP instead of UTP, is 2.5-3 times higher upon replacement of Mg2+ by Mn2+ ions. The dinucleotide ApU serving as an initiator rises the incorporation level of 8-oxy-GTP both for Mg2+ and Mn2+ ions. 8-oxy-GTP slightly inhibits poly[r(A-U)] synthesis, but UTP strongly inhibits the incorporation of 8-oxy-GTP. [alpha-32P] 8-oxy-GTP is incorporated mainly instead of UTP, but it can be incorporated also during the substitution of 8-oxy-GTP for ATP.

DNA-Directed RNA Polymerases↗

PubMed1999

A role for RNA metabolism in inducing the heat shock response.

Yeast HSF is constitutively trimeric and DNA bound. Heat shock is thought to activate HSF by inducing a conformational change. We have developed an assay in which we can follow a conformational change of HSF that correlates with activity and thus appears to be the active conformation. This conformational change requires two HSF trimers bound cooperatively to DNA. The conformational change can be induced in whole cell extracts, and is thus amenable to biochemical analysis. We have purified a factor that triggers the conformational change. The factor is sensitive to dialysis, insensitive to NEM, and is not extractable by phenol. It is small, and apparently not a peptide. Mass spectroscopy identifies a novel guanine nucleotide that tracks with activity on columns. This novel nucleotide, purchased from Sigma, induces the conformational change (although this does not prove the identity of the activating factor unambiguously, because Sigma's preparation is contaminated with other compounds). What is the source of this nucleotide in cells? Activity can be generated by treating extracts with ribonuclease; this implicates RNA degradation as a source of HSF-activating activity. The heat shock response is primarily responsible for monitoring the levels of protein chaperones; how can RNA degradation be involved? Synthetic lethal interactions link HSF activity to ribosome biogenesis, suggesting a possible model. Ribosomal proteins are produced in large quantities, and in excess of rRNA; unassembled r-proteins are rapidly degraded (t1/2 approximately 3 min). Unassembled r-proteins aggregate readily. It is likely that unassembled r-proteins represent a major target of chaperones in vivo, and for proteasome-dependent degradation. Interference with rRNA processing (e.g., by heat shock) requires hsp70s to handle the aggregation-prone r-proteins, and proteasome proteins to help degrade the unassembled r-proteins before they aggregate. A nucleotide signal could be generated from the degradation products of the rRNA itself.

DNA↗

PubMed1977

The distribution of poly(A)+ and poly(A)- protamine messenger RNA sequences in the developing trout testis.

Protamine messenger RNA was isolated in a very pure form from trout testes and used as a template for the synthesis of labeled complementary DNA (cDNA) of high specifiv activity. The cDNA was found to be a full-length transcript of protamine messenger RNA and was used as a probe for hybridization reactions with RNA preparations isolated from three subcellular compartments of differentiating trout testis cells. The RNA populations from the nuclei, polysomes, and postribosomal supernatant of these cells were fractionated into poly(A)-containing [poly(A)+] and poly(A)-free [poly(A)-] RNA to determine the distribution of these two forms of protamine mRNA in these cell compartments. At the early protamine stage of testis development, polysomal and postribosomal supernatant fractions contain almost equal quantities of poly(A)+ protamine mRNA, but poly(A)- protamine mRNA was found almost entirely in the polysomes.

Animals↗

PubMed1970

Synthetic capabilities of plasmolyzed cells and spheroplasts of Escherichia coli.

Effects of plasmolysis and spheroplast formation on deoxyribonucleic acid (DNA), ribonucleic acid (RNA), protein, and phospholipid synthesis by Escherichia coli strain THU were studied. RNA and protein synthesis were severely diminished. DNA and phospholipid synthesis were inhibited, but less so; they could be partly restored. DNA synthesis could be restored by replacing thymine in the medium with thymidine, and phospholipid synthesis, by adding back small quantities of soluble cell extract. Plasmolysis effected marked reductions in rates of growth and macro-molecule synthesis, and temporarily reduced culture viability. Plasmolysis also caused an anomalous stimulation of phospholipid synthesis. Spheroplasts and plasmolyzed cells synthesized small amounts of ribosomal RNA that sedimented normally. However, this ribosomal RNA was very inefficiently packaged to ribosome subunits. Spheroplasts were unable to carry out induced synthesis of beta-galactosidase, and plasmolyzed cells were delayed in this function. Radioautographs examined in an electron microscope showed that DNA synthesis in plasmolyzed cells and spheroplasts was performed by a substantial fraction of the culture populations. That DNA and membrane were associated in the spheroplasts used in this study was suggested by formation of M-bands containing membrane and most of the cell's DNA. The results are discussed in terms of alterations of membrane structure and conformation attending plasmolysis and spheroplasting.

Bacterial Proteins↗

PubMed1999

Cleavage of double-stranded copy RNA by RNase 1 and RNase T1 provides a robust means to detect p53 gene mutations in clinical specimens.

Detecting somatic mutations in patient specimens is challenging because of the wide variation in quality and quantity of genomic DNA in clinically derived material. In cancer specimens, the challenge of detecting mutations is usually compounded by the presence of large numbers of nonmutated normal cells that dampen the relative signal that can be obtained from employing any mutation detection strategy. In the case of somatic mutations in the gene encoding the tumor suppressor, p53, a clinically useful mutation detection assay must be able to detect a wide variety of types of mutations scattered over five coding exons and their flanking intron sequences. This study examined the ability of a mutation detection strategy, termed NIRCA, to identify single-base mutations in the clinically relevant domain of the p53 gene. This strategy relies on RNase digestion-mediated cleavage of double-stranded copy RNA transcribed in vitro from polymerase chain reaction (PCR)-amplified genomic templates to detect mismatched base pairs resulting from hybridization of complimenting mutant and wild-type copy RNA strands. This assay system was found to robustly detect all twelve possible mismatches and the plus one and minus one frame shifts. Furthermore, the assay could detect mutations in clinical specimens when the mutant alleles composed as few as 4% of the total population of alleles isolated in bulk specimen genomic DNA. This mutation detection strategy worked efficiently in bladder, breast, colon and lung tumors as well as sediments from bladder cytology specimens.

Humans↗

PubMed1969

Foot-and-mouth disease virus inhibition induced in mice by synthetic double-stranded RNA (polyriboinosinic and polyribocytidylic acids).

Synthetic 2-stranded RNA-a helical complex formed by duplexing homopolymers of polyriboinosinic and polyribocytidylic acids (poly I:C)-induced host resistance to foot-and-mouth disease virus when microgram quantities were injected into mice. There was a graded response as shown by titrations of polynucleotide complex or virus. Protection was effective for >48 hours after a single injection of polynucleotide complex. Survival and serum interferon titers were directly related.

Animals↗

PubMed1993

Determination of mRNA fate by different RNA polymerase II promoters.

Translational stop mutations of the human beta-globin gene cause a reduction of cytoplasmic mRNA accumulation in thalassemia patients and in transfection models. The exact mechanism underlying this phenomenon has remained enigmatic but is known to be post-transcriptional. We have used transfected HeLa cells to study the expression of beta-globin mRNAs with nonsense or frameshift mutations within the three exons of this gene. Mutations in exons 1 or 2 reduce cytoplasmic mRNA accumulation whereas a mutation in exon 3 permits essentially normal expression. We report here that the post-transcriptional fate of mutated beta-globin mRNAs is differentially affected by the type of RNA polymerase II promoter driving expression. Replacement of the beta-globin promoter with the herpes simplex virus type 1 thymidine kinase gene promoter but not the cytomegalovirus immediate early promoter rescues the cytoplasmic accumulation of mutated mRNA to wild-type levels. This effect is shown to be independent of the absolute quantity and the kinetics of accumulation of mutated mRNA synthesized, and primer-extension analyses confirm that both viral promoters accurately utilize identical transcription start sites. These data thus reveal an unexpected property of RNA polymerase II promoters: determination of the post-transcriptional fate of the maturing mRNA, presumably by influencing alternative choices between as yet undefined processing and/or transport pathways.

Base Sequence↗

PubMed1987

The sorangicins, novel and powerful inhibitors of eubacterial RNA polymerase isolated from myxobacteria.

A new antibiotic, sorangicin, was isolated from the culture supernatant of the myxobacterium, Sorangium (Polyangium) cellulosum strain So cel2. It is a macrocyclic lactone carbonic acid and is produced in two structural variants, sorangicins A and B. In addition small quantities of the respective glycosides, sorangiosids A and B, may be found. The antibiotic acts mainly against Gram-positive bacteria, including myocobacteria, with MIC values between 0.01 and 0.1 microgram/ml, but at higher concentrations (MIC 3 approximately 30 micrograms/ml) Gram-negatives are also inhibited. Yeasts and molds are completely resistant. The new antibiotic is a specific inhibitor of eubacterial RNA polymerase which it blocks, however, only if added before RNA polymerization has started.

Aminoglycosides↗

PubMed2004

Histone release during transcription: NAP1 forms a complex with H2A and H2B and facilitates a topologically dependent release of H3 and H4 from the nucleosome.

Transcription through a multinucleosomal template was studied to determine why histones are released to the nascent RNA. It was first determined in competition experiments between DNA and RNA that histones H2A and H2B have a 20-fold preference for binding RNA over DNA; a preference was not seen for histones H3 and H4. Histones H3 and H4 would preferentially bind RNA, provided they were in an octameric complex with H2A and H2B. In transcription studies with T7 RNA polymerase, H3 and H4 were transferred to the nascent RNA, provided the template was linear. If the DNA was topologically restrained, which is a condition that more closely maintains transcription-induced stresses, H3 and H4 would not release. Histones H3 and H4 would be released from this template when H2A and H2B were present, a release that was enhanced by the presence of nucleosome assembly protein-1 (NAP1). Since a small quantity of H2A and H2B is sufficient to facilitate this transfer, it is proposed that H2A and H2B function to repeatedly shuttle H3 and H4 from the template DNA to the RNA. Cross-linked histones (dimethylsuberimidate-cross-linked octamer) were reconstituted into nucleosomes and found to be transferred to the RNA at the same frequency as un-cross-linked histones, an indication that such large complexes can be released during transcription. Transcription was carried out in the presence of Escherichia coli topoisomerase I so that positive coils would accumulate on the DNA. Histones H3 and H4 would again not be transferred from this DNA, unless H2A and H2B were present. In this instance, however, when NAP1 was present, the shuttling of H3 and H4 to the RNA caused a significant depletion of H2A and H2B from the positively coiled DNA. These results are discussed with regard to current models for transcription through nucleosomes.

Animals↗

PubMed1994

Gastrin-releasing peptide is produced in the pregnant ovine uterus.

Our previous finding of appreciable quantities of a gastrin-releasing peptide (GRP)-like immunoreactive (GRPLI) entity in ovine fetal and maternal plasma led us to examine the ovine pregnant uterus as a possible source of this material. At term, intense immunohistochemical staining for GRPLI occurred in the endometrial epithelial cells, and the term ovine uterus also contained abundant GRP messenger RNA (mRNA). In contrast, GRP mRNA was not detected in fetal membranes. GRP mRNA was present in the uterus on gestational day 63; a significant increase in GRP mRNA had occurred by day 100. Thereafter, levels remained elevated until term, but 3 months postpartum, GRP mRNA levels were greatly reduced. As previous studies suggested the GRPLI entity to be of greater molecular size than GRP-(1-27), we deduced the primary structure of ovine uterus GRP by sequencing a complementary DNA clone isolated from a complementary DNA library constructed from term ovine uterus polyadenylated RNA. Ovine uterine GRP is composed of 27 amino acid residues and has a conserved C-terminal region, similar to GRP structures in other species. We conclude that during pregnancy, the ovine uterus produces considerable quantities of GRP, which may play an important but hitherto unrecognized role in utero-placental development and possibly in fetal development after transfer to the fetus.

Amino Acid Sequence↗

PubMed1983

Use of a cDNA library for the study of mRNA changes during muscle differentiation.

A cDNA library was used to measure changes in many individual mRNAs during muscle differentiation in culture. A library of 1000 clones was constructed from total myofiber poly(A) RNA. About 23% of these clones gave a detectable colony hybridization signal using end-labeled myofiber mRNA, the remainder containing muscle sequences too rare to be detected with this assay. The 230 positive clones were grouped into four classes based on relative visual intensity. Reconstruction experiments using pure globin mRNA enable us to determine the approximate percentage of total RNA made up by each mRNA hybridizing to a cDNA clone. Those clones containing sequences complementary to developmentally regulated mRNAs were identified by a differential hybridization procedure. The cDNA library was screened with end-labeled mRNA from both undifferentiated myoblasts and differentiated myofibers. Although the bulk of the clones hybridized essentially the same with both RNA populations, several dozen were found which hybridized differentially. Some clones contained sequences which were not present at all in myoblasts and present in very high quantities in myofibers. Others contained sequences found in both myoblasts and myofibers but in increased quantities in the differentiated cells. Still others contained sequences which decreased in quantity during muscle differentiation. The clones in the first group were chosen for immediate analysis since they likely contain contractile protein mRNA sequences. However, all the characterized cDNA clones can now be used as probes to study the chromosomal organization and developmental expression of genes active during muscle differentiation.

Animals↗

PubMedDate not supplied

[Thyroglobulin gene expression in human thyroid cells in various types of thyroid pathology].

Highly purified thyroglobulin mRNA was isolated from human nodal euthyroid goiter. Full length cDNA was synthesized from 33S RNA by using reverse transcriptase in the presence of human placenta ribonuclease inhibitor. DNA complementary to human Tg mRNA was used in liquid hybridization experiments to determine the quantity of Tg mRNA. The amount of Tg mRNA in euthyroid nodal and congenital goiter was reduced. Tg specific mRNA was absent in thyroid cancer cells.

Cells, Cultured↗

PubMed1975

Characteristics of the prolactin stimulation of uridine metabolism in mammary gland explants.

Experiments were carried out to characterize the prolactin stimulation of labeled uridine uptake into mammary gland explants which were initially preincubated for 2 days in medium containing insulin plus hydrocortisone. Prolactin was found to enhance labeled uridine uptake after 4 h but not after 2 h when uridine concentrations ranging between 0.1 muM and 1 mM were tested. The effect of prolactin on labeled uridine uptake also appears to require ongoing RNA and protein synthesis since incubation with a variety of inhibitors of RNA and protein synthesis abolished the prolactin effect. It was further discovered that prolactin stimulates the labeling of the cellular pools of the phosphorylated derivatives of uridine while the quantity of label present in the uridine and uracil pools was not affected. It is thus possible that the effect of prolactin on labeled uridine uptake may be caused by the enhanced phosphorylation of the uridine. It was also found that the onset of the effect of prolactin on the phosphorylation of uridine to UTP was not different from the onset of the effect of this hormone on labeled uridine uptake and its incorporation into RNA. Additional studies were carried out to determine if the effect of prolactin on RNA synthesis could be dissociated from its effect on the uptake of precursor substances. For this purpose the effect of prolactin on the uptake of radiolabeled phosphate and its incorporation into RNA was studied. Prolactin stimulated the incorporation of phosphate into RNA after 4 h but the uptake of phosphate was not affected by the hormone at that time. Further, the effect of prolactin on phosphate incorporation into RNA was temporally identical to the hormonal effect on the incorporation of 3H-uridine into RNA.

Animals↗