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PubMed1966

Nature of ribonucleic acid stimulated by streptomycin in the absence of protein synthesis.

Freda, Celia E. (University of Pennsylvania School of Medicine, Philadelphia), and Seymour S. Cohen. Nature of ribonucleic acid stimulated by streptomycin in the absence of protein synthesis. J. Bacteriol. 92:1680-1688. 1966.-The ribonucleic acid (RNA) synthesized in a thymineless, arginineless, uracil-less Escherichia coli strain 15 in the absence of arginine was characterized by sucrose density gradient centrifugation. About 60% of this RNA had sedimentation rates in the range between 4S and 16S, and the remainder was comprised of the 23S and 16S ribosomal components. On addition of streptomycin for 1 hr in the absence of the amino acid, there was an inhibition of synthesis of material of 4S to 16S, whereas 16S RNA was slightly stimulated. Between 1 and 3 hr after addition of the antibiotic, during the precipitous killing of the bacteria in the arginine-deficient culture, the synthesis of 16S ribosomal RNA was specifically and sharply stimulated.

Arginine↗
PubMed1995

Differential display of messenger ribonucleic acid: a useful technique for analyzing differential gene expression in human brain tumors.

In this study, a differential display method for messenger ribonucleic acid was successfully used to identify genes differentially expressed between normal human brain and malignant glioma tissues. A total of 60 differentially expressed sequences were initially identified, of which 21 were cloned and sequenced. Twenty of the cloned sequences represented novel genes, and one sequence represented a kinesin heavy chain (KHC) gene isoform. The KHC isoform was selected for further characterization. Northern blots of total ribonucleic acid isolated from normal brain and a glioblastoma were probed with our KHC probe and confirmed the differential expression of this gene. Expression analysis of a variety of normal human tissues demonstrated that this KHC isoform is expressed only in brain tissues, with no detectable expression in placenta, spleen, kidney, lung, liver, or skeletal muscle. Our results confirm the rapid and sensitive nature of the differential display technique in identifying differential gene expression. This method offers a means to identify new genes of biological interest in human brain tumors such as oncogenes, tumor suppressor genes, and tumor-specific markers.

Adult↗
PubMed1997

Myocardial damage assessed by indium-111-antimyosin: correlation with persistent enteroviral ribonucleic acid in dilated cardiomyopathy.

The persistence of enteroviral ribonucleic acid (RNA) in the myocardium has been implicated as a pathogenetic factor in idiopathic dilated cardiomyopathy. Enteroviral persistence may lead to myocardial cell membrane damage, resulting in increased uptake of antimyosin antibodies. To further evaluate this hypothesis, a direct comparison of myocardial antimyosin uptake with the presence of enteroviral RNA was performed in ten patients (one female, nine male; 53+/-8 years) with chronic dilated cardiomyopathy. Planar antimyosin images were obtained 48 h after the injection of indium-111-labelled antimyosin Fab. Using a region of interest technique, the heart to lung uptake ratio (HLR) was calculated as a semiquantitative parameter of myocardial tracer uptake. Cardiac catheterization was performed to assess left ventricular function and to obtain myocardial biopsy samples. In the biopsy samples, gene amplification by polymerase chain reaction (PCR) was used to specifically detect enteroviral RNA. In the ten patients, the left ventricular ejection fraction was 39%+/-11% and the end-diastolic volume 131+/-46 ml/m2. The HLR was 1.72+/-0.21 and showed no correlation with functional parameters. In two patients with a positive PCR consistent with persisting enteroviral RNA, the HLR was not higher than that in eight patients with a negative PCR (1.46+/-0. 18 vs 1.78+/-0.18, respectively). These results suggest that increased uptake of 111In-antimyosin in chronic idiopathic dilated cardiomyopathy cannot be explained by pure persistence of enteroviral RNA. Other pathogenetic factors such as myocardial autoantibodies or microvascular spasm may be responsible for myocyte membrane damage detected by antimyosin.

Antibodies, Monoclonal↗
PubMed1978

The ribosomes of Plasmodium berghei: isolation and ribosomal ribonucleic acid analysis.

Ribosomes and high molecular weight ribosomal ribonucleic acid (rRNA) from the blood stages of Plasmodium berghei parasites were studied in preparations free from host ribosome contamination. Purified malarial ribosomes were isolated in high yield from a population of ultrastructurally intact, viable parasites by hypertonic lysis with Triton X-100 and differential centrifugation. These ribosomes were shown to be derived from active polysomes and could be dissociated into subunits by puromycin-0.5 M KCl treatment. Malarial rRNA extracted from purified 40S and 60S ribosomal subunits was characterized by electrophoretic, sedimentation and base ratio analyses. Like certain other protozoa, the P. berghei 40S ribosomal subunit possessed an exceptionally large RNA species (mol. wt 0.9 X 10(6), while RNA isolated from the parasite's 60S subunit (mol. wt 1.5 X 10(6)) was specifically 'nicked' to produce one large component (mol.wt 1.2 X 10(6)) and one small component (mol.wt 0.3 X 10(6)) in equimolar quantities. These rRNA's migrate identically on polyacrylamide gels after heating to 63 degrees C for 5 min or under denaturing conditions in the presence of formamide, indicating an absence of aggregation and non-specific degradation of the rRNA species. Base composition studies showed P. berghei rRNA to be low in guanosine and cytosine content, as is the case for protozoa generally.

Animals↗
PubMed1981

On the function of N-[(9-beta-D-ribofuranosylpurin-6-yl)carbamoyl]threonine in transfer ribonucleic acid. Metal ion binding studies.

The unusual transfer ribonucleic acid (RNA) anticodon adjacent modified nucleoside N-[(9-beta-D-ribofuranosylpurin-6-yl)carbamoyl]threonine, t6A, and its N6-methyl (mt6A) and 5'-phosphate (pt6A) derivatives are efficient ligands for magnesium and manganese ions, as demonstrated by potentiometry and nuclear magnetic resonance spectroscopy. Analysis of the 1H and 13C NMR spectra of t6A in the presence of paramagnetic Mn (II) at 32-34 degrees C has shown that the metal ion binds to the carboxyl group and probably N6 of the side chain as well as the N1 or N7 atom of the adenine ring. A more specific and stronger metal-ligand complex between Mn(II) and pt6A is evident from the 1H, 13C, and 31P NMR data. In this case, the metal forms a complex involving phosphate, N7 of the adenine and the carboxyl group, and N6 of the side chain. Blocking the N6 site as in mt6A attenuates the interaction, as revealed in the proton spectra. Potentiometric titrations at 30 degree C and in 0.1 M KNO3 have produced findings parallel to the NMR data on the interaction of Mn(II) with these ligands and have allowed a quantitative comparisup, and N6 of the side chain. Blocking the N6 site as in mt6A attenuates the interaction, as revealed in the proton spectra. Potentiometric titrations at 30 degree C and in 0.1 M KNO3 have produced findings parallel to the NMR data on the interaction of Mn(II) with these ligands and have allowed a quantitative comparisup, and N6 of the side chain. Blocking the N6 site as in mt6A attenuates the interaction, as revealed in the proton spectra. Potentiometric titrations at 30 degree C and in 0.1 M KNO3 have produced findings parallel to the NMR data on the interaction of Mn(II) with these ligands and have allowed a quantitative comparison between them as well as a comparison of the binding between Mg(II) and Mn(II). The stability constants (log K) for 1:1 metal-ligand complexes between Mg(II) and t6A, mt6A, and pt6A are respectively 5.5, 4.3, and 7.1. For Mn(II), the respective values are 6.0, 4.5, and 7.9. In the case of pt6A, the stability constants are about 5 log K units larger than those obtained for Mg(II) and Mn(II) binding to 5'-AMP [Khan, M. M. T., & Martell, A. E. (1967) J. Am. Chem. Soc. 89, 5585]. Thus the threonine side chain is an important determinant in the interaction between the modified nucleosides and metal ions, and these results are supportive of the idea that a facet of the function of this type of unusual nucleoside in transfer RNA is as a specific ligand for magnesium ion, a postulate promulgated earlier [Miller, J. P., Hussain, Z., & Schweizer, M. P. (1976) Nucleic Acids Res. 3, 1185].

Adenosine↗
PubMed1980

Transfer ribonucleic acid guanine transglycosylase isolated from rat liver.

Transfer ribonucleic acid (tRNA) guanine transglycosylase (guanine insertion enzyme) was isolated from rat liver and extensively purified. The enzyme catalyzes an exchange of queuine (the base of queuosine, Q) as well as its precursors and guanine for guanine originally located in the first position of the anticodon of "undermodified" tRNATyr, tRNAHis, tRNAAsn, and tRNAAsp from an Escherichia coli mutant or rat ascites hepatoma cells. This is in contrast to the previous observation that E. coli tRNA-guanine transglycosylase catalyzes the exchange of queuine precursors, such as 7-(aminoethyl)-7-deazaguanine and 7-cyano-7-deazaguanine, but not of queuine itself [Okada, N., Noguchi, S. Kasai, H., Shindo-Okada, N., Ohgi, T., Goto, T., & Nishimura, S. (1979) J. Biol. Chem. 254, 3067-3073]. The Km value for queuine of the rat liver enzyme is 9.2 X 10(-7) M, much lower than the values for the bases of queuosine precursors or guanine. Thus, the actual substrate for tRNA-guanine transglycosylase in queuosine biosynthesis in vivo in rat liver may not be 7-(aminomethyl)-7-deazaguanine, which is thought to be an actual substrate guanine, the E. coli system. Queuine or some queuine derivative may be the actual substrate for the tRNA-guanine transglycosylase reaction in the biosynthesis of Q in tRNA of mammalian cells. 6-Thioguanine and 8-azaguanine are also found to be good substrates.

Animals↗
PubMed1980

Distances between 3' ends of ribosomal ribonucleic acids reassembled into Escherichia coli ribosomes.

The three ribonucleic acids (RNAs) from Escherichia coli ribosomes were isolated and then labeled at their 3' ends by oxidation with periodate followed by reaction with thiosemicarbazides of fluorescein or eosin. Ribosomal subunits reconstituted with the labeled RNAs were active for polyphenylalanine synthesis. The distances between the 3' ends of the RNAs in 70S ribosomes were estimated by nonradiative energy transfer from fluorescein to eosin. The percentage of energy transfer was calculated from the decrease in fluorescence lifetime of fluorescein in the quenched sample compared to the unquenched sample. Fluorescence lifetime was measured in real time by using a mode-locked laser for excitation and a high-speed electrostatic photomultiplier tube for detection of fluorescence. The distances between fluorophores attached to the 3' ends of 16S RNA and 5S RNA or 23S RNA were estimated to be about 55 and 71 A, respectively. The corresponding distance between the 5S RNA and 23S RNA was too large to be measured reliably with the available probes but was estimated to be greater than 65 A. Comparison of the quantum yields of the labeled RNAs free in solution and reconstituted into ribosomal subunits suggests that the 3' end of 16S RNA does not interact appreciably with other ribosomal components and may be in a relatively exposed position, whereas the 3' ends of the 5S RNA and 23S RNA may be buried in the 70S ribosomal subunit.

Chemical Phenomena↗
PubMed1975

Rifampin susceptibility of ribonucleic acid synthesis in a fragile Saccharomyces cerevisiae mutant.

Ribonucleic acid (RNA) synthesis in the sorbitol-dependent, fragile yeast mutant VY1160 (Venkov et al., 1974) is rapidly inhibited by rifampin. The growth of the mutant cells and protein synthesis are more slowly affected by the antibiotic, apparently as secondary phenomena. Lower doses of rifampin (50 to 100 mug/ml) preferentially inhibit ribosomal RNA synthesis in comparison to that of messenger RNA and transfer RNA. Transcription and translation of messenger RNA continues in the presence of low doses of rifampin, as evidenced by the unimpaired induction of alpha-glucosidase. Partially purified RNA polymerase II from this mutant, in contrast to that from the parental strain, is strongly inhibited by low concentrations (1 mug/ml) of rifampin, whereas RNA polymerase I from the two strains is similar in behavior. The mutant may be useful for the study of regulatory mechanisms of transcription in eukaryotes.

DNA-Directed RNA Polymerases↗
PubMed1969

Methyl-deficient transfer ribonucleic acid in Saccharomyces cerevisiae.

Methyl-deficient transfer ribonucleic acid (tRNA) is found in certain methionine auxotrophs of Saccharomyces cerevisiae during logarithmic growth (at one generation time before the late growth phase) and during residual growth in the absence of exogenous methionine. The former effect seems to be accounted for by the general increase in RNA synthesis that occurs at the time; there is no specific synthesis of tRNA in the absence of ribosomal RNA synthesis, nor is the methyl group deficiency limited to a single tRNA species. During methionine starvation, all species of tRNA are methyl-deficient, but this occurs only in strains with certain blocks in the methionine pathway. The kinetics of disappearance of the methyl group donor, S-adenosylmethionine, during starvation of D73 (which accumulates methyl-deficient tRNA), do not differ from other strains, but D73 loses the methylase inhibitor, S-adenosylhomocysteine, much more slowly.

Carbon Isotopes↗
PubMed1971

Division cycle of Myxococcus xanthus. II. Kinetics of stable and unstable ribonucleic acid synthesis.

The kinetics of stable and unstable ribonucleic acid (RNA) synthesis during the division cycle of Myxococcus xanthus growing in a defined medium was determined. Under these conditions, M. xanthus contains one chromosome which is replicated during 80% of the cell cycle. Stable RNA synthesis was measured by pulselabeling an exponential-phase culture with radioactive uridine and then preparing the cells for quantitative autoradiography. By measuring the size of individual cells as well as the number of grains, the rate of stable RNA synthesis as a function of cell size was determined. Unstable RNA synthesis during the division cycle was determined by correlating the data for stable RNA synthesis with the relative amounts of stable and unstable RNA labeled during the short pulse. The data reported here demonstrate that: (i) cells synthesize both stable and unstable RNA throughout the division cycle; (ii) the rate of stable RNA synthesis increases in two discrete steps, corresponding to average ages of 0.15 and 0.75 generations; (iii) the rate of unstable RNA synthesis exhibits an initial rise, followed by a relatively constant rate of synthesis, and finally, a burst of unstable RNA synthesis prior to septum formation. The half-life of unstable RNA of M. xanthus, generation time of 390 min at 30 C, was 4 min. Comparison of the rates of stable and unstable RNA synthesis indicates noncoordinate RNA synthesis within the normal division cycle.

Autoradiography↗
PubMed1980

Synthesis and activity of ribonucleic acid polymerase in Escherichia coli.

The amounts of ribonucleic acid (RNA) polymerase (beta' subunits) and ribosomes (RNA), and the fraction of RNA polymerase actively engaged in transcription, were measured in Escherichia coli B/r as a function of growth rate. By an improved method of quantitating protein bands on electrophoresis gels, the systematic error and reproducibility of the RNA polymerase determination were estimated to be less than 15 and 6%, respectively. For a threefold increase in growth rate, the fractional synthesis of polymerase (relative to protein) increased 1.5-fold, whereas the fractional synthesis of ribosomal protein increased 2.2-fold. The decrease in the amount of RNA polymerase per ribosome with increasing growth rate is interpreted as an expression of the control of the transcriptional read-through from the genes for ribosomal protein, rplJ,L, to the adjacent genes for RNA polymerase subunits, rpoB,C. The number of active RNA polymerase molecules was determined from the synthesis rates of stable and messenger RNA and the known RNA chain growth rates. Comparison of active and total RNA polymerase indicates that the fraction of active enzyme increases from 20 to 30% in the range of growth rates between 0.6 and 2.0 doublings per hour. Possible causes for the inactive enzyme are discussed.

DNA-Directed RNA Polymerases↗
PubMed1980

Methylation patterns of mycoplasma transfer and ribosomal ribonucleic acid.

The methylation patterns of transfer and ribosomal ribonucleic acid (RNA) from two mycoplasmas, Mycoplasma capricolum and Acholeplasma laidlawii, have been examined. The transfer RNA from the two mycoplasmas resembled that of other procaryotes in degree of methylation and general diversity of methylated nucleotides, and bore particular resemblance to Bacillus subtilis transfer RNA. The only unusual feature was the absence of m5U from M. capricolum transfer RNA. The methylation patterns of the mycoplasma 16S RNAs were also typically procaryotic, retaining the methylated residues previously shown to be highly conserved among eubacterial 16S RNAs. The mycoplasma 23S RNA methylation patterns were, on the other hand, quite unusual. M. capricolum 23S RNA contained only four methylated residues in stoichiometric amounts, all of which were ribose methylated. A. laidlawii 23S RNA contained the same ribose-methylated residues, plus in addition approximately six m5U residues. These findings are discussed in relation to the phylogenetic status of mycoplasma, as well as the possible role of RNA methylation.

Acholeplasma laidlawii↗
PubMed1967

Structural units of reovirus ribonucleic acid and their possible functional significance.

Reovirus contains ribonucleic acid (RNA) equivalent in amount to a molecular weight of approximately 10(7) daltons. On isolation, this RNA is invariably broken into fragments of three different sizes. The three pieces have been separated from each other by chromatography on methylated albumin-kieselguhr columns. Denaturation of the three fragments of RNA in dimethyl sulfoxide led to separation of the strands, as suggested by sucrose gradient sedimentation patterns and by the second-order kinetics of reannealing. Molecular weights of 0.8 x 10(6), 1.4 x 10(6), and 2.4 x 10(6) were determined for the double-stranded fragments from the sedimentation rates of the single-stranded RNA obtained by denaturation. There was little or no homology among the three classes of denatured RNA when taken in pairs in hybridization tests. The three pieces of double-stranded RNA, therefore, did not result from random breaks in the original viral RNA molecule. Virusspecific single-stranded RNA formed in infected cells, and previously found to be largely if not entirely messenger RNA transcribed from the viral genome, was also separated into three size classes by sedimentation through sucrose gradients. Each class of single-stranded RNA corresponded in size to one of the three fragments of double-stranded RNA. The largest piece of single-stranded RNA hybridized uniquely with the largest fragment of denatured viral RNA. By whatever means this fragment of double-stranded RNA may be joined into the viral RNA molecule, it seems to act as a specific unit for transcription of an uninterrupted messenger RNA of equivalent length.

Carbon Isotopes↗
PubMed1968

Double-stranded Ribonucleic Acid from Cytoplasmic Polyhedrosis Virus of the Silkworm.

Ribonucleic acid (RNA) was extracted by phenol treatment from cytoplasmic polyhedrosis virus isolated from the midgut of infected silkworms. This RNA appears as threads when precipitated in alcohol. Two components having different sedimentation constants were observed. The molecular weight of the RNA preparation obtained by sedimentation coefficient (weight-averaged) and intrinsic viscosity was about 2 x 10(6) to 3 x 10(6). It was one-half to one-third the size of the calculated molecular weight for an entire RNA molecule in a virion. Electron micrographs of this RNA preparation showed two peaks in the distribution of contour length, at 0.4 and 1.3 mum, which would correspond to molecular weights of 10(6) and 3 x 10(6), respectively. The extracted RNA seemed to split into segments at a preferential breaking point. This RNA was soluble in concentrated salt solution, differing from single stranded high-molecular-weight RNA. The base composition of this RNA was complementary in the ratios of adenosine to uridine and guanosine to cytosine. It contained 43% guanosine plus cytosine. Based on its filamentous appearance by electron microscopy, typical pattern of optical rotatory dispersion and circular dichroism, sharp transition of the optical properties on heating, great hyperchromicity on degradation, nonreactivity with formaldehyde, and resistance to ribonucleases, it is concluded that this RNA is double-stranded and has regular base pairings of guanosine-cytosine and adenosine-uridine.

Journal Article↗
PubMed1969

Sindbis virus-induced viral ribonucleic acid polymerase.

A cytoplasmic structure containing the viral ribonucleic acid (RNA) polymerase has been isolated by sucrose density centrifugation from cells infected with Sindbis virus. Uninfected cells did not contain any such structure. Preliminary experiments indicated that the structure may be associated with membranes. This structure incorporated (3)H-guanosine triphosphate in vitro in the absence of added template. The RNA synthesized in vitro by the enzyme consisted of single-stranded 40S RNA, the ribonuclease-resistant replicative form, and possibly the replicative intermediate form of viral RNA. The products formed in vitro by the enzyme are identical in sedimentation rates to those formed in the infected cells in vivo.

Animals↗
PubMed1969

Molecular weight of poliovirus ribonucleic acid.

Purified poliovirus single- and double-stranded ribonucleic acids (RNA) were examined by electron microscopy. The length of both molecules was found to be 2.37 mum. The uncorrected sedimentation coefficient for single-stranded RNA is 33S, as compared to 27S for the RNA of tobacco mosaic virus. It is calculated from these results that the molecular weight of the sodium form of poliovirus is 2.6 x 10(6) daltons.

Centrifugation, Density Gradient↗