A covalently linked DNA-RNA molecule from human leukemia cells

An enzyme complex was prepared from the cytoplasm of a continuous line of monocytic human leukemia cells isotopically labeled in culture. Such preparations carry out RNA dependent DNA synthesis using endogenous primers and templates and contain radioactive RNA and DNA. The endogenous [³H]-thymidine labeled DNA in these preparations was characterized by sedimentation in Cs₂SO₄ and neutral sucrose density gradients in conjunction with heat and alkali treatments and digestion with RNase. The resulting data support a view that a portion of the DNA is covalently linked to a larger piece of RNA in a molecule with a sedimentation coefficient of approximately 24S. This in turn may be hydrogen bonded to additional DNA in the native state.     

Evidence for RNA-Oligonucleotides in Plant Vacuoles Isolated from Cultured Tomato Cells

We have shown that highly purified vacuoles of suspension-cultured tomato (Lycopersicon esculentum) cells contain RNA-oligonucleotides, using two different approaches to label and detect RNA: (a) in vivo labeling of cellular RNA with [5-³H]uridine, followed by preparation of vacuoles from protoplasts and by quantification of radioactively labeled material; and (b) in vitro labeling and analysis on sequencing gels of nucleic acids prepared from tomato vacuoles and their identification as RNA. The intravacuolar location of the RNA found in vacuolar preparations was concluded from analyzing for RNA intact organelles after repeated flotation steps as well as ribonuclease A treatment. About 3% of the RNA in protoplasts was localized within vacuoles, exceeding by severalfold the contribution made by contamination with unlysed protoplasts and subcellular organelles. Investigation of the size distribution of vacuolar RNA revealed an oligonucleotide pattern strikingly different from that which would arise from contaminating protoplasts; vacuolar RNA fragments are considerably shorter than 80 nucleotides. Characterization of these oligoribonucleotides (3′-phosphorylated termini; relatively rich in pyrimidines) as possible products of tomato vacuolar ribonuclease I action, and, in addition, enzymatic hydrolysis of vacuolar RNA by inherent enzyme activities in lysed vacuole preparations support the hypothesis that plant vacuoles are involved in cellular nucleolytic processes.     

In vitro biosynthesis of liver cytochrome P450 mature peptide sub-unit by translation of isolated poly(A)+ mRNA from normal and phenobarbital induced rats

The biosynthesis of a cytochrome P₄₅₀ peptide sub-unit by the in vitro translation of total hepatic poly (A)⁺ mRNA in an heterologous cell-free-system is described. The ability of the liver poly (A)⁺ RNA preparations from normal and phenobarbital induced rats to promote protein synthesis and the identification of in vitro synthesized proteins revealed the presence of a cytochrome P₄₅₀ peptide sub-unit presenting the same apparent molecular weight of the native peptide. This fact demonstrates that rat liver poly (A)⁺ mRNA fraction contains an important amount of cytochrome P₄₅₀ peptide messages. Total poly (A)⁺ RNA from rats in an early phenobarbital induction stage exhibits a higher cytochrome P₄₅₀ template activity in good agreement with the enhancement of this hemeprotein concomitantly observed in vivo, in the liver microsomes, it is also concluded that cytochrome P₄₅₀, peptide sub-unit, induced in rat liver by phenobarbital, is translated in its mature form.     

Direct determination of the specific activity of RNA uniformly labeled with 32P

A simple method for the direct determination of the specific activity of RNA uniformly labeled with ³²P is described. The procedure is based on the premise that upon disintegration of ³²P to ³²S, the phosphodiester bond is broken. Analysis of the rate of decay of the full-length molecule by gel electrophoresis and autoradiography can accurately determine the “intramolecular specific activity” of the RNA. An equation that predicts the relative intensity of the intact RNA molecules remaining as a function of time is presented. These predictions are confirmed using in vitro-synthesized RNA labeled at a known specific activity. This procedure has been used to determine the intramolecular specific activity of RNA labeled in vivo in yeast. It can also be employed to choose the best conditions for experiments utilizing uniformly labeled RNA or single-stranded DNA and requiring the detection of intact molecules.     

RNA sequence determination in the nanogram range by a combination of in vitro labeling procedures.

Recently developed methods which allow one to read RNA sequences directly from polyacrylamide gels do not always provide unequivocal results. A combination of primary and secondary in vitro 5′-labeling, as presented here, is methodically and in its results equivalent to fingerprinting and sequencing techniques developed for in vivo labeled RNA. 5 S RNA was used to demonstrate the applicability and reliability of this combination of postlabeling procedures: 5 μg RNA was partially digested, and the resulting overlapping fragments were 5′-³²P-labeled with T4 phage-induced polynucleotide kinase in vitro. After two-dimensional polyacrylamide gel electrophoresis and carrier-free electrophoretic elution, the labeled long fragments, obtained in the 10-ng range, were completely degraded with RNase T₁ and RNase A, respectively. These digests were again ³²P-phosphorylated with T4 kinase and lead to fingerprints which allowed the deduction of the nucleotide sequences of the corresponding long fragments.     

Biosynthesis of the Tonoplast H-ATPase from Oats

To determine whether the tonoplast-type H⁺-ATPase was differentially synthesized in various parts of the oat seedling, sections of 4-day-old oat (Avena sativa L. var Lang) seedlings were labeled in vivo with [³⁵S]methionine and ATPase subunits were precipitated with polyclonal antisera. ATPase subunits were detected in all portions of the seedling with the exception of the seed. Lesser amounts of the 60 and 72 kilodalton polypeptides of the ATPase were found in apical regions (0-5 millimeter) than in maturing regions (10-15, or 20-25 millimeter from the tip) of the roots or shoots. To initiate a study of the biosynthesis of the ATPase, the intracellular site of synthesis for two peripheral ATPase subunits was investigated. Poly(A) RNA from either free or membrane-bound polysomes was isolated and translated in vitro. Message encoding the 72 kilodalton (catalytic) subunit was found predominantly in mRNA isolated from membrane-bound polysomes. In contrast, the message for the 60 kilodalton (putative regulatory) subunit was found predominantly on free polysomes. Polypeptides synthesized in vivo or obtained from RNA translated in vitro exhibited no apparent size differences (limit of resolution, approximately 1 kilodalton), suggesting the absence of cleaved precursors for the 72 or 60 kilodalton subunits. These data suggest a complex mechanism for the synthesis and assembly of the tonoplast ATPase.     

Purification of globin messenger RNA from dimethylsulfoxide-induced friend cells and detection of a putative globin messenger RNA precursor

Procedures are described that permit the detection and isolation of a specific messenger RNA as well as its precursor from total cell extracts. DNA complementary to the mRNA was elongated by the addition of dCMP residues and annealed with labeled cell RNA. The elongated DNA with RNA hybridized to it was isolated by chromatography on a poly(I)-Sephadex column. The method was used to isolate ³²P-labeled globin mRNA from labeled Friend cells, a mouse erythroleukaemic cell line, induced with dimethylsulfoxide to synthesize hemoglobin. ³²P-labeled globin mRNA isolated by this procedure was estimated to be 80% pure by hybridization analysis and sedimented as a single peak at 10 S. Partial sequences were determined for 16 oligonucleotides derived from the purified ³²P-labeled globin mRNA by RNAase T₁ digestion. The partial sequences for nine oligonucleotides corresponded to those predicted from the amino acid sequences of α and β globin; the other oligonucleotides were presumably derived from non-translated regions.In order to detect a possible precursor to globin mRNA, RNA from induced Friend cells pulse-labeled with [³²P]phosphate for 20 minutes was centrifuged through a sucrose gradient and the resulting fractions were analyzed for globinspecific sequences. Two peaks of globin-specific RNA were detected, a larger one at 10 S, the position of mature globin mRNA, and a smaller one at 15 S.     

Cell-free synthesis of opiate binding sites

A procedure is described for the detection of opiate binding sites synthesized during in vitro translation of various mRNA preparations. RNA were isolated from membrane bound polysomes which were prepared from NG 108-15 hybridoma, C6BU1 glioma cells, as well as from N18TG2, NB2aAg and NB41A3 neuroblastoma cells. Polyadenylated [poly(A)⁺] RNA were purified, translated in vitro in a rabbit reticulocyte lysate and the translation products assayed for their ability to bind [³H] bremazocine. Bound and free ligands were separated by column chromatography. After translation of poly(A)⁺ RNA obtained from NG 108-15 cells we demonstrated a stereospecific, saturable binding of [³H]bremazocine (displaced by levorphanol and not by dextrorphan) with a K_d of 2.4 ± 1.0 nM. The total amount of opiate binding sites synthesized was 6.2 ± 0.5 fmol per μg of poly(A)⁺ RNA. Opiate binding sites were undetectable at zero time and a plateau was reached after translation had proceeded for 20 min. Five time less opiate binding sites were synthesized when the poly(A)⁺ RNA purified from N18TG2 neuroblastoma cells were used under the same experimental conditions. There was no detectable binding of opiate ligands with poly(A)⁺ RNA obtained from C6BU1 glioma cells, NB2aAg or NB41A3 neuroblastoma cells.     

Partial purification of the nuclear estrogen receptor from chicken liver by affinity chromatography

The crude nuclear extract from the liver of estrogenized chickens contains 0.3–1 pmol/g tissue of the estrogen receptor. The receptor has been partially purified by ammonium sulphate precipitation and affinity chromatography on 17β-estradiol-17-hemisuccinyl-ovalbumin-Sepharose 4B. A 12% pure receptor preparation (2700-fold purification) with a yield of 17% could be obtained. The partially purified receptor has retained most properties which it displayed in cruder preparations, e.g. the dissociation constant of 10^?9?10^?10 M, the hormone specificity and the sedimentation coefficient of 3.9 S. The size (Stokes radius, 2.9 nm; molecular weight, 49 000) and the asymetry (f/f₀ = 1.10) of the receptor molecule, however, appear slightly reduced after the purification.     

Analysis of the coding activity and stability of messenger RNA in Drosophila oocytes.

The coding activity of the messenger RNA in the ooplasm of late stage 14 (S14) oocytes of Drosophila melanogaster was analyzed by labeling the oocytes in vitro with [³⁵S]methionine and examining the labeled products by two-dimensional gel electrophoresis and fluorography. This analysis was done both with newly formed S14 oocytes from rapidly laying females and with S14 oocytes stored for about 10 days in females that were prevented from laying. Comparison of the fluorographs showed that the proteins labeled in the newly formed oocytes were also labeled in the stored oocytes. Thus, the coding activity of S14 oocyte messenger RNA appears to remain stable during prolonged storage in utero. The oocyte proteins synthesized during oogenesis and incorporated into S14 oocytes were labeled in vivo by injecting [³⁵S]methionine into newly eclosed females, and the S14 oocytes were removed 2 days later for gel electrophoresis and fluorography. Comparison of the fluorographs produced by the in vivo and in vitro labeling procedures showed that most of the oocyte proteins labeled in vivo were also labeled in vitro. The S14 oocytes, therefore, appear to contain messenger RNA for most of the oocyte proteins synthesized during oogenesis. There were also several additional proteins detected only in the fluorographs of the in vivo labeled oocytes; the most prominent of these were identified by immunoprecipitation tests as vitellogenin proteins of yolk granules, which are known to be synthesized outside the oocyte, in fat bodies. The occurrence of stable S14 oocyte messenger RNA for most of the oocyte proteins suggests that the synthesis of those proteins during oogenesis occurs in the developing oocytes, specified by a stable population of oocyte messenger RNA.     

Two ribosome binding sites from the gene 0.3 messenger RNA of bacteriophage T7

Ribosome-protected regions have been isolated and analyzed from the bacteriophage T7 gene 0.3 mRNA labeled in vivo. Two discrete sites which are nearly equally protected by ribosomes are obtained from what was previously assumed to be a monocistronic message. Use of appropriate T7 deletion mutant RNAs has allowed mapping of both ribosome-recognized regions. Site a is positioned very close to the 5′ terminus of the mRNA and is apparently the initiator region for the major gene 0.3 protein, which acts to overcome the host DNA restriction system. Site b is located within several hundred nucleotides of the 3′ end of the RNA and probably initiates synthesis of a small polypeptide of unknown function. Both ribosome binding sites exhibit features common to other initiator regions from Escherichia coli and bacteriophage mRNAs. The proximity of site a to the RNase III cleavage site at the left end of gene 0.3 may explain why processing by RNase III is required for efficient translation of the major gene 0.3 protein.     

Highly charged radioactive initiator methionyl transfer RNA from in vivo labeled HeLa cells

³⁵S-Labeled Met-tRNA_f^Met can be prepared from HeLa cells, for studies of translation in vitro, with both a high degree of charging and a relatively high specific radioactivity. HeLa cells are labeled with [³⁵S]methionine in vivo, in the presence of cycloheximide to reduce translation. Their cytoplasmic RNA is then isolated by phenol extraction and subjected to cellulose ion-exchange chromatography in order to partially purify labeled Met-tRNA_f^Met and resolve it from Met-tRNA_m^Met.     

Identification of discrete disulfide-linked oligomers which distinguish 18 S from 14 S acetylcholinesterase

Acetylcholinesterase (EC 3.1.1.7) purified by affinity chromatography from 1.0 m ionic strength extracts of electric organ from the eel Electrophorus electricus consists of a mixture of 18 and 14 S enzyme forms. When examined by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate without exposure to disulfide reducing agents, these purified preparations show two major high molecular weight bands (>300,000), labeled oligomers A and B, in addition to a major band corresponding to catalytic subunit dimers (150,000 M_r). All these major bands reflect intersubunit disulfide bonding. The 18 and 14 S forms in purified preparations were separated by extensive sucrose gradient centrifugation. Gel analyses of the isolated 18 and 14 S pools indicated that the larger oligomer A derives from the 18 S pool, while oligomer B is found primarily in the 14 S pool. These observations support a previous model for 18 S acetylcholinesterase (T. L. Rosenberry and J. M. Richardson (1977) Biochemistry, in press) which considers this molecule to consist of one oligomer A unit, composed of three pairs of catalytic subunits disulfide-bonded to a collagen-like tail structure, and three catalytic subunit dimers. Proteolytic cleavage of the tail structure in the 18 S form can occur to release an 11 S enzyme tetramer containing a residual tail fragment and to leave a 14 S form. We propose this 14 S form to consist of one oligomer B unit, composed of two pairs of catalytic subunits disulfide-bonded to the remaining tail structure, and two catalytic subunit dimers.     

Products of rat liver mitochondrial protein synthesis: electrophoretic analysis of the number and size of these proteins and their solubility in chloroform: methanol

Rat liver mitochondria were incubated in vitro with radioactive leucine, and submitochondrial particles prepared by several methods. Analysis of the labeled mitochondrial membrane fractions by sodium dodecylsulfate gel electrophoresis revealed three labeled bands of molecular weights corresponding to 40,000; 27,000; and 20,000 daltons. Electrophoresis for longer times at higher concentrations of acrylamide revealed eight labeled bands, ranging in molecular weights from 48,000 to 12,000.Mitochondria were incubated for 5 min with [³H]leucine followed by a chase of unlabeled leucine. Gel electrophoresis of the membranes obtained after labeling for 5 min indicated significant synthesis of polypeptides in the 40,000 M_r, range and very little labeling of low molecular-weight polypeptides. After addition of the chase, increased synthesis of the high molecular-weight polypeptides was observed; however, no significant increase or decrease of radioactivity in the bands of low molecular-weight was observed, suggesting that rat liver mitochondria have the ability to synthesize complete proteins in the M_r 27,000–40,000 range.Approximately 16% of the total leucine incorporated into protein by isolated rat liver mitochondria in vitro could be extracted by chloroform: methanol. Gel electrophoresis of the chloroform: methanol extract revealed several bands containing radioactivity with the majority of counts in a band of 40,000 molecular weight. Gel electrophoresis of the chloroform: methanol extract of lyophilized submitochondrial particles indicated label in two broad bands in the low molecular-weight region of 14,000-10,000 with insignificant counts in the higher molecular-weight regions of the gel.Yeast cells were pulse labeled in vivo with [³H]leucine in the presence of cycloheximide and the submitochondrial particles extracted with chloroform:methanol. The extract separated after gel electrophoresis into four labeled bands ranging in molecular weight from 52,000 to 10,000. Preincubation of the yeast cells with chloramphenicol prior to the pulse labeling caused a 6-fold stimulation of labeling into the band of lowest molecular weight of the chloroform: methanol extract. These results suggest that the accumulation of mitochondrial proteins synthesized in the cytoplasm, when chloramphenicol is present in the medium, may stimulate the synthesis of certain specific mitochondrial proteins which are soluble in chloroform: methanol.     

Determination of nucleotide sequences from double-stranded regions of HeLa cell nuclear RNA

Double-stranded regions which comprise about 4% of isolated HeLa cell heterogeneous nuclear RNA have been characterized by RNA fingerprinting and sequencing analysis. The simplicity of the pattern in two-dimensional RNA fingerprints suggests a sequence complexity of about 1000 nucleotides. The nucleotide sequences of six prominent RNase T₁-resistant oligonucleotides (ranging in size from 7 to 9 bases) have been determined using isolated double-stranded nuclear RNA labeled in vivo with ³²P-labeled inorganic phosphate. We conclude that (here exists a substantial subpopulation of simple, potentially complementary sequences common to much of the heterogeneous nuclear RNA population and interspersed with other kinds of sequences.     

In vitro RNA iodination with the aid of chloramine T

A new method for in vitro RNA radioiodination with the aid of chloramine T has been developed. The ¹²⁵I-labeled RNA preparations obtained by this method were uniformly labeled, nondegraded, and of high specific activity. The method is simple and the results are reproduced easily.     

Accumulation of the early histone messenger RNAs during the development of Strongylocentrotus purpuratus

The developmental profile of amounts of the mRNAs for the early histones was determined. Sea urchin embryos (Strongylocentrotus purpuratus) were labeled with ³H nucleoside, and the RNA was extracted and fractionated by electrophoresis on polyacrylamide gels. Radioactivity in the resolved mRNA bands was determined and converted to molar quantities by knowledge of the precursor pool-specific activity. Between the 16- and the 200-cell stages 7–10 × 10⁶ molecules of each core histone mRNA, and 2.5 × 10⁵ molecules of H1 mRNA accumulate. During the subsequent few hours of cleavage the accumulated mRNAs disappear with a half-life of 1.5–2 hr. It is argued that mRNA half-life may be regulated during cleavage.     

Wheat leaf RNA polymerases. II. Kinetic characterization and template specificities of nuclear, chloroplast, and soluble enzymes

Further comparisons were made of DNA-dependent RNA polymerase (nucleotide triphosphate: RNA nucleotidyl transferase, EC 2.7.7.6) activities, partially purified from purified nuclear fragments and chloroplasts and from the soluble phase of young wheat leaves. All three preparations had the same cation specificities for maximal RNA polymerase activity (Mg²⁺ > Mn²⁺ > Ca²⁺) and showed an absolute dependence on an added divalent cation. All three preparations showed the same thermal stabilities and pH optima, very similar pH-activity profiles, and the same type of kinetics with ATP as substrate. Enzyme activities showed negative cooperativity with respect to ATP concentration; the high and low K_m values for ATP were not significantly different for the three preparations.