Showing papers on "RNA published in 1978"

Inhibition of Rous sarcoma virus replication and cell transformation by a specific oligodeoxynucleotide

Abstract: The tridecamer d(A-A-T-G-G-T-A-A-A-A-T-G-G), which is complementary to 13 nucleotides of the 3'- and 5'-reiterated terminal sequences of Rous sarcoma virus 35S RNA, was added to chick embryo fibroblast tissue cultures infected with Rous sarcoma virus. Inhibition of virus production resulted. The inference emerges that the tridecamer and its counterpart with blocked 3'- and 5'-hydroxyl termini enter the chick fibroblast cells, hybridize with the terminal reiterated sequences at the 3' and 5' ends of the 35S RNA, and interfere with one or more steps involved in viral production and cell transformation. Likely sites of action are (i) the circularization step of the proviral DNA intermediate, and (ii) the initiation of translation, the latter being described in the following communication [Stephenson, M. L. & Zamecnik, P. C. (1978) Proc. Natl. Acad. Sci. USA 75, 285--288].

Complete nucleotide sequence of SV40 DNA

Abstract: The determination of the total 5,224 base-pair DNA sequence of the virus SV40 has enabled us to locate precisely the known genes on the genome. At least 15.2% of the genome is presumably not translated into polypeptides. Particular points of interest revealed by the complete sequence are the initiation of the early t and T antigens at the same position and the fact that the T antigen is coded by two non-contiguous regions of the genome; the T antigen mRNA is spliced in the coding region. In the late region the gene for the major protein VP1 overlaps those for proteins VP2 and VP3 over 122 nucleotides but is read in a different frame. The almost complete amino acid sequences of the two early proteins as well as those of the late proteins have been deduced from the nucleotide sequence. The mRNAs for the latter three proteins are presumably spliced out of a common primary RNA transcript. The use of degenerate codons is decidedly non-random, but is similar for the early and late regions. Codons of the type NUC, NCG and CGN are absent or very rare.

Inhibition of Rous sarcoma viral RNA translation by a specific oligodeoxyribonucleotide

Abstract: A tridecamer oligodeoxynucleotide, d(A-A-T-G-G-T-A-A-A-A-T-G-G), which is complementary to reiterated 3'- and 5'-terminal nucleotides of Rous sarcoma virus 35S RNA, is an efficient inhibitor of the translation of proteins specified by the viral RNA in the wheat embryo cell-free system. The inhibition specificity for oncornavirus RNA is greater than for rabbit reticulocyte mRNA or brome mosaic virus RNA. Other oligodeoxynucleotides of similar size have little or no specific effect on the RNA-directed translation. The tridecamer acts as a primer for the avian myeloblastosis virus DNA polymerase when Rous sarcoma virus heated 70S RNA is used as a template, offering evidence that it can hybridize to the RNA. The possible use of such an oligodeoxynucleotide hybridization competitor to inhibit Rous sarcoma virus replication is described in the preceding paper [Zamecnik, P. C. & Stephenson, M. L. (1978) Proc. Natl. Acad. Sci. USA. 75, 280--284].

Spliced early mRNAs of simian virus 40.

Abstract: Biochemical methods are presented for determining the structure of spliced RNAs present in cells at low concentrations. Two cytoplasmic spliced viral RNAs were detected in CV-1 cells during the early phase of simian virus 40 (SV40) infection. One is 2200 nucleotides in length and is composed of two parts, 330 and 1900 nucleotides, mapping from ∼0.67 to ∼0.60 and from ∼0.54 to ∼0.14, respectively, on the standard viral map. The other is 2500 nucleotides long and also is composed of two parts, 630 and 1900 nucleotides mapping from ∼0.67 to ∼0.54 and from ∼0.54 to ∼0.14, respectively. Correlation of the structure of these mRNAs with the structure of the early SV40 proteins, small T antigen (17,000 daltons) and large T antigen (90,000 daltons), determined by others suggests that: (i) translation of the 2500-nucleotide mRNA yields small T antigen; (ii) translation of the 2200-nucleotide mRNA proceeds through the splice point in the RNA to produce large T antigen (and thus large T antigen is encoded in two separate regions of the viral genome); and (iii) the DNA sequences between ∼0.67 and ∼0.60 present in both mRNAs are translated in the same reading frame in both mRNAs to yield two separate gene products that have the same NH2-terminal sequence. Therefore, expression of the early SV40 genes is partially controlled at the level of splicing of RNAs.

3'-terminal labelling of RNA with T4 RNA ligase.

Abstract: T4 RNA LIGASE catalyses the formation of an internucleotide phosphodiester bond between an oligonucleotide donor molecule with a 5′-terminal phosphate and an oligonucleotide acceptor molecule with a 3′-terminal hydroxyl1–3. Although the minimal acceptor must be a trinucleoside diphosphate, dinucleoside pyrophosphates and mononucleoside 3′,5′-bisphosphates (pNps) are effective donors in the intermolecular reaction4–6. We demonstrate here that various high molecular weight RNA molecules are acceptors in the RNA ligase reaction even when present in very low concentrations in the reaction mixture. One immediate consequence of this observation is that a convenient method for labelling the 3′ end of RNA molecules in vitro becomes available. By using a [5′-32P]pNp as a donor and RNA as an acceptor, the product of the reaction is an RNA molecule one nucleotide longer, with a 3′-terminal phosphate and a 32P-phosphate in the last internucleotide linkage. This reaction is therefore analogous to the in vitro labelling of the 5′ termini of RNA chains with polynucleotide kinase and [γ-32P]ATP and can be used in situations where 5′ labelling is not possible. In addition, the ability to add various donors to an RNA molecule should allow the function of the 3′ terminus of the molecule to be investigated.

Detection of viral sequences of low reiteration frequency by in situ hybridization

Abstract: The sensitivity of in situ hybridization has been increased at least 10-fold by hybridizing in cDNA excess, by increasing the diffusion of the cDNA through the cells, by hybridizing at optimum temperature, and by stabilizing hybrids during autoradiography. Saturation of intracellular RNA with [3H]cDNA has been achieved. The assay is quantitative. In situ hybridization has been used to detect and quantitate visna virus RNA in infected cells. By using [3H]cDNA with specific activity of 2 X 10(8) dpm/micrograms and conditions that reduce background to negligible levels, 10--20 copies of viral RNA per cell can be detected and quantitated after 2 days of autoradiographic exposure.

Recent human influenza A (H1N1) viruses are closely related genetically to strains isolated in 1950

Abstract: Comparison of the oligonucleotide maps of the RNAs of current human influenza (H1N1) virus isolates shows these strains to be much more closely related to viruses isolated in 1950 than to strains which circulated before or after that period.

Structural analysis of spermine and magnesium ion binding to yeast phenylalanine transfer RNA.

Abstract: Refinement of the diffraction data at 2.5-A resolution from orthorhombic crystals of yeast tRNAPhe has proceeded to the point where spermine and magnesium ions can be located in the difference electron density map. Two spermine molecules are found: one is located in the major groove at one end of the anticodon stem; the other is near the variable loop and curls around phosphate 10 in a region where the polynucleotide chain takes a sharp turn. Four distinct magnesium ions have been identified: one in the anticodon loop, two in the D loop, and one coordinated with phosphates 8, 9, 11, and 12, where the polynucleotide chain is coiled. The conformation of the anticodon stem and loop is stabilized by the cations at the end of the molecule. The positions of these ions may be related to aspects of the biological activity of tRNA. The spermine and magnesium ions appear to be important in maintaining the overall folding of the tRNA molecule.

Acetylation of chromosome squashes of Drosophila melanogaster decreases the background in autoradiographs from hybridization with [125I]-labeled RNA.

Abstract: DNA in prepared chromosomes from the larval salivary glands of Drosophila melanogaster was hybridized with [125I]-labeled 5S and tRNA from the same organism. Autoradiography revealed that radioactivity was frequently bound to all regions of the slides, masking labeling of the chromosomes. Acetylation of the preparations before hybridization prevented the formation of this background and revealed the specific chromosomal sites.

Characterization of Rous sarcoma virus src gene products synthesized in vitro.

Abstract: The cell-free synthesis of three major proteins from virion RNA of nondefective Rous sarcoma virus (RSV), but not from RNA of transformation-defective deletion mutants, has been observed. The apparent molecular weights of these transformation-specific proteins are approximately 60,000 (60K), 25K, and 17K. Tryptic maps of methionine-containing peptides revealed the 17K, 25K, and 60K proteins to be overlapping in sequence. However, only partial homology was observed between the 17K, 25K and 60K proteins synthesized from Schmidt-Ruppin strain, subgroup D, RSV RNA and those synthesized from Prague strain, subgroup B, RSV, RNA. About half of the methionine peptides in the Schmidt-Ruppin strain, subgroup D, 60K protein were shared with the Prague strain, subgroup D, 60K protein, and the rest were distinct to each. The virion RNAs coding for the 60K, 25K, and 17K proteins were found to be polyadenylated and to sediment with maximal mRNA activity at about 23, 19 to 20, and 18S, respectively. In addition, transformation-specific proteins with molecular weights of 39K and 33K were observed by in vitro synthesis. These proteins are also related to the 60K, 25K, and 17K proteins and were synthesized from polyadenylated RSV RNA of approximately 21 to 22S. RNase T1-resistant oligonucleotides were analyzed in parallel, and the src-specific oligonucleotides were found to be first present in equimolar amounts in those gradient fractions sedimenting at 21 to 22S. Our data suggest that synthesis of the 60K protein is initiated near the 5' terminus of the src gene, whereas the 39K, 33K, 25K, and 17K proteins are initiated internally in the src gene. All of these proteins appear to be initiated independently, but they may have a common termination site.

Leaky UAG termination codon in tobacco mosaic virus RNA.

Abstract: THE RNA of tobacco mosaic virus (TMV) can be translated in various cell-free systems1–3 and in amphibian oocytes4, to yield two large polypeptides of molecular weights (MW) approximately 110,000 (110K) and 160,000 (160K). Products of the same sizes are found in infected plants2,5 and protoplasts6 and they are probably components of the viral replicase7,8. I show here that synthesis of these two proteins is initiated at the same site; the larger product is generated by partial readthrough of an amber (UAG) termination codon, and in the presence of yeast amber suppressor tRNA, the in vitro synthesis of the 160K protein is increased whereas the yield of the 110K protein is diminished.

Binding of benzo[a]pyrene 7,8-diol-9,10-epoxides to DNA, RNA, and protein of mouse skin occurs with high stereoselectivity

Abstract: The formation, stereostructure, and cellular reactions of the 7,8-diol-9,10-epoxide metabolites of the carcinogen benzo[a]pyrene have been examined after topical application of benzo[a]pyrene to the skin of mice. In this known target tissue, polymer adducts from diastereomeric diol epoxides, (+)-(7S, 8R, 9R, 10R) and (+)-(7R, 8S, 9R, 10R), were formed stereospecifically from their corresponding 7,8-dihydrodiols. Both diol epoxides bind with proteins, RNA, and DNA in vivo. For the nucleic acids, binding occurs preferentially at the 2-amino group of guanine in cellular RNA and DNA in vivo. Methods for establishing the structure of the cellular adducts as well as the possible biological implications of their formation are discussed.

Interferon action may be mediated by activation of a nuclease by pppA2'p5'A2'p5'A.

Abstract: EXPOSURE of cells to the antiviral agent interferon inhibits virus replication1. In interferon-treated cells the adsorption, penetration and uncoating of infecting viruses is not affected, but the synthesis of virus-specific mRNA and viral proteins is inhibited2,3. We have studied a mechanism for degradation of mRNA which may be activated in interferon-treated cells by the presence of double-stranded RNA (dsRNA) of viral origin. Lengyel et al. have reported that an endonuclease present in extracts of cells treated with interferon is activated by dsRNA and ATP4–6. The endonuclease degrades mRNA by a process which can be divided into two phases: an activation phase requiring the presence of both ATP and dsRNA but not of mRNA, and an endonucleolytic phase, which does not require either ATP or dsRNA6. Kerr et al. have at the same time reported that protein synthesis is inhibited in extracts of cells treated with interferon after incubation with dsRNA and ATP7. In these incubation conditions a low molecular weight inhibitor is formed from ATP8,9. The mechanism of action of this inhibitor, the structure of which has recently been determined as pppA2′p5′A2′p5′A (pppApApA)10, is not known. Our results indicate that this trinucleotide mediates the activation of a nuclease which degrades mRNA and may therefore inhibit protein synthesis in this way.

Globin mRNAs are primers for the transcription of influenza viral RNA in vitro

Abstract: Because influenza viral RNA transcription in vitro is greatly enhanced by the addition of a primer dinucleotide, ApG or GpG, we have proposed that viral RNA transcription in vivo requires initiation by primer RNAs synthesized by the host cell, specifically by RNA polymerase II, thereby explaining the α-amanitin sensitivity of viral RNA transcription in vivo. Here, we identify such primer RNAs, initially in reticulocyte extracts, where they are shown to be globin mRNAs. Purified globin mRNAs very effectively stimulated viral RNA transcription in vitro, and the resulting transcripts directed the synthesis of all the nonglycosylated virus-specific proteins in micrococcal nuclease-treated L cell extracts. The viral RNA transcripts synthesized in vitro primed by ApG also directed the synthesis of the nonglycosylated virus-specific proteins, but the globin mRNA-primed transcripts were translated about 3 times more efficiently. The translation of the globin mRNA-primed, but not the ApG-primed, viral RNA transcripts was inhibited by 7-methylguanosine 5′-phosphate in the presence of S-adenosylhomocysteine, suggesting that the globin mRNA-primed transcripts contained a 5′-terminal methylated cap structure. We propose that this cap was transferred from the globin mRNA primer to the newly synthesized viral RNA transcripts, because no detectable de novo synthesis of a methylated cap occurred during globin mRNA-primed viral RNA transcription. Preliminary experiments indicate that other purified eukaryotic mRNAs also stimulate influenza viral RNA transcription in vitro.

Ribonuclease P: an enzyme with an essential RNA component

Abstract: The activity of ribonuclease P on precursor tRNA substrates from Escherichia coli can be abolished by pretreatment of this enzyme with micrococcal nuclease or pancreatic ribonuclease A, as well as by proteases and by thermal denaturation. Highly purified RNase P exhibits one prominent RNA and one prominent polypeptide component when examined in polyacrylamide gels containing sodium dodecyl sulfate. The buoyant density in CsCl of RNase P, 1.71 g/ml, is characteristic of a protein-RNA complex. The activity of RNase P is inhibited by various RNA molecules. The presence of a discrete RNA component in RNase P appears to be essential for enzymatic function. A model is described for enzyme-substrate recognition in which this RNA component plays an important role.

Identification of an Abelson murine leukemia virus-encoded protein present in transformed fibroblast and lymphoid cells

Abstract: Extracts from lymphoid and fibroblast cell lines transformed by Abelson murine leukemia virus (A-MuLV) contain a protein of molecular weight 120,000 (P120). Immunoprecipitation with specific sera shows that P120 contains regions homologous to the 5'-terminal segment of the MULV gag gene complex--p15, p12, and at least part of p30--but lacks detectable determinants of p10, reverse transcriptase, and the envelope glycoprotein. P120 is phosphorylated and has an intracellular half-life of 3--6 hr. In vitro translation of virion RNA from A-MuLV, with Moloney MuLV as helper, yields a product of molecular weight 120,000 with serological reactivity similar to that of the cellular P120. Translation of the RNA from the helper gave no P120. P120 is expressed in all lymphoid and fibroblastic cell lines we have tested that were transformed by A-MuLV but is not detectable in a lymphoid line in which the A-MuLV genome was established by infection but was not responsible for the transformation. Expression of P120 is selectively retained in clones of A-MuLV-transformed lymphocytes that convert to a nonproducer state after loss of expression of helper MuLV intracellular precursors. These results suggest that the P120 product of the A-MuLV genome may be responsible for maintenance of the transformed phenotype of lymphoid and fibroblast cells transformed by the virus.

Identification of a polypeptide encoded by the avian sarcoma virus src gene.

Abstract: Two techniques were used to search for the polypeptide encoded by the avian sarcoma virus (ASV) src gene. First, antiserum from rabbits bearing ASV-induced fibrosarcomas was used to immunoprecipitate a transformation-specific antigen from ASV-transformed chick embryo fibroblasts. This antigen has an apparent molecular weight (Mr) of 60,000. Second, the 3' one-third of the ASV genome, selected by oligo(dT)-cellulose chromatography and sucrose gradient sedimentation, was translated in a mRNA-dependent reticulocyte cell-free lysate. This RNA species programmed the synthesis of a polypeptide that comigrated with the transformation-specific antigen of Mr 60,000 immunoprecipitated from transformed cells. The methionine-containing tryptic peptides from the polypeptides of Mr 60,000 obtained from translation in vitro and from immunoprecipitation were found to be identical upon two-dimensional fractionation.

Heterogeneous nuclear RNA-protein fibers in chromatin-depleted nuclei.

Abstract: The heterogeneous nuclear RNA-protein (hnRNP) fibers in HeLa cell nuclei are visualized by a nuclear subfractionation technique which removes 96% of the chromatin in a single step and 99% in a two-step elution but leaves the bulk of the hnRNA complexed with the remnant nuclear structure or lamina. Both steady-state and newly synthesized (approximately 15-s label) hnRNA are associated with the remnant nuclei to about the same extent. This association does not appear to depend on the presence of chromatin and exists in addition to any possible association of hnRNP with chromatin itself. Electron microscopy of partially purified nuclear hnRNA complexes shows that the hnRNP fibers form a ribonucleoprotein network throughout the nucleus, whose integrity is dependent on the RNA. Autoradiography confirms that hnRNA is a constituent of the fibers. The RNA network visualized in these remnant nuclei may be similar to RNA networks seen in intact cells. The hnRNA molecules appear to be associated with the nuclear lamina, at least in part, by unusual hnRNA sequences. More than half of the recovered poly(A) and double-stranded hnRNA regions remains associated with the nuclear structures or the laminae after digestion with RNase and elution with 0.4 M ammonium sulfate. In contrast, the majority of oligo(A), another ribonuclease resistant segment, is released together with most of the partially digested but still acid-precipitable single-stranded hnRNA and the hnRNP proteins not eluted by the ammonium sulfate alone. These special RNA regions appear to be tightly bound and may serve as points of attachment of the hnRNA to nuclear substructures. It is suggested that hnRNA metabolism does not take place in a soluble nucleoplasmic compartment but on organized structures firmly bound to the nuclear structure.

O4-(5'-uridylyl)tyrosine is the bond between the genome-linked protein and the RNA of poliovirus

Abstract: Virion RNA of poliovirus type 1 has been analyzed for the linkage between genome-protein VPg and the polyribonucleotide chain. Hydrolysis of the linkage with acid or alkali and enzymatic degradation lead to the conclusion that the bond is neither a phosphodiester such as nucleotidyl-(P-O)-serine (or threonine) nor a phosphoramidate such as nucleotidyl-(P-N)-amino acid. VPg-RNA can be iodinated by the Bolton and Hunter reagent [iodinated 3-(4-hydroxyphenyl)propionic acid N-hydroxysuccinimide ester] but not by the chloramine-T or lactoperoxidase procedures, an observation suggesting that VPg does not contain accessible tyrosine. However, VPg can be labeled with [3H]tyrosine in vivo. Hydrolysis of VPg-[32P]pUp with 5.6 M HCl at 110 degrees yielded 32P-labeled O4-(3'-phospho-5'-uridylyl)tyrosine that could be cleaved with micrococcal nuclease to O4-[32P]phosphotyrosine and uridine 3'-[32P]phosphate. These data establish that VPg is linked to the poliovirus genome by a bond between the O4 of tyrosine and the 5'-P atom of the terminal uridylic acid residue. The 5' end of polio genome RNA can now be described as VPg(Tyr-O)-pU-U-A-A-A-A-C-A-G.