Showing papers on "RNA published in 1982"

Rapid evolution of RNA genomes

Abstract: RNA viruses show high mutation frequencies partly because of a lack of the proofreading enzymes that assure fidelity of DNA replication. This high mutation frequency is coupled with high rates of replication reflected in rates of RNA genome evolution which can be more than a millionfold greater than the rates of the DNA chromosome evolution of their hosts. There are some disease implications for the DNA-based biosphere of this rapidly evolving RNA biosphere.

RNA tumor viruses

Abstract: This book contains 12 selections Some of the titles are: Genome Structure;Genetics of Retroviruses;Functions and Origins of Retroviral Transforming Genes;Human T-cell Retroviruses;Replications of Retroviruses;and Endogenous Viruses

Signal recognition particle contains a 7S RNA essential for protein translocation across the endoplasmic reticulum.

Abstract: In addition to its previously characterized, six different polypeptide components, signal recognition protein--which functions in protein translocation across and integration into the endoplasmic reticulum membrane--contains a 7S RNA molecule. The RNA is closely identified with the small cytoplasmic 7SL RNA and is required for both structural and functional properties of signal recognition protein--which we therefore rename signal recognition particle.

Nucleotide sequence of tobacco mosaic virus RNA

Abstract: Oligonucleotide primers have been used to generate a cDNA library covering the entire tobacco mosaic virus (TMV) RNA sequence. Analysis of these clones has enabled us to complete the viral RNA sequence and to study its variability within a viral population. The positive strand coding sequence starts 69 nucleotides from the 5' end with a reading frame for a protein of Mr 125,941 and terminates with UAG. Readthrough of this terminator would give rise to a protein of Mr 183,253. Overlapping the terminal five codons of this readthrough reading frame is a second reading frame coding for a protein of Mr 29,987. This gene terminates two nucleotides before the initiator codon of the coat protein gene. Potential signal sequences responsible for the capping and synthesis of the coat protein and Mr 29,987 protein mRNAs have been identified. Similar sequences within these reading frames may be used in the expression of sets of proteins that share COOH-terminal sequences.

Amplification of endogenous myc-related DNA sequences in a human myeloid leukaemia cell line.

Abstract: Malignant transformation of cells by acute transforming RNA tumour viruses is mediated by the expression of certain specific pro viral DNA sequences (‘oncogenes’). These sequences have been well characterized and, in many cases, molecularly cloned1–8. These viral oncogenes are related to similar genes found in normal uninfected cells9,10. Moreover, these particular sequences are highly conserved in evolution4,11, suggesting that these genes have an important, albeit unknown, role in normal cell function. It has been suggested that an increased dosage of products of such endogenous oncogenes may be responsible for malignant transformation10,12,13. For example, increased expression of the endogenous chick c-myc oncogene has been observed in avian leukosis virus-induced transformation of chick bursal lymphocytes12. Here we demonstrate that sequences in normal human DNA homologous to the avian myc oncogene are present in multiple copies in the chromosomal DNA of the human leukaemia cell line HL-60. Other transformation-specific genes derived from the Abelson leukaemia virus4 and feline sarcoma virus6 are not amplified in HL-60. This myc-related gene amplification is not present in other cultured human myeloid leukaemia cells, including K-56214 and KG-115.

Form and function of retroviral proviruses

Abstract: Retroviruses have proved to be useful reagents for studying genetic and epigenetic (such as regulatory) changes in eukaryotic cells, for assessing functional and structural relationships between transposable genetic elements, for inducing insertional mutations, including some important in oncogenesis, and for transporting genes into eukaryotic cells, either after natural transduction of putative cellular oncogenes or after experimental construction of recombinant viruses. Many of these properties of retroviruses depend on their capacity to establish a DNA (proviral) form of their RNA genomes as a stable component of host chromosomes, in either somatic or germinal cells.

Nucleosides useful in the preparation of polynucleotides

Abstract: New and useful intermediate nucleotides bound to an inorganic polymer support, including the preparation thereof, and processes for the conversion to oligonucleotides which are especially useful for the synthesis of polynucleotides, particularly ribonucleic (RNA) and deoxyribonucleic acids (DNA).

Cloning and characterization of five overlapping cDNAs specific for the human proα 1(I) collagen chain

Abstract: We report the cloning of five overlapping cDNAs bearing sequences specific for the human pro alpha 1(I) collagen chain. Poly-A RNA enriched for collagen sequences was purified from normal human fibroblasts and used as template to synthesize double stranded cDNA. The cDNA was inserted into the Eco RI site of pBR 322 by blunt-ending and dG:dC tailing. The clones were screened by colony hybridization using the original RNA population and the resulting five positive clones subjected to restriction endonuclease mapping analysis and DNA sequencing. These overlapping clones cover from residue 247 in the alpha chain to part of the 3' end untranslated region of the pro alpha 1(I) mRNA for a total of 3400 nucleotides.

Failure of RNA synthesis to recover after UV irradiation: an early defect in cells from individuals with Cockayne's syndrome and xeroderma pigmentosum

Abstract: Previous work has shown that in cells from the ultraviolet-sensitive genetic disorder, Cockayne's syndrome, DNA synthesis fails to recover after ultraviolet irradiation, despite the fact that these cells have no detectable defect in either excision or daughter-strand repair pathways We now show that Cockayne cells, as well as cells from a number of patients with xeroderma pigmentosum, are sensitive to the lethal effects of UV irradiation in stationary phase under conditions in which no DNA is synthesized after irradiation Furthermore, in normal and defective human fibroblasts, RNA synthesis is depressed after UV irradiation In normal (dividing) cells, RNA synthesis recovers very rapidly, but this recovery does not occur in Cockayne cells, and it is reduced or absent in xeroderma pigmentosum cells from different complementation groups Qualitatively, similar results are obtained with cells in stationary phase The recovery of RNA synthesis in the various defective cell strains is not correlated with the overall extent of excision repair, but there is some correlation between recovery of RNA synthesis and cell survival after ultraviolet irradiation These results implicate recovery of RNA synthesis as an important early response to ultraviolet irradiation

Transcripts from the cellular homologs of retroviral oncogenes: distribution among chicken tissues.

Abstract: The oncogenes (v-onc genes) of rapidly transforming retroviruses have homologs (c-onc genes) in the genomes of normal cells. In this study, we characterized and quantitated transcription from four c-onc genes, c-myb, c-myc, c-erb, and c-src, in a variety of chicken cells and tissues. Electrophoretic analysis of polyadenylated RNA, followed by transfer to nitrocellulose and hybridization to cloned onc probes showed that c-myb, c-myc, and c-src each give rise to a single mature transcript, whereas c-erb gives rise to multiple transcripts (B. Vennstrom and J. M. Bishop, Cell, in press) which vary in abundance among different cells and tissues. Transcription from c-myb, c-myc, c-erb, and c-src was quantitated by a "dot-blot" hybridization assay. We found that c-myc, c-erb, and c-src transcription could be detected in nearly all cells and tissues examined, whereas c-myb transcription was detected only in some hemopoietic cells; these cells, however, belong to several different lineages. Thus, in no case was expression of a c-onc gene restricted to a single cell lineage. There appeared to be a correlation between levels of c-myb expression and hemopoietic activity of the tissues and cells examined, which suggests that c-myb may be expressed primarily in immature hemopoietic cells. An examination of c-onc RNA levels in target cells and tissues for viruses carrying the corresponding v-onc genes revealed no obvious correlation, direct or inverse, between susceptibility to transformation by a given v-onc gene and expression of the homologous c-onc gene.

Temporal Patterns of Human Cytomegalovirus Transcription: Mapping the Viral RNAs Synthesized at Immediate Early, Early, and Late Times After Infection

Abstract: The transcription of the human cytomegalovirus genome was investigated at immediate early, early, and late times after infection. Viral RNAs associated with either the whole cell, the nucleus, the cytoplasm, or the polyribosomes were analyzed. At immediate early times, i.e., in the absence of de novo viral protein synthesis, the viral RNA in high abundance originated from a region of the long unique section of the prototype arrangement of the viral genome (0.660 to 0.770 map units). The viral RNA in low abundance originated from the long repeat sequences (0.010 to 0.035 and 0.795 to 0.825 map units) and a region in the long unique section (0.201 to 0.260 map units). Viral RNAs associated with the polyribosomes as polyadenylated RNA were mapped to these restricted regions of the viral genome and characterized according to size class in kilobases. At 24 h after infection in the presence of an inhibitor of viral DNA replication, i.e., at early times, the stable viral RNAs in highest abundance mapped in the long repeat sequences. Viral RNAs at intermediate abundance under these conditions mapped in two regions of the long unique section of the viral genome (0.325 to 0.460 and 0.685 to 0.770 map units). Stable viral RNAs that were associated with the polyribosomes in high abundance as polyadenylated RNA orginated from the long repeat sequences, but not from the long unique section of the viral genome. An analysis of whole-cell RNA at late times (72 h) indicated that the abundant transcription was in the regions of the long unique sequences (0.325 to 0.460 and 0.660 to 0.685 map units), and transcription of intermediate abundance was from the long repeat sequences. However, stable viral mRNA's derived from the long repeat sequences were associated with the polyribosomes at late times after infection. In addition, mRNA's originating from the long and short unique sequences were found associated with the polyribosomes at higher relative concentration than at early times after infection. It is proposed that expression of the immediate early viral genes is required to transcribe the early viral genes in the long repeat and adjacent sequences. These sequences are also transcribed at late times after infection while viral DNA synthesis continues. The expression of viral genes in most of the long and short unique sequences appears to require viral DNA replication.

Isolation and characterization of c-myc, a cellular homolog of the oncogene (v-myc) of avian myelocytomatosis virus strain 29.

Abstract: The chicken genome contains nucleotide sequences homologous to transforming genes (oncogenes) of a number of avian retroviruses. We have isolated chicken DNA (c-myc) that is homologous to the oncogene (v-myc) of the avian myelocytomatosis virus MC29 and have compared the structures of the cellular and viral genes. Results from restriction endonuclease mapping of c-myc and from analysis of heteroduplexes between the DNAs of the cellular and viral genes show that c-myc is homologous to 1,500 nucleotides in v-myc DNA. This homologous region is interrupted in c-myc by an intron-like sequence of 1,100 nucleotides which is absent from v-myc. Nuclear RNA from normal chicken cells contains at least five species of transcripts from c-myc ranging from 2.5 to 6.5 kilobases in length. By contrast, cytoplasm contains only the 2.5-kilobase c-myc RNA. These features of the c-myc gene and its nuclear transcripts are characteristic of normal cellular genes and suggest that the myc gene is of cellular rather than viral origin. The exons in c-myc may define two functional domains in the gene and may therefore facilitate the dissection of the different oncogenic potentials of the MC29 virus.

Complete nucleotide sequence of the attenuated poliovirus Sabin 1 strain genome

Abstract: The complete nucleotide sequence of the genome of the type 1 poliovirus vaccine strain (LSc,2ab) was determined by using molecular cloning and rapid sequence analysis techniques. The restriction fragments of double-stranded cDNA synthesized from the vaccine strain RNA were inserted into the adequate sites of cloning vector pBR322. Sequence analysis of the cloned DNAs revealed that the virion RNA molecule was 7,441 nucleotides long and polyadenylylated at the 3' terminus. When the nucleotide sequence was compared with that of the genome of the virulent parental strain (Mahoney), 57 base substitutions were observed to be scattered all over the genome. Of these, 21 resulted in amino acid changes in a number of viral proteins. A cluster of amino acid changes is located in the viral coat proteins, especially in the NH2-terminal half of the viral capsid protein VP1. These results may imply that the mutations in the VP1 coding region contribute to attenuation.

Chromosomal localization of human cellular homologues of two viral oncogenes.

Abstract: Acute transforming RNA tumour viruses represent genetic recombinants between type C retro viral sequences and transformation-specific sequences of cellular origin. Of the known mammalian cell-derived transforming genes (oncogenes), two have been shown to encode proteins with either intrinsic or highly associated tyrosine-specific protein kinase activity. One such gene, c-fes, is of cat cellular origin, while the second, c-abl, was derived from mouse cellular sequences. We now show that the human equivalents of c-fes and c-abl are localized on human chromosomes 15 and 9, respectively. These findings exclude the possibility that these transformation-related genes are clustered at a single locus within the human genome. It is of interest that both of these chromosomes are involved in specific rearrangements found in certain forms of human cancer.

Deletion mapping of DNA regions required for SV40 early region promoter function in vivo.

Abstract: The SV40 early region promoter, previously localized to the DNA segment bounded by the HpaII and HindIII restriction sites (nucleotides 346 and 5171), was further defined by construction of an extensive set of deletions within this region and measurement of their effects on (a) viral DNA replication, (b) virus multiplication and the ability to complement early and late mutations, (c) transformation of rat cells, (d) large T antigen formation, and (e) the location of the 5' ends of early mRNAs. One set of mutations is represented by deletions that begin at the HpaII site and extend unidirectionally for varying lengths toward the BglI site at ori. A second set of mutants contains deletions that start at ori and extend unidirectionally for varying lengths towards the HpaII site. A third set of mutants, with deletions or duplications of various lengths and boundaries, lie between the HpaII and BglI sites. Our studies indicate the following. (a) Ori, the sequence needed for initiating SV40 DNA replication, extends from the sequences needed for initiating SV40 DNA replication, extends from the sequences needed to bind T antigen to the palindrome in site II to nucleotide 34, the late region edge of the AT block. Flanking sequences adjacent to the AT block facilitate DNA replication. (b) The SV40 early region promoter comprises two functionally distinct nucleotide sequence elements. One is flanked by nucleotides 5231 and 107, and contains the RNA initiation sites at nucleotides 5231-5237, a positioning element resembling the TATAAATA consensus sequence about 20-25 nucleotides upstream, and an RNA polymerase II recognition sequence contributed by short GC-rich sequences clustered between nucleotides 35 and 107; we refer to this as the RNA polymerase II interaction site. The second distinct sequence element is contained within each of two 72-bp segments located between nucleotides 107 and 250; the behavior of this element suggests that it may influence the accessibility of RNA polymerase II for the interaction site or the efficiency of RNA chain initiation. Large T antigen binding sites I, II, and III overlap with the putative RNA polymerase II interaction site; since large T antigen does not prevent elongation of RNA transcripts initiated upstream, T antigen probably represses early region expression by preventing RNA polymerase II binding to the promoter.

Light-stimulated transcription of genes for two chloroplast polypeptides in isolated pea leaf nuclei.

Abstract: Nuclei isolated from both light-grown and dark-grown leaves of Pisum sativum by Percoll density gradient centrifugation incorporate labelled UTP into RNA when supplemented with the other three nucleoside triphosphates. The RNA is heterodisperse, with transcripts up to at least 25S in size. Among these transcripts are sequences hybridizing to cloned DNA probes for wheat rRNA and two abundant chloroplast polypeptides of Pisum, viz. the small subunit of ribulose bisphosphate carboxylase and a polypeptide of the light-harvesting chlorophyll a/b binding complex. Transcription of small subunit and light-harvesting complex sequences is greater (18-fold and 9-fold, respectively) in nuclei from light-grown leaves than in nuclei from dark-grown leaves. Transcription of ribosomal genes, by contrast, is only doubled by growth in the light. Small subunit and light-harvesting complex sequences transcribed in dark-grown nuclei are not degraded in a 120 min chase. These results suggest that the stimulation of accumulation of small subunit and light-harvesting complex mRNAs by exposure of Pisum seedlings to light is mediated by an increase in transcription rather than by a decrease in RNA degradation.

Control of rRNA and tRNA syntheses in Escherichia coli by guanosine tetraphosphate.

Abstract: The expression of stable RNA (rRNA and tRNA) genes and the concentration of guanosine tetraphosphate (ppGpp) were measured in an isogenic pair of relA+ and relA derivatives of Escherichia coli B/r. The cells were either growing exponentially at different rates or subject to amino acid starvation when they were measured. The specific stable RNA gene activity (rs/rt, the rate of rRNA and tRNA synthesis relative to the total instantaneous rate of RNA synthesis) was found to decrease from 1.0 at a ppGpp concentration of 0 (extrapolated value) to 0.24 at saturating concentrations of ppGpp (above 100 pmoles per optical density at 460 nm unit of cell mass). The same relationship between the rs/rt ratio and ppGpp concentration was obtained independent of the physiological state of the bacteria (i.e., independent of the growth rate or of amino acid starvation) and independent of the relA allele. It can be concluded that ppGpp is an effector for stable RNA gene control and that stable RNA genes are not controlled by factors other than the ppGpp-mediated system. The results were shown to be qualitatively and quantitatively consistent with data on in vitro rRNA gene control by ppGpp, and they were interpreted in the light of reported ideas derived from those in vitro experiments.