Nucleic Acids Research

, Van Knippenberg,, P.H.;, Van Kimmenade, J.M.A.;Heus,, H.A.

doi: 10.1093/nar/12.6.2595pmid: 6709501

Abstract The strongest conserved part of the RNA of small ribosomal subunits is probably located near the 3′ end. This paper reviews the primary and secondary structures of some 40 sequenced 3′ termini and tries to classify these structures according to common features and differences The regions under consideration contain at the 5′ side an almost universal, supposedly single-stranded stretch of nucleotides with the sequence --AAGUCGUAACAAGGU--. This is followed by a stem-loop structure. The stem always contains 9 basepairs (including U-G pairs) and no mismatches or bulged nucleotides. The loop of the hairpin is either (m 2 ) GGm26 Am26 A (bacteria, chloroplasts and mitochondria) or UGm26 Am26 A (cytoplasm). The hairpin is, in most cases, followed at the 3′side by --GGAUCA--. Next to it bacteria and chloroplasts contain the so-called “Shine and Dalgarno” sequence --CCUCC-- The stem region of the hairpin contains a conserved U-GA-U junction. The two basepairs between this junction and the loop are either of type 1 (G-CG-C) or type 2 C-GC-G . Classification according to type links certain bacteria with mitochondria of yeast and plants and others with chloroplasts and with animal mitochondria This content is only available as a PDF. © 1984 IRL Press Ltd.

Travers, Andrew, A.

doi: 10.1093/nar/12.6.2605pmid: 6369249

Abstract E.coli promoters which are coordinately regulated in response to amino acid limitation contain conserved nucleotide sequences immediately 3′ to −10 region. These sequences contain predominantly either GC or AT residues depending on whether the response is respectively negative or positive. Certain classes of promoters also contain conserved sequences upstream of the primary promoter. In tRNA genes these sequences could act as a secondary polymerase binding site. This content is only available as a PDF. © 1984 IRL Press Ltd.

Schmid,, Kurt;Thomm,, Michael;Laminet,, Axel;Laue, Frank, G.;Kessler,, Christoph;Stetter, Karl, O.;Schmitt,, Rüdiger

doi: 10.1093/nar/12.6.2619pmid: 6324124

Abstract Three type II restriction endonucleases, MaeI, MaeII and MaeIII, with novel site specificities have been isolated and purified from the archaebacterium Methanococcus aeolicus PL-15/H. The recognition sequences of these enzymes are C↓T A G                 (MaeI)                   A↓C G T                  (MaeII)                  ↓G T N A C            (MaeIII)                 with the sites of cleavage as indicated by the arrows. The sequences were confirmed by restriction and computer analyses on sequenced DNA's of plasmid pBR322, bacteriophages λ and ØX174 and virus SV 4O. This content is only available as a PDF. © 1984 IRL Press Ltd.

Vaquero,, Catherine;Sanceau,, Josiane;Sondermeyer,, Paul;Falcoff,, Rébéca

doi: 10.1093/nar/12.6.2629pmid: 6200833

Abstract Exposure of human lymphocytes to a mitogen induces the appearance of newly synthesized RNAs and proteins. This study describes the changes in overall synthesis as measured by pulse labelling of PHA treated lymphocytes as well as a qualitative analysis of the protein synthetic patterns “in vivo” and “in vitro”. Both the levels of RNA and protein synthesis increase drastically in PHA stimulated cells, while cultures incubated without mitogen remained at background levels. The low translational activity in control cells is not due to the absence of messengers since the extracted RNAs clearly direct the synthesis of high molecular weight proteins when translated “in vitro”. A number of qualitative differences are seen in the “in vitro” translation of RNA extracted from induced and non-induced lymphocytes, although the apparent protein synthetic pattern “in vivo” remains identical. The secretion of IFN-γ is one of the newly expressed functions in stimulated lymphocytes and therefore has been studied more detailed in a time-course of the messenger level compared to the secreted activity of the medium. A specific probe was used to quantitate in Northern blot's the accumulation of mRNA coding for IFN- γ. This content is only available as a PDF. © 1984 IRL Press Ltd.

Panayotatos,, Nikos

doi: 10.1093/nar/12.6.2641pmid: 6369250

Abstract ColE1 derivative plasmids were constructed in which the natural promoter that primes replication or, in addition, the region coding for the RNA I control element had been deleted. In all of these molecules priming of the origin was effected by read-through transcription from constitutive or inducible ( lac UV5) promoters inserted farther upstream. In the latter case, regulation of lac repressor activity with IPTG resulted in controlled plasmid levels invivo . These results indicated that, at least in the absence of other control elements, regulation of the priming promoter was sufficient to control DNA replication and determine plasmid copy number. This content is only available as a PDF. © 1984 IRL Press Ltd.

Atmadja,, Johannes;Brimacombe,, Richard;Maden, B. Edward, H.

doi: 10.1093/nar/12.6.2649pmid: 6424099

Abstract 18S ribosomal RNA from X . laevis was subjected to partial digestion with ribonucleases A or T1 under a variety of conditions, and base-paired fragments were isolated. Sequence analysis of the fragments enabled five base-paired secondary structural elements of the 18S RNA to be established. Four of these elements (covering bases 221–256, 713–757, 1494–1555 and 1669–1779) confirm our previous secondary structure predictions, whereas the fifth (comprising bases 1103–1125) represents a phylogenetically conserved “switch” structure, which can also form in prokaryotic 16S RNA. The results are incorporated into a refined model of the 18S RNA secondary structure, which also includes the locations of the many methyl groups in X.laevis 18S RNA. In general the methyl groups occur in non-helical regions, at hairpin loop ends, or at helix boundaries and imperfections. One large cluster of 2′-O-methyl groups occurs in a region of complicated secondary structure in the 5′-one third of the molecule This content is only available as a PDF. Author notes * Present address: Department of Biochemistry, University of Liverpool, PO Box 147, Liverpool L69 3BX, UK © 1984 IRL Press Ltd.

Sun,, Lily;Paulson,, K.Eric;Schmid, Carl, W.;Kadyk,, Lisa;Leinwand,, Leslie

doi: 10.1093/nar/12.6.2669pmid: 6546796

Abstract Randomly selected human genomic clones have been surveyed for the presence of non-Alu family interspersed repeats. Four such families of repeats have been isolated and characterized with respect to repetition frequency, interspersion, base sequence, sequence divergence, in vitro RNA polymerase III transcription, elongation of transcripts in isolated nuclei, and in vivo transcription. The two most abundant of the four families of repeats correspond to previously reported families of repeats, namely the Kpn I family and poly (CA). We conclude that most of the highly repetitive (> 50,000 copies) human interspersed repeats have already been identified. Two lower abundance repeats families are also described here The abundance with which each of these families is represented in nuclear RNA qualitatively corresponds to their genomic reiteration frequencies. Further, the complementary strands of each repeat family are approximately symmetrically transcribed. The abundance of these repeats in cytoplasmic RNA is qualitatively less than in nuclear RNA. The bulk of the in vivo transcriptional activity of these repeats thus appears to be nonspecific read through from other promoters This content is only available as a PDF. © 1984 IRL Press Ltd.

Spadafora,, Corrado;Crippa,, Marco

doi: 10.1093/nar/12.6.2691pmid: 6709502

Abstract Micrococcal nuclease digestion was used as a tool to study the organization of the ribosomal chromatin in liver, blood and embryo cells of X. laevis . It was found that in liver and blood cells, ribosomal DNA is efficiently protected from nuclease attack in comparison to bulk chromatin. Although ribosomal chromatin is fragmented in a typical nucleosomal pattern, a considerable portion of ribosomal DNA retains a high molecular weight even after extensive digestion. A greater accessibility of the coding region in comparison to the non-coding spacer was found. In embryos, when ribosomal DNA is fully transcribed, these genes are even more highly protected than in adult tissues: in fact, the nucleosomal ladder can hardly be detected and rDNA is preserved in high molecular weight. Treatment of chromatin with 0.8 M NaCl abolishes the specific resistance of the ribosomal chromatin to digestion. The ribosomal chromatin, particularly in its active state, seems to be therefore tightly complexed with chromosomal proteins which protect its DNA from nuclease degradation This content is only available as a PDF. © 1984 IRL Press Ltd.

Haumont,, Etienne;Fournier,, Michel;Henau, Suzy, de;Grosjean,, Henri

doi: 10.1093/nar/12.6.2705pmid: 6369251

Abstract We have investigated the specificity of the tRNA modifying enzyme that transforms the adenosine at position 34 (wobble position) into inosine in the anticodon of several tRNAs. For this purpose, we have constructed sixteen recombinants of yeast tRNA Asp harboring an AXY anticodon (where X or Y was one of the four nucleotides A, G, C or U). This was done by enzymatic manipulations in vitro of the yeast tRNA Asp , involving specific hydrolysis with S1-nuclease and RNAase A, phosphorylation with T4-polynucleotide kinase and ligation with T4-RNA ligase: it allowed us to replace the normal anticodon GUC by trinucleotides AXY and to introduce simultaneously a 32 P-labelled phosphate group between the uridine at position 33 and the newly inserted adenosine at position 34. Each of these 32 P-labelled AXY “anticodon-substituted” yeast tRNA Asp were microinjected into the cytoplasm of Xenopus laevis oocytes and assayed for their capacity to act as substrates for the A 34 to I 34 transforming enzyme. Our results indicate that: 1/A34 in yeast tRNA Asp harboring the arginine anticodon ACG or an AXY anticodon with a purine at position 35 but with A, G or C but not U at position 36 were efficiently modified into I 34 ; 2/ all yeast tRNA Asp harboring an AXY anticodon with a pyrimidine at position 35 (except ACG) or uridine at position 36 were not modified at all. This demonstrates a strong dependence on the anticodon sequence for the A 3 4 to I 34 transformation in yeast tRNA Asp by the putative cytoplasmic adenosine deaminase of Xenopus laevis oocytes. This content is only available as a PDF. Author notes * Present address : Institut de Biologie Cellulaire et de Neurochimie. 1, rue Camille Saint-Saëns, F - 33077 Bordeaux, France. ** to whom reprint request should be sent. © 1984 IRL Press Ltd.

Wiid, Ian, J.F.;Boyd, Charles, D.;Bester, Andre, J.;, Van Helden, Paul D.

doi: 10.1093/nar/12.6.2717pmid: 6200834

Abstract One of the changes accompanying skeletal muscle cell (myoblast) fusion is a dramatic increase in synthesis of muscle specific proteins, one of which is myosin. The underlying mechanism for this burst in synthesis is not yet understood but may occur by two mechanisms: (a) gradual storage of mRNA and translational control as found by others or (b) gene activation and rapid synthesis of mRNA for immediate translation. In this paper we show that the myosin gene changes its organization such that postfusion skeletal muscle cells show an increased susceptibility to DNase I, a recognized probe for gene activation. We also show that this change accompanies an increase in rate of transcription and an increased cell content of myosin heavy chain mRNA. This work shows that transcriptional control is an important mechanism during muscle cell development in addition to the translational control shown by other workers This content is only available as a PDF. © 1984 IRL Press Ltd.