Nucleic Acids Research

Vincent,, Alain

doi: 10.1093/nar/14.11.4385pmid: 3086841

Abstract Differential regulation of gene expression , in a precise temporal and spatial pattern during development, is thought to be partly mediated by site specific DNA binding proteins which promote a selective activation of gene transcription (I). From studies on Xenopas TFIIIA, a factor selectively required for transcription of 5 S ribosomal RNA genes. Miller et al . (2) proposed a novel structural model of interaction between DNA and DNA binding protein. The striking homology of TFIIIA with several recently sequenced Drosophil and yeast gene products suggests that multiple regulatory proteins may have evolved from a small ancestral DNA binding protein domain and that the characteristic features of TFIIIA and TFIIIA-5S DNA interactions may be of general significance. This content is only available as a PDF. © IRL Press Limited, Oxford, England

Watanabe,, Kunihiko;Yamano,, Yoshinori;Murata,, Kousaku;Kimura,, Akira

doi: 10.1093/nar/14.11.4393pmid: 2872655

Abstract The nudeotide sequence of the gsh I gene for γ- glutamylcysteine synthetase(GSH I) of Escherichia coli B has been determined. The gsh I structural gene contains 1557 bases in length and predicted a ploypeptide of 518 amino acids with a calculated molecular weight of 58,251. The value is in good agreement with that obtained from gel filtration and SDS/PAGE of GSH I. The initiation codon 5 bp downstream of putative Shine- Dalgarno sequence was an unusual TTG, which encoded methionine. For transcription, two sets of consensus promoter signals(−10 and −35 regions) overlapping each other were identified. The terminator signal shows the favored stem-loop structure with an adequate free energy △G = −22.80 kcal/mol. This content is only available as a PDF. © IRL Press Limited, Oxford, England

Snell, R., G.;Willrins, R., J.

doi: 10.1093/nar/14.11.4401pmid: 3520483

Abstract Modifications have been made to standard pulse field gel eledrophoresis (PFGE) systems to enable very large DNA molecules to be resolved. The single most important modification was to elevate the temperature of ekctrophoresls to 35°C. This enabled the largest SaccharomTces cerevlslat chromosome to be reprodbcibly resolved. More impressively, it enabled the DNA of Candida albkans to be clearly resolved Into six bands, a feat which was very difficult at lower temperatures. Even so, optimal resolution could only be obtained by carefully adjusting field voltages and switching times. The DNA from the two largest C. albkans chromosomes, which was estimated to be at least 5–10Mbp in size, ran somewhat anomalously, giving fuzzy bands which did not migrate in the direction of the average electric field. That the highestmolecnlar weight band was a distinct chromosome was demonstrated by specific hybridisation to the C. albkans ADE2 gene probe. With further fine tuning, the PFGE system described here should be capable of resolving DNA from the smallest human chromosomes. This content is only available as a PDF. © IRL Press Limited, Oxford, England

Fukunaga,, Rikiro;Matsuyama,, Masako;Okamura,, Hamki;Nagata,, Kumiko;Nagata,, Shigekazu;Sokawa,, Yoshihiro

doi: 10.1093/nar/14.11.4421pmid: 3086842

Abstract The relative levels of DNA methylation at CCGG sequences within and around the interferon-γ (IFN-γ) gene in normal human tissues and cell lines were examined by Southern blot analysis using isoschizomeric restriction enzymes, HpaII and MspI. On the test of normal tissues, the IFN-γ gene was under-methylated only in a small population of T lymphocyte, whereas the gene was fully methylated in T cell-depleted lymphocytes and uterus cells. In TCL-Fuj cell line which is a T cell line producing a high level of IFN-γ spontaneously, the IFN-γ gene was undermethylated. Moreover, the extent of DNA methylation was inversely correlated to the level of expression of the IFN-γ gene in several T cell lines including sublines derived from TCL-Fuj cells. However, partial or complete unmethylation at the CCGG sites of IFN-γ gene was observed in a promyelocytic leukemia cell line and two epithelial cell lines that fail to produce IFN-γ irrespective of induction. These results suggest that undermethy-lation of IFN-γ gene is necessary but not sufficient for its efficient expression. This content is only available as a PDF. © IRL Press Limited, Oxford, England

Finch, Paul, W.;Wilson, Rosemary, E.;Brown,, Kate;Hickson, Ian, D.;Tomkinson, Alan, E.;Emmerson, Peter, T.

doi: 10.1093/nar/14.11.4437pmid: 3520484

Abstract The nuoleotide sequenoe of a 6,000 bp region of the E. coli ohromosome that inoludea the 3' end of the coding region for the thyA gene and the entire recC gene has been determined. The proposed coding region for the RecC protein is 3369 nucleotides long, which would encode a polypeptide consisting of 1122 ami no acids with a calculated moleoular mass of 129 kDa. Hung bean nuolease mapping of a recC specific transcript produced in vivo indioates that transcription of recC is initiated 80 bp upstream of the trans lational start point. A weak promoter sequenoe situated 5' to the transcription initiation point has been identified. In the 1953 bp thyA-recC intergenic region there are three open reading frames that would code for polypeptides of moleoular mass 30 kDa, 13.5 kDa and 12 kDa, respectively. Although the first and third of these open reading frames are preoeded by possible ribosome binding sites, no obvious promoter sequences oould be identified. Moreover, transorlpts for these reading frames could not be detected. This content is only available as a PDF. Author notes * Present address: Department of Biochemistry, University of California, Berkeley, CA 94720, USA © IRL Press Limited, Oxford, England

Thomas, Christopher, M.;Smith, Christopher, A.

doi: 10.1093/nar/14.11.4453pmid: 3520485

Abstract We report the nucleotide sequence of the trfB region of broad host range plasmid RK2. This region encodes the following loci: trfB, identical to korA and korD, which encodes a key transcriptional repressor of certain RK2 operona; incC, which appears to be involved in plasoid maintenance, possibly through post-tranacriptional regulation of trfA product levels; the start of korB, which encodes a second transcriptional repressor of operons involved in stable inheritance of RK2. These loci are expressed as part of the trfB operon. In combination with deletion analysis, transcriptional and translation fusions and ‘maxicell’ analysis of polypeptides, the DNA sequence allows a number of conclusions to be drawn. First, the korB ORF start codon overlaps the IncC ORP stop codon, suggesting the possibility of translational coupling between these two genes. Second, the trfB ORF lies entirely within the first third of the incC ORF using a different phase. Third, the incC ORF appears to contain a second transcriptional start whose function appears to be coupled to translation of the trfB ORF. Analysis of codon usage in the region of overlap between IncC and trfB suggests that the IncC gene may have evolved before the trfB gene. Determination of the DNA sequence of a mutant in which the product of trfB is rendered defective for transcriptional repression reveals an amino acid alteration within a region of this polypeptide which exhibits homology to the αhelix-turn-αhelix motif characteristic of many DNA binding proteins, and which is probably responsible for recognition of the trfB operator by this protein. This content is only available as a PDF. © IRL Press Limited, Oxford, England

Chen, X., J.;Saliola,, M.;Falcone,, C.;Bianchi, M., M;Fukuhara,, H.

doi: 10.1093/nar/14.11.4471pmid: 3520486

Abstract pKDl is the only circular plasmid known in the genus Kluyveromyces. Nucleotide sequence analysis has revealed that this 4757 base-pairs long plasmid contained three major open reading frames, A, B, and C, and a pair of inverted repeats of 346 base-pairs. The molecule exists in two isomeric forms generated by internal recombination at these repeats. The functional organization of pKDl genome appears to be quite analogous to that of the 2u plasmid of Saccharomyces cerevisiae. There is however little homology of sequences between these plasmids, except that the gene A has a dispersed but significant homology with the FLP recombinase gene of the 2u plasmid. S.cerevisiae cells can be transformed by derivatives of pKDl carrying URA3 gene as a selection marker. This content is only available as a PDF. © IRL Press Limited, Oxford, England

Young, Marian, F.;Bolander, Mark, E.;Day, Agnes, A.;Ramis, Camille, I.;Robey, Pamela, Gehron;Yamadav,, Yoshihiko;Termine, John, D.

doi: 10.1093/nar/14.11.4483pmid: 3012473

Abstract Overlapping cDNA clones encoding bovine osteonectin were isolated from a γgtll expression library constructed from bovine bone cell mRNA. The longest clone, γOn 17 (insert size 2.0 kb) was studied in detail. The clone was shown to encode osteonectin by hybrid select translation experiments and by DNA sequence analysis. Northern analysis of bone cell RNA showed the length of the osteonectin mRNA to be 2.0 kb. Osteonectin message was found in bone but not in soft tissue (liver and brain) preparations consistent with the distribution of the protein in these tissues. On the other hand, osteonectin message was observed in tendon, a tissue in which little or no osteonectin protein is found in vivo. Hybridization of osteonectin cDNA was detected in cells from a number of species including human, rat, mouse and chick. The level of osteonectin mRNA was drastically decreased in chick embryo fibroblasts transformed by Rous sarcoma virus. This content is only available as a PDF. © IRL Press Limited, Oxford, England

Myers, Jeanne, C.;Brinker, Jane, M.;Kefalides, Nicholas, A.;Rosenbloom,, Joel;Wang,, Sho-Ya;Gudas, Lorraine, J.

doi: 10.1093/nar/14.11.4499pmid: 3714485

Abstract The DNA sequence corresponding to the 1.3 kb 3' untranslated region of the 6.5 kb human procoilagen α1(IV) mRNA was determined and compared with the mouse sequence obtained from 3' cDNA and genomic clones overlapping the reported 5' half (Oberbaumer et al., 1985, Eur. J. Biochem. 147:217). Although four AAUAAA hexanucleotides are found In the human and seven 1n the mouse RNAs, Northern blot hybridization showed almost exclusive utilization of the most 3' sequence, in contrast to the pattern seen when using αl(I), α2(I), αl(III) and α2(V) procollagen probes. Moreover, the ninety nucleotides 5' to the poly A tall 1n the major αl(IV) mRNAs exhibit a much greater degree of interspecies homology than those encompassing the other three shared AAUAAA recognition signals. Further examination of this highly conserved area revealed the presence of two “consensus sequences” found 1n the 3' noncoding region of a number of RNA polymerase II transcribed genes (Mattaj and Zeller, 1983, Embo J. 2:1883) and, unexpectedly, some similarity with the nucleotides 5' to the poly A attachment signals 1n other procollagen mRNAs. This content is only available as a PDF. © IRL Press Limited, Oxford, England

Berthier,, F.;Renaud,, M.;Alziari,, S.;Durand,, R.

doi: 10.1093/nar/14.11.4519pmid: 3086843

Abstract Drosophila melanogoster mitochondrial DNA (mtDNA) is closely related to the mammalian and amphibian mtDNA except for gene organization. In Drosophila, genes are distributed in clusters alternatively coded on each strand. Besides the eleven major foreseeable transcripts previously described (MERTEN and PARDUE, 1981, J. Mol. Biol, 153, 1–21), we have characterized two poly A + transcripts, one major and one minor which could correspond respectively to the ND3 and ND6 reading frames, and 27 poly A+ minor transcripts (0.2 to < 3.2 Kb) which are distributed along the mtDNA except In the rRNAs, NO 1 and A + T rich regions . The mapping end length of 25 of these transcripts strongly suggest a precursor role. They would be processed at the level of tRNA or tRNA-like sequences. Most of them are transcribed from the template strand of each gene cluster and their distribution is in agreement with the hypothesis of several transcription origins and terminations located near the extremities of each gene cluster. Quantitatively our results show a large variation In each presumptive mature transcript compared to the other, even in a given gene cluster, suggesting a specific degradation of some of the mature transcripts. This content is only available as a PDF. © IRL Press Limited, Oxford, England