Nucleic Acids Research

Brown, John, W.S.

doi: 10.1093/nar/14.24.9549pmid: 3808952

Abstract Splice junction and possible branch point sequences have been collected from 177 plant introns. Consensus sequences for the 5' and 3' splice junctions and for possible branch points have been derived. The splice junction consensus sequences were virtually identical to those of animal introns except that the polypyrimidine stretch at the 3' splice junction was less pronounced in the plant introns. A search for possible branch points with sequences related to the yeast, vertebrate and fungal consensus sequences revealed a similar sequence in plant introns. This content is only available as a PDF. © IRL Press Limited, Oxford, England

Najarian,, Diana;Shu, Hsiao, Hsueh;Martin, Nancy, C.

doi: 10.1093/nar/14.24.9561pmid: 3543841

Abstract Expression of the mitochondrial tRNA Asp gene of Saccharomyces cerevisiae has been examined in five syn− mutants known to affect tRNA Asp function, and in a rho− mutant which accumulates precursor tRNAs. By comparison of wild-type versus mutant DNA sequence, the lesion in each syn− mutant has been identified as a single base change within the mitochondrial tRNAAsp structural gene. The mutant tRNA Asp genes are transcribed, and the transcripts can be processed to mature 45-size tRNA Asp. The steady-state level of each mutant tRNA Asp is lower than that of wild-type tRNA Asp. The RNA from two of the syn− mutants contained a second, slow-migrating from of mitochondrial tRNA Asp which is correctly processes at the 5' end. We conclude that the lesions in the syn− mitochondrial tRNA genes block neither transcription of these genes, nor 5' end processing of the transcripts. The effects of each point mutation must be manifested at the level of 3' end processing, or at a functional level. This content is only available as a PDF. © IRL Press Limited, Oxford, England

Tomkinson, Alan, E.;Linn,, Stuart

doi: 10.1093/nar/14.24.9579pmid: 3027656

Abstract A nuclease was purified from mitochondria of the mouse plasmacytoma cell line, MCP-11 which acts on single-stranded DNA endonucleolytically and appears to have no activity upon native DNA. It degrades unordered RNA somewhat more effectively than it does DNA. The enzyme activity and the major detectable polypeptide migrate to a position corresponding to an Mr of 37, 400 on denaturing polyacrylamide gels; in its native from the activity has an S value of 4.7, which corresponds to a molecular weight of roughly 73, 000. The singlestrand DNase activity has a pH optimum near 7.5, requires a divalent cation and is inhibited by EDTA, phosphate, KC1 and NaCl. The enzyme is remarkably similar to fungal mitochondrial enzymes whose absence in various mutants correlates with defective DNA repair and recombination. It reacts weakly with antibody to a form of such an enzyme from Neurospora crassa. This content is only available as a PDF. © IRL Press Limited, Oxford, England

Piette,, Jacques;Yaniv,, Moshe

doi: 10.1093/nar/14.24.9595pmid: 3027657

Abstract The fine contacts of a mouse nuclear factor, called PEB1. with the B enhancer of polyoma virus were analyzed. It protects against DNasel attack a region of about 50 base pairs that can be divided in two domains. The first contains a GC-rich palindrome and the homology to the SV40 enhancer. The second is homologous to a sequence in the immunoglobulin (Ig) heavy chain gene enhancer. Methylation interference and protection experiments reveal strong specific contacts only with a purine rich track on the late coding strand of the early proximal part of the palindrome. Deletion analysis show that the minimal sequences necessary for binding include only the first domain. The Ig homology contributes only weakly to the binding. The minimal core is similar to the core of the B enhancer defined in vivo. The interactions we observe here are reminiscent of those of TFIIIA positive transcription factor and the SSRNA gene of xenopus. This content is only available as a PDF. © IRL Press Limited, Oxford, England

Steger,, G.;Tabler,, M.;Brūggemann,, W.;Colpan,, M.;Klotz,, G.;Sänger,, H.-L.;Riesner,, D.

doi: 10.1093/nar/14.24.9613pmid: 3808953

Abstract The structure and structural transitions of transcripts of cloned oligomeric viroid were studied in physico-chemical experiments and stability calculations. Transcripts of (+) and (−) polarity, from unit up to sixfold length, were synthesized from DNA clones of the potato spindle tuber viroid (PSTV) with the SP6 transcription system. Their structural properties were investigated by optical denaturation curves, high performance liquid chromato-graphy (HPLC), electron microscopy, sedimentation-diffusion equilibrium and velocity sedimentation. Secondary structures of the RNAs and theoretical denaturation curves were calculated using an energy optimization program. The secondary structure of lowest free energy for unit length and oligomeric transcripts is a rod-like structure similar to that of the mature circular viroids. When this structure is used as a model for calculations, there is a large degree of agreement between the theoretical and the experimental denaturation curves. At high temperatures, however, (+) strand transcripts exhibited a transition which was more stable than expected from the calculations or than was known from curves of mature viroids. This transition arises from a rearrangement of the central conserved region of viroids to a helical region of 28 stable base pairs either intermolecularly leading to bimolecular complexes, or intramolecularly giving rise to a branched secondary structure. The rearrangement could be detected by electron microscopy, HPLC, and analytical ultracentrifugation. The helical region serves to divide up the oligomeric (+) strand into structural units which may be recognized by cleavage and ligation enzymes which process the oligomeric intermediates to circular mature viroids. This content is only available as a PDF. © IRL Press Limited, Oxford, England

Petersen, Jens, G.Litske;Holmberg,, Steen

doi: 10.1093/nar/14.24.9631pmid: 3027658

Abstract The nucleotide sequence of the yeast ILV5gene, which codes for the branched-chain amlno acid biosynthesis enzyme acetohydroxyacid reductoiso-merase, has been determined. The ILV5coding region is 1, 185 nucleotides, corresponding to a polypeptide with a molecular weight of 44, 280. Transcription of the ILV5mRNA initiates at position -81 upstream from the ATG translation start codon and terminates between 218 and 222 bases downstream from the stop codon. Consensus sequences have been identified for initiation and termination of transcription, and for general control of amino acid biosynthesis, as well as repression by leucine. The ILV5gene is regulated slightly by general amino acid control. Codon usage of the ILV5gene has the strong bias observed in yeast genes that are highly expressed. In agreement with this, the reductoisomerase monomer, with an apparent molecular weight of 40, 000, has been identified in an SDS polyacrylamide gel pattern of total soluble yeast proteins as a gene dosage dependent band. This content is only available as a PDF. © IRL Press Limited, Oxford, England

Mechti,, N.;Piechaczyk,, M.;Blanchard,, J-M.;Marty,, L.;Bonnieu,, A.;Jeanteur,, Ph.;Lebleu,, B.

doi: 10.1093/nar/14.24.9653pmid: 3468485

Abstract C-myc RNA rapidly decreases to barely detectable levels in Friend erythroleukemia cells induced to differentiate upon the addition of dimethylsul foxide. We show here that c-myc gene is down-regulated both at the transcriptional level presumably by a block in the elongation of primary transcripts and at the post-transcriptional level by an increase in the degradation of its mRNA. This content is only available as a PDF. © IRL Press Limited, Oxford, England

Nakamaye, Kay, L.;Eckstein,, Fritz

doi: 10.1093/nar/14.24.9679pmid: 3027659

Abstract M13 RF IV DNA where phosphorothioate groups are incorporated at restriction endonuclease Nci I recognition sites in the (−) strand is efficiently nicked by the action of this enzyme. Incubation of such nicked DNA with exonuclease III produces gapped DNA. The gap can be filled by reaction with deoxynuclease side triphosphates and DNA polymerase I. When this sequence of reactions is performed with DNA containing a mismatch oligonucleotide primer in the (−)strand mutational frequencies of 70–90 % can be obtained upon transformation. The general nature of this methodology has been further shown to be applicable to other restriction enzymes such as Hind II, Pst I and Fsp I. The mutational frequency obtained using these enymes is between 40–80% mainly because of less efficient nicking and gapping. Studies on inhibition of Nci I cleavage show that in addition to a phosphorothioate group at the position of cleavage an additional group in the 5'-neighbouring position is necessary for complete inhibition. This content is only available as a PDF. Author notes 1Present address: Department of Chemistry, Gonzaga University, Spokane, WA 99258, USA © IRL Press Limited, Oxford, England

Caughey,, P.A.;, de Feyter, R.;Lane,, H.E.D.

doi: 10.1093/nar/14.24.9699pmid: 3027660

Abstract The C (PifC) protein of miniF represses transcription of its own gene by binding to the Pif operator (pifO); it is also needed for replication initiated from the miniF primary origin (ori-1). We have determined the nucleotide sequence of the C gene. The gene has been inserted into an expression vector under Ptrp control where it is expressed at high levels. The C protein has been purified from cells carrying the Ptxp-C plasmid, and a preliminary study of C protein-DNA binding properties has Been carried out. C protein binds strongly to PifO, and weakly to sequences in the ori-1 region. This content is only available as a PDF. © IRL Press Limited, Oxford, England

Buzayan, Jamal, M.;Hampel,, Arnold;Bruening,, George

doi: 10.1093/nar/14.24.9729pmid: 2433680

Abstract The satellite RNA of tobacco ringspot virus (STobRV RNA) replicates and becomes encapsidated in association with tobacco ringspot virus. Previous results show that the infected tissue produces multimeric STobRV RNAs of both polarities. RNA that is complementary to encapsidated STobRV RNA, designated as having the (−) polarity, cleaves autolytically at a specific ApG bond. Purified autolysis products spontaneously join in a non-enyzymic reaction. We report characteristics of this RNA ligation reaction: the terminal groups that react, the type of bond in the newly formed junction and the nucleotide sequence of the joined RNA. The nucleotide sequence of the ligated RNA shows that joining of the reacting RNAs restored an ApG bond. The junction ApG has a 3'-to-5' phosphodiester bond. Thus the net ligation reaction of STobRV (−)RNA is the precise reversal of autolysis. We discuss this new type of RNA ligation reaction and its implications for the formation of multimeric STobRV RNAs during replication. This content is only available as a PDF. Author notes *Present address: Departments of Biological Sciences and Chemistry. Northern Illinois University, DeKalb, IL 60115, USA © IRL Press Limited, Oxford, England