Extensive RNA editing of U to C in addition to C to U substitution in the rbcL transcripts of hornwort chloroplasts and the origin of RNA editing in green plants.


:We cloned and sequenced a portion of chloroplast DNA from the hornwort Anthoceros formosae. A nucleotide sequence of 7556 bp contained structures similar to those of ndhK, ndhC, trnV, trnM, atpE, atpB, rbcL, trnR and accD. The arrangement of these was the same as that of other chloroplast DNA. However, two nonsense codons were located within the putative coding region of rbcL, although they were used as putative termination codons of the genes. RNA was extensively edited in the transcripts of rbcL when cDNA sequences were analyzed. The unusual nonsense codons of TGA and TAA became CGA and CAA respectively. These are examples of U to C type RNA editing, which was never been found before in chloroplast mRNA. In general, 13 Cs of genomic DNA were found as Ts in the cDNA sequence and seven Ts were found as Cs. This is the first finding of RNA editing on the transcripts of rbcL and also in bryophytes. This event had been thought to arise in land plants after the split of bryophytes. The origin of RNA editing is discussed in relation to the landing of green plants.


Nucleic Acids Res


Nucleic acids research


Yoshinaga K,Iinuma H,Masuzawa T,Uedal K




Has Abstract


1996-03-15 00:00:00














  • Transcription and processing of the rodent ID repeat family in germline and somatic cells.

    abstract::ID elements comprise a rodent SINE (short interspersed DNA repetitive element) family that has amplified by retroposition of a few master genes. In order to understand the important factors of SINE amplification, we investigated the transcription of rat ID elements. Three different size classes of ID transcripts, BC1,...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kim J,Kass DH,Deininger PL

    更新日期:1995-06-25 00:00:00

  • Binding and repair of O6-ethylguanine in double-stranded oligodeoxynucleotides by recombinant human O6-alkylguanine-DNA alkyltransferase do not exhibit significant dependence on sequence context.

    abstract::Double-stranded (ds) oligodeoxynucleotides (29mers) containing an O6-ethylguanine (O6-EtGua) flanked 5' and 3' by different bases (5'..TGT..3'; 5'..CGG..3', 5'..GGT..3'; 5'..GGG..3'; 5'..GGA..3') were synthesized to investigate the binding and repair characteristics of recombinant human O6-alkylguanine-DNA alkyltransf...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bender K,Federwisch M,Loggen U,Nehls P,Rajewsky MF

    更新日期:1996-06-01 00:00:00

  • Structure of HIV-1 TAR RNA in the absence of ligands reveals a novel conformation of the trinucleotide bulge.

    abstract::Efficient transcription from the human immunodeficiency virus (HIV) promoter depends on binding of the viral regulatory protein Tat to a cis-acting RNA regulatory element, TAR. Tat binds at a trinucleotide bulge located near the apex of the TAR stem-loop structure. An essential feature of Tat-TAR interaction is that t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Aboul-ela F,Karn J,Varani G

    更新日期:1996-10-15 00:00:00

  • Meiosis-specific yeast Hop1 protein promotes synapsis of double-stranded DNA helices via the formation of guanine quartets.

    abstract::In most eukaryotes, genetic exchange between paired homologs occurs in the context of a tripartite proteinaceous structure called the synaptonemal complex (SC). Genetic analyses have revealed that the genes encoding SC proteins are vital for meiotic chromosome pairing and recombination. However, the number, nature and...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Anuradha S,Muniyappa K

    更新日期:2004-04-28 00:00:00

  • DNA CTG triplet repeats involved in dynamic mutations of neurologically related gene sequences form stable duplexes.

    abstract::DNA triplet repeats, 5'-d(CTG)n and 5'-d(CAG)n, are present in genes which have been implicated in several neurodegenerative disorders. To investigate possible stable structures formed by these repeating sequences, we have examined d(CTG)n, d(CAG)n and d(CTG).d(CAG)n (n = 2 and 3) using NMR and UV optical spectroscopy...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Smith GK,Jie J,Fox GE,Gao X

    更新日期:1995-11-11 00:00:00

  • Involvement of a nuclear matrix association region in the regulation of the SPRR2A keratinocyte terminal differentiation marker.

    abstract::The small proline-rich protein genes ( SPRRs ) code for precursors of the cornified cell envelope, and are specifically expressed during keratinocyte terminal differentiation. The single intron of SPRR2A enhanced the activity of the SPRR2A promoter in transient transfection assays. This enhancement was position depend...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Fischer DF,van Drunen CM,Winkler GS,van de Putte P,Backendorf C

    更新日期:1998-12-01 00:00:00

  • Interaction of N-acetyl-phenylalanyl-tRNAPhe with 70S ribosomes of Escherichia coli.

    abstract::The interaction of N--Acetyl--Phe--tRNA Phe with 70 S ribosomes is a reversible process in the absence as well as in the presence of messenger. The equilibrium binding constants of these interactions were measured at different magnesium concentrations and temperatures and thermodynamical quantities computed. The entha...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Odinzov VB,Kirillov SV

    更新日期:1978-10-01 00:00:00

  • Structural analysis of an RNA molecule involved in replication control of plasmid R1.

    abstract::The replication control circuit of the FII plasmids R1, R100 and R6-5 involves a small untranslated RNA molecule of about 93 nucleotides. This RNA, designated CopA RNA in plasmid R1, acts in vivo as a post-transcriptional inhibitor of the expression of the RepA protein whose synthesis is required for each round of pla...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Gerhart E,Wagner H,Nordström K

    更新日期:1986-03-25 00:00:00

  • Experimental maps of DNA structure at nucleotide resolution distinguish intrinsic from protein-induced DNA deformations.

    abstract::Recognition of DNA by proteins depends on DNA sequence and structure. Often unanswered is whether the structure of naked DNA persists in a protein-DNA complex, or whether protein binding changes DNA shape. While X-ray structures of protein-DNA complexes are numerous, the structure of naked cognate DNA is seldom availa...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Azad RN,Zafiropoulos D,Ober D,Jiang Y,Chiu TP,Sagendorf JM,Rohs R,Tullius TD

    更新日期:2018-03-16 00:00:00

  • Molecular recognition of RhlB and RNase D in the Caulobacter crescentus RNA degradosome.

    abstract::The endoribonuclease RNase E is a key enzyme in RNA metabolism for many bacterial species. In Escherichia coli, RNase E contributes to the majority of RNA turnover and processing events, and the enzyme has been extensively characterized as the central component of the RNA degradosome assembly. A similar RNA degradosom...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Voss JE,Luisi BF,Hardwick SW

    更新日期:2014-12-01 00:00:00

  • PLSDB: a resource of complete bacterial plasmids.

    abstract::The study of bacterial isolates or communities requires the analysis of the therein included plasmids in order to provide an extensive characterization of the organisms. Plasmids harboring resistance and virulence factors are of especial interest as they contribute to the dissemination of antibiotic resistance. As the...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Galata V,Fehlmann T,Backes C,Keller A

    更新日期:2019-01-08 00:00:00

  • Conditional DNA repair mutants enable highly precise genome engineering.

    abstract::Oligonucleotide-mediated multiplex genome engineering is an important tool for bacterial genome editing. The efficient application of this technique requires the inactivation of the endogenous methyl-directed mismatch repair system that in turn leads to a drastically elevated genomic mutation rate and the consequent a...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Nyerges Á,Csorgő B,Nagy I,Latinovics D,Szamecz B,Pósfai G,Pál C

    更新日期:2014-04-01 00:00:00

  • OmicsNet: a web-based tool for creation and visual analysis of biological networks in 3D space.

    abstract::Biological networks play increasingly important roles in omics data integration and systems biology. Over the past decade, many excellent tools have been developed to support creation, analysis and visualization of biological networks. However, important limitations remain: most tools are standalone programs, the majo...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Zhou G,Xia J

    更新日期:2018-07-02 00:00:00

  • Fluorescent labelling of tRNA and oligodeoxynucleotides using T4 RNA ligase.

    abstract::3'-O-(5'-phosphoryldeoxycytidyl) phosphorothioate and fluorescent 3'-O-(5'-phosphoryldeoxycytidyl) S-bimane phosphorothioate can be ligated to tRNA by T4 RNA ligase. They are also efficient donors for the enzymatic ligation to oligodeoxynucleotides bearing a 3'-cytidine terminus. Cytidine 3',5'-bisphosphate is also a ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Cosstick R,McLaughlin LW,Eckstein F

    更新日期:1984-02-24 00:00:00

  • Methylase-limited partial NotI cleavage for physical mapping of genomic DNA.

    abstract:UNLABELLED:Partial cleavage of DNA with the restriction endonuclease NotI (5'...GC/GGCCGC...3') is an important technique for genomic mapping. However, partial genomic cleavage with this enzyme is impaired by the agarose matrix in which the DNA must be suspended. To solve this problem we have purified the blocking meth...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Hanish J,McClelland M

    更新日期:1990-06-11 00:00:00

  • A new minor groove binding asymmetric cyanine reporter dye for real-time PCR.

    abstract::The minor groove binding asymmetric cyanine dye 4-[(3-methyl-6-(benzothiazol-2-yl)-2,3-dihydro- (benzo-1,3-thiazole)-2-methylidene)]-1-methyl-pyridin ium iodide (BEBO) is tested as sequence non- specific label in real-time PCR. The fluorescence intensity of BEBO increases upon binding to double-stranded DNA allowing e...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bengtsson M,Karlsson HJ,Westman G,Kubista M

    更新日期:2003-04-15 00:00:00

  • Long internal inverted repeat in a yeast viral double-stranded RNA.

    abstract::The Saccharomyces cerevisiae viruses are non-infectious double-stranded (ds) RNA viruses present in most laboratory strains of yeast. Their genome consists of one or more dsRNAs separately encapsidated in particles composed mainly of one polypeptide, which has a Mr of 88 kdaltons in the best-studied viral subtype. A l...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bruenn J,Madura K,Siegel A,Miner Z,Lee M

    更新日期:1985-03-11 00:00:00

  • Roles for TbDSS-1 in RNA surveillance and decay of maturation by-products from the 12S rRNA locus.

    abstract::The Trypanosoma brucei exoribonuclease, TbDSS-1, has been implicated in multiple aspects of mitochondrial RNA metabolism. Here, we investigate the role of TbDSS-1 in RNA processing and surveillance by analyzing 12S rRNA processing intermediates in TbDSS-1 RNAi cells. RNA fragments corresponding to leader sequence upst...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Mattiacio JL,Read LK

    更新日期:2008-01-01 00:00:00

  • TcSNP: a database of genetic variation in Trypanosoma cruzi.

    abstract::The TcSNP database (http://snps.tcruzi.org) integrates information on genetic variation (polymorphisms and mutations) for different stocks, strains and isolates of Trypanosoma cruzi, the causative agent of Chagas disease. The database incorporates sequences (genes from the T. cruzi reference genome, mRNAs, ESTs and ge...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Ackermann AA,Carmona SJ,Agüero F

    更新日期:2009-01-01 00:00:00

  • Rational evolution of Cd2+-specific DNAzymes with phosphorothioate modified cleavage junction and Cd2+ sensing.

    abstract::In vitro selection of RNA-cleaving DNAzymes is a powerful method for isolating metal-specific DNA. A few successful examples are known, but it is still difficult to target some thiophilic metals such as Cd(2+) due to limited functional groups in DNA. While using modified bases expands the chemical functionality of DNA...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Huang PJ,Liu J

    更新日期:2015-07-13 00:00:00

  • IMP1 KH1 and KH2 domains create a structural platform with unique RNA recognition and re-modelling properties.

    abstract::IGF2 mRNA-binding protein 1 (IMP1) is a key regulator of messenger RNA (mRNA) metabolism and transport in organismal development and, in cancer, its mis-regulation is an important component of tumour metastasis. IMP1 function relies on the recognition of a diverse set of mRNA targets that is mediated by the combinator...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Dagil R,Ball NJ,Ogrodowicz RW,Hobor F,Purkiss AG,Kelly G,Martin SR,Taylor IA,Ramos A

    更新日期:2019-05-07 00:00:00

  • Expression of the human interferon-gamma cDNA in yeast.

    abstract::Several plasmids which direct the expression of human interferon-gamma (IFN-gamma) cDNA in the yeast Saccharomyces cerevisiae under the transcriptional control of the 3-phosphoglycerate kinase (PGK) promoter have been constructed. Up to 25 x 10(6) units per liter culture of biologically active IFN-gamma are synthesize...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Derynck R,Singh A,Goeddel DV

    更新日期:1983-03-25 00:00:00

  • Characterization of genome-wide p53-binding sites upon stress response.

    abstract::The tumor suppressor p53 is a sequence-specific transcription factor, which regulates the expression of target genes involved in different stress responses. To understand p53's essential transcriptional functions, unbiased analysis of its DNA-binding repertoire is pivotal. In a genome-wide tiling ChIP-on-chip approach...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Smeenk L,van Heeringen SJ,Koeppel M,van Driel MA,Bartels SJ,Akkers RC,Denissov S,Stunnenberg HG,Lohrum M

    更新日期:2008-06-01 00:00:00

  • The Frog Prince: a reconstructed transposon from Rana pipiens with high transpositional activity in vertebrate cells.

    abstract::Members of the Tc1/mariner superfamily of transposable elements isolated from vertebrates are transpositionally inactive due to the accumulation of mutations in their transposase genes. A novel open reading frame-trapping method was used to isolate uninterrupted transposase coding regions from the genome of the frog s...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Miskey C,Izsvák Z,Plasterk RH,Ivics Z

    更新日期:2003-12-01 00:00:00

  • The Saccharomyces cerevisiae TRT2 tRNAThr gene upstream of STE6 is a barrier to repression in MATalpha cells and exerts a potential tRNA position effect in MATa cells.

    abstract::A growing body of evidence suggests that genes transcribed by RNA polymerase III exhibit multiple functions within a chromosome. While the predominant function of these genes is the synthesis of RNA molecules, certain RNA polymerase III genes also function as genomic landmarks. Transfer RNA genes are known to exhibit ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Simms TA,Miller EC,Buisson NP,Jambunathan N,Donze D

    更新日期:2004-09-30 00:00:00

  • SLIRP stabilizes LRPPRC via an RRM-PPR protein interface.

    abstract::LRPPRC is a protein that has attracted interest both for its role in post-transcriptional regulation of mitochondrial gene expression and more recently because numerous mutated variants have been characterized as causing severe infantile mitochondrial neurodegeneration. LRPPRC belongs to the pentatricopeptide repeat (...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Spåhr H,Rozanska A,Li X,Atanassov I,Lightowlers RN,Chrzanowska-Lightowlers ZM,Rackham O,Larsson NG

    更新日期:2016-08-19 00:00:00

  • Properties of a small transcribed poly A sequence in heterogeneous nuclear RNA of HeLa cells.

    abstract::A class of heterogeneous nuclear RNA (hnRNA) molecules contain an internal transcribed poly A sequence of close to 25 uninterrupted AMP residues. HnRNA molecules containing this sequence are separable from those containing the large 3' terminal poly A sequence on the basis of their differential affinity for oligo dT c...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Venkatesan S,Nakazato H,Kopp DW,Edmonds M

    更新日期:1979-03-01 00:00:00

  • Purification and properties of the Eco57I restriction endonuclease and methylase--prototypes of a new class (type IV).

    abstract::The Eco57I restriction endonuclease and methylase were purified to homogeneity from the E.coli RR1 strain carrying the eco57IRM genes on a recombinant plasmid. The molecular weight of the denaturated methylase is 63 kDa. The restriction endonuclease exists in a monomeric form with an apparent molecular weight of 104-1...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Janulaitis A,Petrusyte M,Maneliene Z,Klimasauskas S,Butkus V

    更新日期:1992-11-25 00:00:00

  • Rapid and efficient cDNA library screening by self-ligation of inverse PCR products (SLIP).

    abstract::cDNA cloning is a central technology in molecular biology. cDNA sequences are used to determine mRNA transcript structures, including splice junctions, open reading frames (ORFs) and 5'- and 3'-untranslated regions (UTRs). cDNA clones are valuable reagents for functional studies of genes and proteins. Expressed Sequen...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Hoskins RA,Stapleton M,George RA,Yu C,Wan KH,Carlson JW,Celniker SE

    更新日期:2005-12-02 00:00:00

  • Thyroid-specific transcription factors control Hex promoter activity.

    abstract::The homeobox-containing gene Hex is expressed in several cell types, including thyroid follicular cells, in which it regulates the transcription of tissue- specific genes. In this study the regulation of Hex promoter activity was investigated. Using co- transfection experiments, we demonstrated that the transcriptiona...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Puppin C,D'Elia AV,Pellizzari L,Russo D,Arturi F,Presta I,Filetti S,Bogue CW,Denson LA,Damante G

    更新日期:2003-04-01 00:00:00