A trans-splicing group I intron and tRNA-hyperediting in the mitochondrial genome of the lycophyte Isoetes engelmannii.

Abstract:

:Plant mitochondrial genomes show much more evolutionary plasticity than those of animals. We analysed the first mitochondrial DNA (mtDNA) of a lycophyte, the quillwort Isoetes engelmannii, which is separated from seed plants by more than 350 million years of evolution. The Isoetes mtDNA is particularly rich in recombination events, and chloroplast as well as nuclear DNA inserts document the incorporation of foreign sequences already in this most ancestral vascular plant lineage. On the other hand, particularly small group II introns and short intergenic regions reveal a tendency of evolution towards a compact mitochondrial genome. RNA editing reaches extreme levels exceeding 100 pyrimidine exchanges in individual mRNAs and, hitherto unobserved in such frequency, also in tRNAs with 18 C-to-U conversions in the tRNA for proline. In total, some 1500 sites of RNA editing can be expected for the Isoetes mitochondrial transcriptome. As a unique molecular novelty, the Isoetes cox1 gene requires trans-splicing via a discontinuous group I intron demonstrating disrupted, but functional, RNAs for yet another class of natural ribozymes.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Grewe F,Viehoever P,Weisshaar B,Knoop V

doi

10.1093/nar/gkp532

subject

Has Abstract

pub_date

2009-08-01 00:00:00

pages

5093-104

issue

15

eissn

0305-1048

issn

1362-4962

pii

gkp532

journal_volume

37

pub_type

杂志文章
  • ssDNA diffuses along replication protein A via a reptation mechanism.

    abstract::Replication protein A (RPA) plays a critical role in all eukaryotic DNA processing involving single-stranded DNA (ssDNA). Contrary to the notion that RPA provides solely inert protection to transiently formed ssDNA, the RPA-ssDNA complex acts as a dynamic DNA processing unit. Here, we studied the diffusion of RPA alon...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkz1202

    authors: Mishra G,Bigman LS,Levy Y

    更新日期:2020-02-28 00:00:00

  • Visualization of novel simian virus 40 DNA recombination intermediates induced by ultraviolet light irradiation.

    abstract::Electron microscopic technique was used to examine the structures of SV40 DNA recombination intermediates induced by ultraviolet irradiation as an approach for understanding recombination mechanisms in animal cells. Putative recombination intermediate with the characteristic Holliday junction was observed in both SV40...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/19.25.7193

    authors: Hsu MT

    更新日期:1991-12-01 00:00:00

  • The guanine-rich fragile X chromosome repeats are reluctant to form tetraplexes.

    abstract::Using circular dichroism spectroscopy, UV absorption spectroscopy and polyacrylamide gel electrophoresis, we studied conformational properties of guanine-rich DNA strands of the fragile X chromosome repeats d(GGC)n, d(GCG)n and d(CGG)n, with n = 2, 4, 8 and 16. These strands are generally considered in the literature ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkh179

    authors: Fojtík P,Kejnovská I,Vorlícková M

    更新日期:2004-01-12 00:00:00

  • A Ku80 fragment with dominant negative activity imparts a radiosensitive phenotype to CHO-K1 cells.

    abstract::DNA non-homologous end joining, the major mechanism for the repair of DNA double-strands breaks (DSB) in mammalian cells requires the DNA-dependent protein kinase (DNA-PK), a complex composed of a large catalytic subunit of 460 kDa (DNA-PKcs) and the heterodimer Ku70-Ku80 that binds to double-stranded DNA ends. Mutati...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/28.23.4778

    authors: Marangoni E,Foray N,O'Driscoll M,Douc-Rasy S,Bernier J,Bourhis J,Jeggo P

    更新日期:2000-12-01 00:00:00

  • Construction and characterization of recombinant plasmid DNAs containing sequences of the origin of bacteriophage phi X174 DNA replication.

    abstract::The synthetic DNA fragment (formula, see text) (corresponding to nucleotides 4299-4314 of the phi X DNA sequence) was cloned into either the AmpR gene or the KmR gene of plasmid pACYC 177. The DNA sequence of the KmR gene around the insertion site was determined by nucleotide sequence analysis of the pACYC 177 FnudII ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/9.14.3335

    authors: Heidekamp F,Baas PD,van Boom JH,Veeneman GH,Zipursky SL,Jansz HS

    更新日期:1981-07-24 00:00:00

  • Structure and transcription of the Drosophila mulleri alcohol dehydrogenase genes.

    abstract::The D. melanogaster Adh gene is transcribed from two different promoters; a proximal (larval) promoter is active during late embryonic and larval stages, and a distal (adult) promoter is active primarily in third instar larvae and in adult flies (1). Genetic analyses suggest that several species of the mulleri subgrou...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/13.19.6899

    authors: Fischer JA,Maniatis T

    更新日期:1985-10-11 00:00:00

  • Evidence for three distinct D proteins, which react differentially with anti-Sm autoantibodies, in the cores of the major snRNPs U1, U2, U4/U6 and U5.

    abstract::Electrophoresis of the mixture of proteins from purified snRNPs U1, U2, U4/U6 and U5 on SDS-polyacrylamide gels that had been allowed to polymerise in the presence of high TEMED concentrations have revealed the presence of proteins in the snRNPs that previously had eluded detection. The most striking case is that of p...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/18.22.6475

    authors: Lehmeier T,Foulaki K,Lührmann R

    更新日期:1990-11-25 00:00:00

  • A simple polypyrimidine repeat acts as an artificial Rho-dependent terminator in vivo and in vitro.

    abstract::In this paper, we present evidence that an efficient Rho-dependent terminator can be created by introducing a simple (AG/TC) n DNA repeat into a transcription unit. The Rho termination activity in vivo and in vitro is dependent on the length and the orientation of the insert. The transcription of at least 30 bp of the...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/26.21.4895

    authors: Guérin M,Robichon N,Geiselmann J,Rahmouni AR

    更新日期:1998-11-01 00:00:00

  • Naturally occurring mutations in the human HNF4alpha gene impair the function of the transcription factor to a varying degree.

    abstract::The hepatocyte nuclear factor (HNF)4alpha, a member of the nuclear receptor superfamily, regulates genes that play a critical role in embryogenesis and metabolism. Recent studies have shown that mutations in the human HNF4alpha gene cause a rare form of type 2 diabetes, maturity onset diabetes of the young (MODY1). To...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/28.2.430

    authors: Lausen J,Thomas H,Lemm I,Bulman M,Borgschulze M,Lingott A,Hattersley AT,Ryffel GU

    更新日期:2000-01-15 00:00:00

  • Alkemio: association of chemicals with biomedical topics by text and data mining.

    abstract:UNLABELLED:The PubMed® database of biomedical citations allows the retrieval of scientific articles studying the function of chemicals in biology and medicine. Mining millions of available citations to search reported associations between chemicals and topics of interest would require substantial human time. We have im...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gku432

    authors: Gijón-Correas JA,Andrade-Navarro MA,Fontaine JF

    更新日期:2014-07-01 00:00:00

  • Pseudorevertants of a lac promoter mutation reveal overlapping nascent promoters.

    abstract::Four pseudorevertants of a -10 region lacP mutation were isolated. Three of these mutations were found to activate nascent promoters. These mutations were: a -2 G/C----A/T change (-2A) promoting transcription at position +11, a +1 A/T----T/A change (+1T) promoting transcription initiation at position +13, and a +10 C/...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/17.10.3927

    authors: Karls R,Schulz V,Jovanovich SB,Flynn S,Pak A,Reznikoff WS

    更新日期:1989-05-25 00:00:00

  • Molecular characterization of the MT-family of dispersed middle-repetitive DNA in rodent genomes.

    abstract::We report the consensus sequence of members of a new dispersed middle-repetitive DNA family, MT, which is present in mouse and rat genomes. This family is shown to be as abundant as the described rodent B1 and B2 families. Hybridization experiments with radioactive single-stranded cDNAs from different tissues indicate...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/14.16.6403

    authors: Heinlein UA,Lange-Sablitzky R,Schaal H,Wille W

    更新日期:1986-08-26 00:00:00

  • Contributions of discrete tRNA(Ser) domains to aminoacylation by E.coli seryl-tRNA synthetase: a kinetic analysis using model RNA substrates.

    abstract::The aminoacylation kinetics of T7 transcripts representing defined regions of Escherichia coli serine tRNAs were determined using purified E.coli seryl-tRNA synthetase (SerRS) and the kinetic values were used to estimate the relative contribution of various tRNA(Ser) domains to recognition by SerRS. The analysis revea...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/21.19.4467

    authors: Sampson JR,Saks ME

    更新日期:1993-09-25 00:00:00

  • RNA-dependent association with myosin IIA promotes F-actin-guided trafficking of the ELAV-like protein HuR to polysomes.

    abstract::The role of the mRNA-binding protein human antigen R (HuR) in stabilization and translation of AU-rich elements (ARE) containing mRNAs is well established. However, the trafficking of HuR and bound mRNA cargo, which comprises a fundamental requirement for the aforementioned HuR functions is only poorly understood. By ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkt663

    authors: Doller A,Schulz S,Pfeilschifter J,Eberhardt W

    更新日期:2013-10-01 00:00:00

  • Palingol: a declarative programming language to describe nucleic acids' secondary structures and to scan sequence database.

    abstract::At the DNA/RNA level, biological signals are defined by a combination of spatial structures and sequence motifs. Until now, few attempts had been made in writing general purpose search programs that take into account both sequence and structure criteria. Indeed, the most successful structure scanning programs are usua...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/24.8.1395

    authors: Billoud B,Kontic M,Viari A

    更新日期:1996-04-15 00:00:00

  • PALI-a database of Phylogeny and ALIgnment of homologous protein structures.

    abstract::PALI (release 1.2) contains three-dimensional (3-D) structure-dependent sequence alignments as well as structure-based phylogenetic trees of homologous protein domains in various families. The data set of homologous protein structures has been derived by consulting the SCOP database (release 1.50) and the data set com...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/29.1.61

    authors: Balaji S,Sujatha S,Kumar SS,Srinivasan N

    更新日期:2001-01-01 00:00:00

  • ChIPprimersDB: a public repository of verified qPCR primers for chromatin immunoprecipitation (ChIP).

    abstract::Chromatin immunoprecipitation (ChIP) has ushered in a new era of scientific discovery by allowing new insights into DNA-protein interactions. ChIP is used to quantify enriched genomic regions using qPCR, and more recently is combined with next generation sequencing (ChIP-seq) to obtain a genome wide profile of protein...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky813

    authors: Kurtenbach S,Reddy R,Harbour JW

    更新日期:2019-01-08 00:00:00

  • Intermediates in plasmid pT181 DNA replication.

    abstract::Staphylococcus aureus plasmid pT181 is thought to replicate via an asymmetric rolling-circle mechanism. By studying pulse labeled replicative intermediates, here we report that pT181 replication involves: (1) a post-replicative hypersupercoiled monomer and (2) a partially replicated intermediate which lacks superhelic...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/16.7.2897

    authors: Majumder S,Novick RP

    更新日期:1988-04-11 00:00:00

  • Complexes of the arginine-rich histone tetramer (H3)2(H4)2 with negatively supercoiled DNA: electron microscopy and chemical cross-linking.

    abstract::Tetramers of the arginine-rich histones H3 and H4 associate with supercoiled SV40 DNA either singly, giving tetrameric nucleoprotein complexes or in pairs giving octameric complexes, both of which are visualized as beads in the electron microscope. The relative amounts of the two complexes may be revealed by complete ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/7.3.611

    authors: Thomas JO,Oudet P

    更新日期:1979-10-10 00:00:00

  • Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes.

    abstract::The 338.5 kb of the Escherichia coli genome described here together with previously described segments bring the total of contiguous finished sequence of this genome to > 1 Mb. Of 319 open reading frames (ORFs) found in this 338.5 kb segment, 147 (46%) are potential new genes. The positions of several genes which had ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/23.12.2105

    authors: Burland V,Plunkett G 3rd,Sofia HJ,Daniels DL,Blattner FR

    更新日期:1995-06-25 00:00:00

  • SNP@Domain: a web resource of single nucleotide polymorphisms (SNPs) within protein domain structures and sequences.

    abstract::The single nucleotide polymorphisms (SNPs) in conserved protein regions have been thought to be strong candidates that alter protein functions. Thus, we have developed SNP@Domain, a web resource, to identify SNPs within human protein domains. We annotated SNPs from dbSNP with protein structure-based as well as sequenc...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl323

    authors: Han A,Kang HJ,Cho Y,Lee S,Kim YJ,Gong S

    更新日期:2006-07-01 00:00:00

  • The effects of mercury-substitution on the hybridisation characteristics of nucleic acids.

    abstract::The effect of different levels of mercury substitution on the rate and extent of hybridisation of globin mRNA with a complementary DNA (cDNA) copy has been investigated. It was found that mercuration significantly reduces both the rate of hybridisation and the extent of the reaction, but that these effects are abolish...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/7.8.2357

    authors: Brown TD,Balmain A

    更新日期:1979-12-20 00:00:00

  • Rapid synthesis of oligodeoxyribonucleotides. IV. Improved solid phase synthesis of oligodeoxyribonucleotides through phosphotriester intermediates.

    abstract::A phosphotriester solid phase method on a polyamide support has been used to prepare oligodeoxyribonucleotides up to 12 units long. Compared to solid phase phosphodiester synthesis the new methodology is quicker, more flexible and gives 10-60-fold better overall yields. ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/8.5.1081

    authors: Gait MJ,Singh M,Sheppard RC,Edge MD,Greene AR,Heathcliffe GR,Atkinson TC,Newton CR,Markham AF

    更新日期:1980-03-11 00:00:00

  • Ligation of oligonucleotides to nucleic acids or proteins via disulfide bonds.

    abstract::We have developed general methods for joining together, via cleavable disulfide bonds, either two unprotected polynucleotides or a polynucleotide and a peptide or protein. To join two oligonucleotides, each is first converted to an adduct in which cystamine is joined to the 5'-terminal phosphate of the oligonucleotide...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/16.9.3671

    authors: Chu BC,Orgel LE

    更新日期:1988-05-11 00:00:00

  • Retrotransposon-like nature of Tp1 elements: implications for the organisation of highly repetitive, hypermethylated DNA in the genome of Physarum polycephalum.

    abstract::The repetitive fraction of the genome of the eukaryotic slime mould Physarum polycephalum is dominated by the Tp1 family of highly repetitive retrotransposon-like sequences. Tp1 elements consist of two terminal direct repeats of 277bp which flank an internal domain of 8.3kb. They are the major sequence component in th...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/19.2.279

    authors: Rothnie HM,McCurrach KJ,Glover LA,Hardman N

    更新日期:1991-01-25 00:00:00

  • 'Genome design' model and multicellular complexity: golden middle.

    abstract::Human tissue-specific genes were reported to be longer than housekeeping genes (both in coding and intronic parts). The competing neutralist and adaptationist models were proposed to explain this observation. Here I show that in human genome the longest are genes with the intermediate expression pattern. From the stan...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl773

    authors: Vinogradov AE

    更新日期:2006-01-01 00:00:00

  • Initiation of phage phi 29 DNA replication by the terminal protein modified at the carboxyl end.

    abstract::A mutant at the carboxyl end of the terminal protein, p3, of phage phi 29 DNA has been constructed by inserting an containing the stop translation codon TGA in the three possible reading frames, immediately downstream of a phage phi 29 DNA fragment coding for all but the last five amino acids of protein p3. The activ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/11.21.7397

    authors: Mellado RP,Salas M

    更新日期:1983-11-11 00:00:00

  • Genome-wide analyses reveal the extent of opportunistic STAT5 binding that does not yield transcriptional activation of neighboring genes.

    abstract::Signal Transducers and Activators of Transcription (STAT) 5A/B regulate cytokine-inducible genes upon binding to GAS motifs. It is not known what percentage of genes with GAS motifs bind to and are regulated by STAT5. Moreover, it is not clear whether genome-wide STAT5 binding is modulated by its concentration. To cla...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks056

    authors: Zhu BM,Kang K,Yu JH,Chen W,Smith HE,Lee D,Sun HW,Wei L,Hennighausen L

    更新日期:2012-05-01 00:00:00

  • Fine mapping of replication origins (ori A and ori B) in Nicotiana tabacum chloroplast DNA.

    abstract::Using a partially purified replication complex from tobacco chloroplasts, replication origins have been localized to minimal sequences of 82 (pKN8, positions 137 683-137 764) and 243 bp (pKN3, positions 130 513-130 755) for ori A and ori B respectively. Analysis of in vitro replication products by two-dimensional agar...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/25.18.3681

    authors: Kunnimalaiyaan M,Nielsen BL

    更新日期:1997-09-15 00:00:00

  • Entirely enzymatic nanofabrication of DNA-protein conjugates.

    abstract::While proteins are highly biochemically competent, DNA offers the ability to program, both reactions and the assembly of nanostructures, with a control that is unprecedented by any other molecule. Their joining: DNA-protein conjugates - offer the ability to combine the programmability of DNA with the competence of pro...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkx707

    authors: Bernardinelli G,Högberg B

    更新日期:2017-10-13 00:00:00