当前位置： SCI文献检索 > NUCLEIC ACIDS RESEARCH期刊下所有文献 > Survey of chimeric IStron elements in bacterial genomes: multiple molecular symbioses between group I intron ribozymes and DNA transposons.

Survey of chimeric IStron elements in bacterial genomes: multiple molecular symbioses between group I intron ribozymes and DNA transposons.

Abstract：

:IStrons are chimeric genetic elements composed of a group I intron associated with an insertion sequence (IS). The group I intron is a catalytic RNA providing the IStron with self-splicing ability, which renders IStron insertions harmless to the host genome. The IS element is a DNA transposon conferring mobility, and thus allowing the IStron to spread in genomes. IStrons are therefore a striking example of a molecular symbiosis between unrelated genetic elements endowed with different functions. In this study, we have conducted the first comprehensive survey of IStrons in sequenced genomes that provides insights into the distribution, diversity, origin and evolution of IStrons. We show that IStrons have a restricted phylogenetic distribution limited to two bacterial phyla, the Firmicutes and the Fusobacteria. Nevertheless, diverse IStrons representing two major groups targeting different insertion site motifs were identified. This taken with the finding that while the intron components of all IStrons belong to the same structural class, they are fused to different IS families, indicates that multiple intron-IS symbioses have occurred during evolution. In addition, introns and IS elements related to those that were at the origin of IStrons were also identified.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Tourasse NJ,Stabell FB,Kolstø AB

doi

10.1093/nar/gku939

subject

Has Abstract

pub_date

2014-11-10 00:00:00

pages

12333-51

issue

20

eissn

0305-1048

issn

1362-4962

pii

gku939

journal_volume

42

pub_type

杂志文章

相关文献

NUCLEIC ACIDS RESEARCH文献大全
  • FlyBase at 25: looking to the future.

    abstract：:Since 1992, FlyBase (flybase.org) has been an essential online resource for the Drosophila research community. Concentrating on the most extensively studied species, Drosophila melanogaster, FlyBase includes information on genes (molecular and genetic), transgenic constructs, phenotypes, genetic and physical interacti...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkw1016

    authors： Gramates LS,Marygold SJ,Santos GD,Urbano JM,Antonazzo G,Matthews BB,Rey AJ,Tabone CJ,Crosby MA,Emmert DB,Falls K,Goodman JL,Hu Y,Ponting L,Schroeder AJ,Strelets VB,Thurmond J,Zhou P,the FlyBase Consortium.

    更新日期：2017-01-04 00:00:00

  • Alternatively spliced p53 RNA in transformed and normal cells of different tissue types.

    abstract：:The alternatively spliced RNA species of tumor suppressor gene p53, containing an additional 96 bases derived from intron 10, is present at approximately 25 to 30% the level of regularly spliced p53 RNA in both normal epidermal and carcinoma cells. The presence of this alternatively spliced RNA in 10T1/2 fibroblast ce...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/20.8.1979

    authors： Han KA,Kulesz-Martin MF

    更新日期：1992-04-25 00:00:00

  • Topoisomerase II regulates yeast genes with singular chromatin architectures.

    abstract：:Eukaryotic topoisomerase II (topo II) is the essential decatenase of newly replicated chromosomes and the main relaxase of nucleosomal DNA. Apart from these general tasks, topo II participates in more specialized functions. In mammals, topo IIα interacts with specific RNA polymerases and chromatin-remodeling complexes...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkt707

    authors： Nikolaou C,Bermúdez I,Manichanh C,García-Martinez J,Guigó R,Pérez-Ortín JE,Roca J

    更新日期：2013-11-01 00:00:00

  • Characteristic arrangement of nucleosomes is predictive of chromatin interactions at kilobase resolution.

    abstract：:High-throughput chromosome conformation capture (3C) technologies, such as Hi-C, have made it possible to survey 3D genome structure. However, obtaining 3D profiles at kilobase resolution at low cost remains a major challenge. Therefore, we herein present an algorithm for precise identification of chromatin interactio...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkx885

    authors： Zhang H,Li F,Jia Y,Xu B,Zhang Y,Li X,Zhang Z

    更新日期：2017-12-15 00:00:00

  • Direct sequencing of polymerase chain reaction amplified DNA fragments through the incorporation of deoxynucleoside alpha-thiotriphosphates.

    abstract：:The direct sequencing of DNA generated by the polynucleotide chain reaction, via the incorporation of phosphorothioate nucleotides and followed by treatment with an alkylating reagent that cleaves specifically at the phosphorothioate positions, is described. The Taq polymerase used in the amplification reaction incorp...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/16.21.9947

    authors： Nakamaye KL,Gish G,Eckstein F,Vosberg HP

    更新日期：1988-11-11 00:00:00

  • A novel human cytochrome P450 gene (P450IIB): chromosomal localization and evidence for alternative splicing.

    abstract：:We have isolated from a single human liver cDNA library two clones which are highly homologous (78% over the coding region) to the major phenobarbital-inducible P450 from rat (P450IIB1). This is the first direct demonstration of the presence of the P450IIB gene subfamily in humans. This subfamily is much less extensiv...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/16.13.5783

    authors： Miles JS,Spurr NK,Gough AC,Jowett T,McLaren AW,Brook JD,Wolf CR

    更新日期：1988-07-11 00:00:00

  • Identification of new eukaryotic tRNA genes in genomic DNA databases by a multistep weight matrix analysis of transcriptional control regions.

    abstract：:A linear method for the search of eukaryotic nuclear tRNA genes in DNA databases is described. Based on a modified version of the general weight matrix procedure, our algorithm relies on the recognition of two intragenic control regions known as A and B boxes, a transcription termination signal, and on the evaluation ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/22.7.1247

    authors： Pavesi A,Conterio F,Bolchi A,Dieci G,Ottonello S

    更新日期：1994-04-11 00:00:00

  • Identification of a novel epigenetic regulatory region within the pluripotency associated microRNA cluster, EEmiRC.

    abstract：:The miR-290 cluster is expressed in embryonic stem cells (ESCs) and is important for the maintenance of pluripotency, but little is known about the mechanisms regulating the early embryonic microRNA cluster (EEmiRC) expression. Here we report the identification of a 332-bp intragenic enhancer (IE) able to modulate the...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkq1344

    authors： Tata PR,Tata NR,Kühl M,Sirbu IO

    更新日期：2011-05-01 00:00:00

  • The initiator element of the Drosophila beta2 tubulin gene core promoter contributes to gene expression in vivo but is not required for male germ-cell specific expression.

    abstract：:The tissue-specific expression of the Drosophila beta 2 tubulin gene ( B2t ) is accomplished by the action of a 14-bp activator element (beta2UE1) in combination with certain regulatory elements of the TATA-less, Inr-containing B2t core promoter. We performed an in vivo analysis of the Inr element function in the B2t ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/28.6.1439

    authors： Santel A,Kaufmann J,Hyland R,Renkawitz-Pohl R

    更新日期：2000-03-15 00:00:00

  • Europe PMC: a full-text literature database for the life sciences and platform for innovation.

    abstract：:This article describes recent developments of Europe PMC (http://europepmc.org), the leading database for life science literature. Formerly known as UKPMC, the service was rebranded in November 2012 as Europe PMC to reflect the scope of the funding agencies that support it. Several new developments have enriched Europ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gku1061

    authors： Europe PMC Consortium.

    更新日期：2015-01-01 00:00:00

  • Initiation of DNA replication at the Chinese hamster origin oriGNAI3 relies on local sequences and/or chromatin structures, but not on transcription of the nearby GNAI3 gene.

    abstract：:We recently identified a region of preferential replication initiation, oriGNAI3, near the 3' end of the Chinese hamster GNAI3 gene. oriGNAI3 is co-amplified in mutants selected for AMPD2 amplification, a process generating chromosomal rearrangements. In this report we have taken advantage of cell lines with truncated...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/27.7.1600

    authors： Toledo F,Lachagès AM,Mayau V,Debatisse M

    更新日期：1999-04-01 00:00:00

  • Analysis of neonatal brain lacking ATRX or MeCP2 reveals changes in nucleosome density, CTCF binding and chromatin looping.

    abstract：:ATRX and MeCP2 belong to an expanding group of chromatin-associated proteins implicated in human neurodevelopmental disorders, although their gene-regulatory activities are not fully resolved. Loss of ATRX prevents full repression of an imprinted gene network in the postnatal brain and in this study we address the mec...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gku564

    authors： Kernohan KD,Vernimmen D,Gloor GB,Bérubé NG

    更新日期：2014-07-01 00:00:00

  • Finely tuned conformational dynamics regulate the protective function of the lncRNA MALAT1 triple helix.

    abstract：:Nucleic acid triplexes may regulate many important biological processes. Persistent accumulation of the oncogenic 7-kb long noncoding RNA MALAT1 is dependent on an unusually long intramolecular triple helix. This triplex structure is positioned within a conserved ENE (element for nuclear expression) motif at the lncRN...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gky1171

    authors： Ageeli AA,McGovern-Gooch KR,Kaminska MM,Baird NJ

    更新日期：2019-02-20 00:00:00

  • PigGIS: Pig Genomic Informatics System.

    abstract：:Pig Genomic Information System (PigGIS) is a web-based depository of pig (Sus scrofa) genomic learning mainly engineered for biomedical research to locate pig genes from their human homologs and position single nucleotide polymorphisms (SNPs) in different pig populations. It utilizes a variety of sequence data, includ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkl808

    authors： Ruan J,Guo Y,Li H,Hu Y,Song F,Huang X,Kristiensen K,Bolund L,Wang J

    更新日期：2007-01-01 00:00:00

  • Determinants of redox sensitivity in RsrA, a zinc-containing anti-sigma factor for regulating thiol oxidative stress response.

    abstract：:Various environmental oxidative stresses are sensed by redox-sensitive regulators through cysteine thiol oxidation or modification. A few zinc-containing anti-sigma (ZAS) factors in actinomycetes have been reported to respond sensitively to thiol oxidation, among which RsrA from Streptomyces coelicolor is best charact...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkr477

    authors： Jung YG,Cho YB,Kim MS,Yoo JS,Hong SH,Roe JH

    更新日期：2011-09-01 00:00:00

  • Purification and characterization of the MspI DNA methyltransferase cloned and overexpressed in E. coli.

    abstract：:The MspI restriction-modification system, which recognizes the sequence 5'-CCGG-3', has been previously cloned and sequenced (1). We subcloned the methyltransferase gene (M.MspI) downstream of the ptac promoter in the multicopy vector pUC119 and overexpressed it in E. coli. Upon induction with IPTG, M.MspI constitutes...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/20.7.1579

    authors： Dubey AK,Mollet B,Roberts RJ

    更新日期：1992-04-11 00:00:00

  • Roles of yeast eIF2α and eIF2β subunits in the binding of the initiator methionyl-tRNA.

    abstract：:Heterotrimeric eukaryotic/archaeal translation initiation factor 2 (e/aIF2) binds initiator methionyl-tRNA and plays a key role in the selection of the start codon on messenger RNA. tRNA binding was extensively studied in the archaeal system. The γ subunit is able to bind tRNA, but the α subunit is required to reach h...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gks1180

    authors： Naveau M,Lazennec-Schurdevin C,Panvert M,Dubiez E,Mechulam Y,Schmitt E

    更新日期：2013-01-01 00:00:00

  • Insights into structure, dynamics and hydration of locked nucleic acid (LNA) strand-based duplexes from molecular dynamics simulations.

    abstract：:Locked nucleic acid (LNA) is a chemically modified nucleic acid with its sugar ring locked in an RNA-like (C3'-endo) conformation. LNAs show extraordinary thermal stabilities when hybridized with DNA, RNA or LNA itself. We performed molecular dynamics simulations on five isosequential duplexes (LNA-DNA, LNA-LNA, LNA-R...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkm1182

    authors： Pande V,Nilsson L

    更新日期：2008-03-01 00:00:00

  • The repair of psoralen monoadducts by the Escherichia coli UvrABC endonuclease.

    abstract：:We have examined the interactions of UvrABC endonuclease with DNA containing the monoadducts of 8-methoxypsoralen (8-MOP) and 4,5',8-trimethylpsoralen (TMP). The UvrA and UvrB proteins were found to form a stable complex on DNA that contains the psoralen monoadducts. Subsequent binding of UvrC protein to this complex ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/15.12.4957

    authors： Yeung AT,Jones BK,Capraro M,Chu T

    更新日期：1987-06-25 00:00:00

  • The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution.

    abstract：:We report the latest release (version 3.0) of the CATH protein domain database (http://www.cathdb.info). There has been a 20% increase in the number of structural domains classified in CATH, up to 86 151 domains. Release 3.0 comprises 1110 fold groups and 2147 homologous superfamilies. To cope with the increases in di...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkl959

    authors： Greene LH,Lewis TE,Addou S,Cuff A,Dallman T,Dibley M,Redfern O,Pearl F,Nambudiry R,Reid A,Sillitoe I,Yeats C,Thornton JM,Orengo CA

    更新日期：2007-01-01 00:00:00

  • The role of N-terminus of Plasmodium falciparum ORC1 in telomeric localization and var gene silencing.

    abstract：:Plasmodium falciparum origin recognition complex 1 (ORC1) protein has been implicated in DNA replication and silencing var gene family. However, the mechanism and the domain structure of ORC1 related to the regulation of var gene family are unknown. Here we show that the unique N-terminus of PfORC1 (PfORC1N(1-238)) is...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gks202

    authors： Deshmukh AS,Srivastava S,Herrmann S,Gupta A,Mitra P,Gilberger TW,Dhar SK

    更新日期：2012-07-01 00:00:00

  • Unusual 2-aminopurine fluorescence from a complex of DNA and the EcoKI methyltransferase.

    abstract：:The methyltransferase, M.EcoKI, recognizes the DNA sequence 5'-AACNNNNNNGTGC-3' and methylates adenine at the underlined positions. DNA methylation has been shown by crystallography to occur via a base flipping mechanism and is believed to be a general mechanism for all methyltransferases. If no structure is available...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkh531

    authors： Su TJ,Connolly BA,Darlington C,Mallin R,Dryden DT

    更新日期：2004-04-23 00:00:00

  • The moonlighting RNA-binding activity of cytosolic serine hydroxymethyltransferase contributes to control compartmentalization of serine metabolism.

    abstract：:Enzymes of intermediary metabolism are often reported to have moonlighting functions as RNA-binding proteins and have regulatory roles beyond their primary activities. Human serine hydroxymethyltransferase (SHMT) is essential for the one-carbon metabolism, which sustains growth and proliferation in normal and tumour c...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkz129

    authors： Guiducci G,Paone A,Tramonti A,Giardina G,Rinaldo S,Bouzidi A,Magnifico MC,Marani M,Menendez JA,Fatica A,Macone A,Armaos A,Tartaglia GG,Contestabile R,Paiardini A,Cutruzzolà F

    更新日期：2019-05-07 00:00:00

  • An oxidized nucleotide affects DNA replication through activation of protein kinases in Xenopus egg lysates.

    abstract：:To elucidate the response to oxidative stress in eukaryotic cells, the effect of an oxidized nucleotide, 8-oxo-2'-deoxyguanosine 5'-triphosphate (8-oxo-dGTP), generated from dGTP with an active oxygen, on DNA synthesis was studied using a cell-free DNA replication system derived from Xenopus egg lysates with a single-...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/30.2.569

    authors： Kai T,Matsunaga R,Eguchi M,Kamiya H,Kasai H,Suzuki M,Izuta S

    更新日期：2002-01-15 00:00:00

  • SAHG, a comprehensive database of predicted structures of all human proteins.

    abstract：:Most proteins from higher organisms are known to be multi-domain proteins and contain substantial numbers of intrinsically disordered (ID) regions. To analyse such protein sequences, those from human for instance, we developed a special protein-structure-prediction pipeline and accumulated the products in the Structur...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkq1057

    authors： Motono C,Nakata J,Koike R,Shimizu K,Shirota M,Amemiya T,Tomii K,Nagano N,Sakaya N,Misoo K,Sato M,Kidera A,Hiroaki H,Shirai T,Kinoshita K,Noguchi T,Ota M

    更新日期：2011-01-01 00:00:00

  • MetaQC: objective quality control and inclusion/exclusion criteria for genomic meta-analysis.

    abstract：:Genomic meta-analysis to combine relevant and homogeneous studies has been widely applied, but the quality control (QC) and objective inclusion/exclusion criteria have been largely overlooked. Currently, the inclusion/exclusion criteria mostly depend on ad-hoc expert opinion or naïve threshold by sample size or platfo...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkr1071

    authors： Kang DD,Sibille E,Kaminski N,Tseng GC

    更新日期：2012-01-01 00:00:00

  • Dissecting the function of the adult β-globin downstream promoter region using an artificial zinc finger DNA-binding domain.

    abstract：:Developmental stage-specific expression of the β-type globin genes is regulated by many cis- and trans-acting components. The adult β-globin gene contains an E-box located 60 bp downstream of the transcription start site that has been shown to bind transcription factor upstream stimulatory factor (USF) and to contribu...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gku107

    authors： Barrow JJ,Li Y,Hossain M,Huang S,Bungert J

    更新日期：2014-04-01 00:00:00

  • Genetic manipulation of an exogenous non-immunoglobulin protein by gene conversion machinery in a chicken B cell line.

    abstract：:During culture, a chicken B cell line DT40 spontaneously mutates immunoglobulin (Ig) genes by gene conversion, which involves activation-induced cytidine deaminase (AID)-dependent homologous recombination of the variable (V) region gene with upstream pseudo-V genes. To explore whether this mutation mechanism can targe...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gnj013

    authors： Kanayama N,Todo K,Takahashi S,Magari M,Ohmori H

    更新日期：2006-01-18 00:00:00

  • Tandem phage-display for the identification of non-overlapping binding pairs of recombinant affinity reagents.

    abstract：:The 'sandwich' binding format, which uses two reagents that can bind simultaneously to a given analyte, is the gold standard in diagnostics and many biochemical techniques. One of the bottlenecks in creating a sandwich assay is identifying pairs of reagents that bind non-competitively to the target. To bridge this gap...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkx688

    authors： Gorman KT,Roby LC,Giuffre A,Huang R,Kay BK

    更新日期：2017-10-13 00:00:00

  • Orphon spliced-leader sequences form part of a repetitive element in Angiostrongylus cantonensis.

    abstract：:In nematodes, the 22 nucleotide (nt) spliced leader (SL) is normally encoded by a multi-copy, tandemly reiterated SL gene and is trans-spliced from SL-RNA onto the 5' end of a subset of mRNAs. We have found that the SL is also encoded at multiple (> 100) orphon genomic sites in the parasitic nematode Angiostrongylus c...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/23.6.1030

    authors： Joshua GW,Perler FB,Wang CC

    更新日期：1995-03-25 00:00:00