当前位置： SCI文献检索 > NUCLEIC ACIDS RESEARCH期刊下所有文献 > A common feature from different subunits of a homomeric AAA+ protein contacts three spatially distinct transcription elements.

A common feature from different subunits of a homomeric AAA+ protein contacts three spatially distinct transcription elements.

Abstract：

:Initiation of σ(54)-dependent transcription requires assistance to melt DNA at the promoter site but is impeded by numerous protein-protein and nucleo-protein interactions. To alleviate these inhibitory interactions, hexameric bacterial enhancer binding proteins (bEBP), a subset of the ATPases associated with various cellular activities (AAA+) protein family, are required to remodel the transcription complex using energy derived from ATP hydrolysis. However, neither the process of energy conversion nor the internal architecture of the closed promoter complex is well understood. Escherichia coli Phage shock protein F (PspF), a well-studied bEBP, contains a surface-exposed loop 1 (L1). L1 is key to the energy coupling process by interacting with Region I of σ(54) (σ(54)(RI)) in a nucleotide dependent manner. Our analyses uncover new levels of complexity in the engagement of a multimeric bEBP with a basal transcription complex via several L1s. The mechanistic implications for these multivalent L1 interactions are elaborated in the light of available structures for the bEBP and its target complexes.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Zhang N,Joly N,Buck M

doi

10.1093/nar/gks661

subject

Has Abstract

pub_date

2012-10-01 00:00:00

pages

9139-52

issue

18

eissn

0305-1048

issn

1362-4962

pii

gks661

journal_volume

40

pub_type

杂志文章

相关文献

NUCLEIC ACIDS RESEARCH文献大全
  • Sequence complexity and diversity of polyadenylated RNA molecules of human normal resting, PHA-stimulated and leukemic lymphocytes.

    abstract：:The abundance and complexity of total poly(A)+RNA of human normal unstimulated lymphocytes, PHA-stimulated and leukemic lymphocytes were examined using the cDNA-poly(A)+ RNA hybridization technique. It was found that in both PHA-stimulated and leukemic lymphocytes the complexity of total poly(A)+RNA is strongly reduce...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/9.24.7013

    authors： Torelli G,Ferrari S,Donelli A,Cadossi R,Ferrari S,Bosi P,Torelli U

    更新日期：1981-12-21 00:00:00

  • A novel virus-inducible enhancer of the interferon-β gene with tightly linked promoter and enhancer activities.

    abstract：:Long-range enhancers of transcription are a key component of the genomic regulatory architecture. Recent studies have identified bi-directionally transcribed RNAs emanating from these enhancers known as eRNAs. However, it remains unclear how tightly coupled eRNA production is with enhancer activity. Through our system...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gku1018

    authors： Banerjee AR,Kim YJ,Kim TH

    更新日期：2014-11-10 00:00:00

  • NotI clones in the analysis of the human genome.

    abstract：:Not I linking clones contain sequences flanking Not I recognition sites and were previously shown to be tightly associated with CpG islands and genes. To directly assess the value of Not I clones in genome research, high density grids with 50 000 Not I linking clones originating from six representative Not I linking l...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/28.7.1635

    authors： Zabarovsky ER,Gizatullin R,Podowski RM,Zabarovska VV,Xie L,Muravenko OV,Kozyrev S,Petrenko L,Skobeleva N,Li J,Protopopov A,Kashuba V,Ernberg I,Winberg G,Wahlestedt C

    更新日期：2000-04-01 00:00:00

  • Twin-primer non-enzymatic DNA assembly: an efficient and accurate multi-part DNA assembly method.

    abstract：:DNA assembly forms the cornerstone of modern synthetic biology. Despite the numerous available methods, scarless multi-fragment assembly of large plasmids remains challenging. Furthermore, the upcoming wave in molecular biological automation demands a rethinking of how we perform DNA assembly. To streamline automation...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkx132

    authors： Liang J,Liu Z,Low XZ,Ang EL,Zhao H

    更新日期：2017-06-20 00:00:00

  • AKAP12 mediates PKA-induced phosphorylation of ATR to enhance nucleotide excision repair.

    abstract：:Loss-of-function in melanocortin 1 receptor (MC1R), a GS protein-coupled receptor that regulates signal transduction through cAMP and protein kinase A (PKA) in melanocytes, is a major inherited melanoma risk factor. Herein, we report a novel cAMP-mediated response for sensing and responding to UV-induced DNA damage re...

    journal_title：Nucleic acids research

    pub_type： 杂志文章,收录出版

    doi：10.1093/nar/gkw871

    authors： Jarrett SG,Wolf Horrell EM,D'Orazio JA

    更新日期：2016-12-15 00:00:00

  • Multiple heterogeneities in the transcribed spacers of ribosomal DNA from Xenopus laevis.

    abstract：:Ribosomal DNA (rDNA) from Xenopus laevis contains several heterogeneities in all three transcribed spacers, as revealed by analysis of cloned and uncloned amplified rDNA from oocytes and cloned chromosomal rDNA from erythrocytes. Heterogeneities include single base changes and length variants of one to several nucleot...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/11.3.629

    authors： Stewart MA,Hall LM,Maden BE

    更新日期：1983-02-11 00:00:00

  • Theoretical melting profiles and denaturation maps of DNA with known sequence: fdDNA.

    abstract：:Differential melting profiles and denaturation maps are calculated for fdDNA whose sequence of nucleotides has been determined recently. The melting profiles for the total DNA and a number of its restriction fragments are compared with experimental data taken from literature. The comparison enables one to correlate a ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/5.7.2547

    authors： Vologodskii AV,Frank-Kamenetskii MD

    更新日期：1978-07-01 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

    doi：10.1093/nar/gky510

    authors： Zhou G,Xia J

    更新日期：2018-07-02 00:00:00

  • Development of bis-locked nucleic acid (bisLNA) oligonucleotides for efficient invasion of supercoiled duplex DNA.

    abstract：:In spite of the many developments in synthetic oligonucleotide (ON) chemistry and design, invasion into double-stranded DNA (DSI) under physiological salt and pH conditions remains a challenge. In this work, we provide a new ON tool based on locked nucleic acids (LNAs), designed for strand invasion into duplex DNA (DS...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkt007

    authors： Moreno PM,Geny S,Pabon YV,Bergquist H,Zaghloul EM,Rocha CS,Oprea II,Bestas B,Andaloussi SE,Jørgensen PT,Pedersen EB,Lundin KE,Zain R,Wengel J,Smith CI

    更新日期：2013-03-01 00:00:00

  • Mechanistic studies on the DNA linking activity of Epstein-Barr nuclear antigen 1.

    abstract：:The DNA replication, plasmid segregation and transactivation functions of Epstein-Barr nuclear antigen 1 (EBNA1) require the binding of EBNA1 to specific DNA recognition sites in the two non-contiguous functional elements of the Epstein-Barr virus latent origin of replication, oriP . EBNA1 molecules bound to these ele...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/26.19.4462

    authors： Avolio-Hunter TM,Frappier L

    更新日期：1998-10-01 00:00:00

  • DeAnnIso: a tool for online detection and annotation of isomiRs from small RNA sequencing data.

    abstract：:Small RNA (sRNA) Sequencing technology has revealed that microRNAs (miRNAs) are capable of exhibiting frequent variations from their canonical sequences, generating multiple variants: the isoforms of miRNAs (isomiRs). However, integrated tool to precisely detect and systematically annotate isomiRs from sRNA sequencing...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkw427

    authors： Zhang Y,Zang Q,Zhang H,Ban R,Yang Y,Iqbal F,Li A,Shi Q

    更新日期：2016-07-08 00:00:00

  • Update of the Diatom EST Database: a new tool for digital transcriptomics.

    abstract：:The Diatom Expressed Sequence Tag (EST) Database was constructed to provide integral access to ESTs from these ecologically and evolutionarily interesting microalgae. It has now been updated with 130,000 Phaeodactylum tricornutum ESTs from 16 cDNA libraries and 77,000 Thalassiosira pseudonana ESTs from seven libraries...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkn905

    authors： Maheswari U,Mock T,Armbrust EV,Bowler C

    更新日期：2009-01-01 00:00:00

  • Cloning of multiple copies of immunoglobulin variable kappa genes in cosmid vectors.

    abstract：:The possibility of cloning large segments of DNA in cosmid vectors offers distinct advantages, in particular for the study of multigene families. Large size fragments of mouse embryo DNA were successfully cloned in the cosmid pHC 79. Twelve recombinants hybridizing specifically to an immunoglobulin kappa chain variabl...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/9.12.2777

    authors： Cattaneo R,Gorski J,Mach B

    更新日期：1981-06-25 00:00:00

  • Construction of a FRS1-FRS2 operon encoding the structural genes for the alpha and beta subunits of yeast phenylalanyl-tRNA synthetase and its use in deletion analysis.

    abstract：:FRS1 and FRS2, the structural genes encoding the large (alpha) and small (beta) subunits of yeast phenylalanyl-tRNA synthetase (PheRS) were placed under the control of the lacZ promoter by creating an artificial operon. The FRS2 gene was fused next to the promoter, followed by a 14 base pair intergenic sequence contai...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/18.8.2087

    authors： Sanni A,Walter P,Ebel JP,Fasiolo F

    更新日期：1990-04-25 00:00:00

  • Base excision repair processing of abasic site/single-strand break lesions within clustered damage sites associated with XRCC1 deficiency.

    abstract：:Ionizing radiation induces clustered DNA damage, which presents a challenge to the cellular repair machinery. The repair efficiency of a single-strand break (SSB) is approximately 4x less than that for repair of an abasic (AP) site when in a bistranded cluster containing 8-oxoG. To explore whether this difference in r...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkm947

    authors： Mourgues S,Lomax ME,O'Neill P

    更新日期：2007-01-01 00:00:00

  • IEDB-AR: immune epitope database-analysis resource in 2019.

    abstract：:The Immune Epitope Database Analysis Resource (IEDB-AR, http://tools.iedb.org/) is a companion website to the IEDB that provides computational tools focused on the prediction and analysis of B and T cell epitopes. All of the tools are freely available through the public website and many are also available through a RE...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkz452

    authors： Dhanda SK,Mahajan S,Paul S,Yan Z,Kim H,Jespersen MC,Jurtz V,Andreatta M,Greenbaum JA,Marcatili P,Sette A,Nielsen M,Peters B

    更新日期：2019-07-02 00:00:00

  • The human estrogen receptor can regulate exogenous but not endogenous vitellogenin gene promoters in a Xenopus cell line.

    abstract：:Transfection of a human estrogen receptor cDNA expression vector (HEO) into cultured Xenopus kidney cells confers estrogen responsiveness to the recipient cells as demonstrated by the hormone dependent expression of co-transfected Xenopus vitellogenin-CAT chimeric genes. The estrogen stimulation of these vit-CAT genes...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/16.17.8291

    authors： Seiler-Tuyns A,Mérillat AM,Haefliger DN,Wahli W

    更新日期：1988-09-12 00:00:00

  • Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations.

    abstract：:The allele frequency net database (http://www.allelefrequencies.net) is an online repository that contains information on the frequencies of immune genes and their corresponding alleles in different populations. The extensive variability observed in genes and alleles related to the immune system response and its signi...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkq1128

    authors： Gonzalez-Galarza FF,Christmas S,Middleton D,Jones AR

    更新日期：2011-01-01 00:00:00

  • Role of an upstream open reading frame in the translation of polycistronic mRNAs in plant cells.

    abstract：:The influence of an upstream small open reading frame (URF) on the translation of two consecutive coding regions on an eukaryotic mRNA was studied. The cis effects of leader length, URF length, the sequences of the URF and neighboring regions, and the trans effects of the Cauliflower mosaic virus transactivator (TAV) ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/20.15.3851

    authors： Fütterer J,Hohn T

    更新日期：1992-08-11 00:00:00

  • Different sequence signatures in the upstream regions of plant and animal tRNA genes shape distinct modes of regulation.

    abstract：:In eukaryotes, the transcription of tRNA genes is initiated by the concerted action of transcription factors IIIC (TFIIIC) and IIIB (TFIIIB) which direct the recruitment of polymerase III. While TFIIIC recognizes highly conserved, intragenic promoter elements, TFIIIB binds to the non-coding 5'-upstream regions of the ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkq1257

    authors： Zhang G,Lukoszek R,Mueller-Roeber B,Ignatova Z

    更新日期：2011-04-01 00:00:00

  • Apurinic endonucleases from Saccharomyces cerevisiae.

    abstract：:Three endonuclease activities have been partially purified from Saccharomyces cerevisiae on the basis of their activity against x-irradiated closed-circular supercoiled bacteriophage PM2 DNA. These endonucleases also nick apurinic DNA and two out of the three activities incise DNA UV-irradiated with high doses. The en...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/5.9.3347

    authors： Armel PR,Wallace SS

    更新日期：1978-09-01 00:00:00

  • BRENDA, enzyme data and metabolic information.

    abstract：:BRENDA is a comprehensive relational database on functional and molecular information of enzymes, based on primary literature. The database contains information extracted and evaluated from approximately 46 000 references, holding data of at least 40 000 different enzymes from more than 6900 different organisms, class...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/30.1.47

    authors： Schomburg I,Chang A,Schomburg D

    更新日期：2002-01-01 00:00:00

  • S/MARt DB: a database on scaffold/matrix attached regions.

    abstract：:S/MARt DB, the S/MAR transaction database, is a relational database covering scaffold/matrix attached regions (S/MARs) and nuclear matrix proteins that are involved in the chromosomal attachment to the nuclear scaffold. The data are mainly extracted from original publications, but a World Wide Web interface for direct...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/30.1.372

    authors： Liebich I,Bode J,Frisch M,Wingender E

    更新日期：2002-01-01 00:00:00

  • Cloning whole bacterial genomes in yeast.

    abstract：:Most microbes have not been cultured, and many of those that are cultivatable are difficult, dangerous or expensive to propagate or are genetically intractable. Routine cloning of large genome fractions or whole genomes from these organisms would significantly enhance their discovery and genetic and functional charact...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkq119

    authors： Benders GA,Noskov VN,Denisova EA,Lartigue C,Gibson DG,Assad-Garcia N,Chuang RY,Carrera W,Moodie M,Algire MA,Phan Q,Alperovich N,Vashee S,Merryman C,Venter JC,Smith HO,Glass JI,Hutchison CA 3rd

    更新日期：2010-05-01 00:00:00

  • Dynamic binding of Ku80, Ku70 and NF90 to the IL-2 promoter in vivo in activated T-cells.

    abstract：:IL-2 gene expression in activated T-cells is initiated by chromatin remodeling at the IL-2 proximal promoter and conversion of a transcriptional repressor into a potent transcriptional activator. A purine-box regulator complex was purified from activated Jurkat T-cell nuclei based on sequence-specific DNA binding to t...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkm117

    authors： Shi L,Qiu D,Zhao G,Corthesy B,Lees-Miller S,Reeves WH,Kao PN

    更新日期：2007-01-01 00:00:00

  • Sequence requirements for mammalian topoisomerase II mediated DNA cleavage stimulated by an ellipticine derivative.

    abstract：:Various antitumor drugs stabilize DNA topoisomerase II-DNA transient covalent complexes. The complexes distribution along pBR322 DNA was shown previously to depend upon the nature of the drug (Tewey et al. (1984) Science 226, 466-468). The position in pBR322 of DNA cleavage by calf DNA topoisomerase II for 115 such si...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/19.11.2861

    authors： Fossé P,René B,Le Bret M,Paoletti C,Saucier JM

    更新日期：1991-06-11 00:00:00

  • The major transcription initiation site of the SV40 late promoter is a potent thyroid hormone response element.

    abstract：:Thyroid hormone receptors (TRs) are members of the nuclear hormone receptor superfamily, which act as transcription factors upon binding to specific DNA sequences called thyroid hormone (T3) response elements (TREs). Such elements are found in the upstream regulatory region of promoters as well as in intragenic sequen...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/25.9.1774

    authors： Desvergne B,Favez T

    更新日期：1997-05-01 00:00:00

  • UV stalled replication forks restart by re-priming in human fibroblasts.

    abstract：:Restarting stalled replication forks is vital to avoid fatal replication errors. Previously, it was demonstrated that hydroxyurea-stalled replication forks rescue replication either by an active restart mechanism or by new origin firing. To our surprise, using the DNA fibre assay, we only detect a slightly reduced for...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkr420

    authors： Elvers I,Johansson F,Groth P,Erixon K,Helleday T

    更新日期：2011-09-01 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

  • The genes for yeast ribosomal proteins S24 and L46 are adjacent and divergently transcribed.

    abstract：:Unlike most yeast ribosomal protein genes studied so far the genes coding for S24 and L46 are adjacent on the genome. Sequence analysis showed that the two genes are transcribed divergently, their initiation codons being 630 bp apart. Taking the respective ATG translation start sites as reference points, the 5'- end o...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/13.3.701

    authors： Leer RJ,van Raamsdonk-Duin MM,Kraakman P,Mager WH,Planta RJ

    更新日期：1985-02-11 00:00:00