The promoter spacer influences transcription initiation via sigma70 region 1.1 of Escherichia coli RNA polymerase.

Abstract:

:Transcription initiation is a dynamic process in which RNA polymerase (RNAP) and promoter DNA act as partners, changing in response to one another, to produce a polymerase/promoter open complex (RPo) competent for transcription. In Escherichia coli RNAP, region 1.1, the N-terminal 100 residues of sigma(70), is thought to occupy the channel that will hold the DNA downstream of the transcription start site; thus, region 1.1 must move from this channel as RPo is formed. Previous work has also shown that region 1.1 can modulate RPo formation depending on the promoter. For some promoters region 1.1 stimulates the formation of open complexes; at the P(minor) promoter, region 1.1 inhibits this formation. We demonstrate here that the AT-rich P(minor) spacer sequence, rather than promoter recognition elements or downstream DNA, determines the effect of region 1.1 on promoter activity. Using a P(minor) derivative that contains good sigma(70)-dependent DNA elements, we find that the presence of a more GC-rich spacer or a spacer with the complement of the P(minor) sequence results in a promoter that is no longer inhibited by region 1.1. Furthermore, the presence of the P(minor) spacer, the GC-rich spacer, or the complement spacer results in different mobilities of promoter DNA during gel electrophoresis, suggesting that the spacer regions impart differing conformations or curvatures to the DNA. We speculate that the spacer can influence the trajectory or flexibility of DNA as it enters the RNAP channel and that region 1.1 acts as a "gatekeeper" to monitor channel entry.

authors

Hook-Barnard IG,Hinton DM

doi

10.1073/pnas.0808133106

subject

Has Abstract

pub_date

2009-01-20 00:00:00

pages

737-42

issue

3

eissn

0027-8424

issn

1091-6490

pii

0808133106

journal_volume

106

pub_type

杂志文章
  • Social isolation uncovers a circuit underlying context-dependent territory-covering micturition.

    abstract::The release of urine, or micturition, serves a fundamental physiological function and, in many species, is critical for social communication. In mice, the pattern of urine release is modulated by external and internal factors and transmitted to the spinal cord via the pontine micturition center (PMC). Here, we exploit...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.2018078118

    authors: Hyun M,Taranda J,Radeljic G,Miner L,Wang W,Ochandarena N,Huang KW,Osten P,Sabatini BL

    更新日期:2021-01-05 00:00:00

  • Ribosome recycling step in yeast cytoplasmic protein synthesis is catalyzed by eEF3 and ATP.

    abstract::After each round of protein biosynthesis, the posttermination complex (PoTC) consisting of a ribosome, mRNA, and tRNA must be disassembled into its components for a new round of translation. Here, we show that a Saccharomyces cerevisiae model PoTC was disassembled by ATP and eukaryotic elongation factor 3 (eEF3). GTP ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1006247107

    authors: Kurata S,Nielsen KH,Mitchell SF,Lorsch JR,Kaji A,Kaji H

    更新日期:2010-06-15 00:00:00

  • Comutagenic effect of norharman and harman with 2-acetylaminofluorene derivatives.

    abstract::Norharman enhanced the known mutagenicity of 2-acetylaminofluorene derivatives in the Salmonella test system. The mutagenicities of 2-acetylaminofluorene, 2-aminofluorene, and N-hydroxy-2-acetylaminofluorene were enhanced by norharman only when rat liver microsomal enzymes were added, whereas the mutagenicity of N-ace...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.75.2.928

    authors: Umezawa K,Shirai A,Matsushima T,Sugimura T

    更新日期:1978-02-01 00:00:00

  • Modeling the cell division cycle: cdc2 and cyclin interactions.

    abstract::The proteins cdc2 and cyclin form a heterodimer (maturation promoting factor) that controls the major events of the cell cycle. A mathematical model for the interactions of cdc2 and cyclin is constructed. Simulation and analysis of the model show that the control system can operate in three modes: as a steady state wi...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.88.16.7328

    authors: Tyson JJ

    更新日期:1991-08-15 00:00:00

  • High-resolution chromosomal localization of human genes for amylase, proopiomelanocortin, somatostatin, and a DNA fragment (D3S1) by in situ hybridization.

    abstract::The method of in situ hybridization has become a significant technique for specific-site chromosome mapping. We show that the resolution of in situ hybridization can be increased by hybridizing the probe to stretched prometaphase chromosomes with high-resolution banding obtained after 5-bromodeoxyuridine treatment of ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.80.22.6932

    authors: Zabel BU,Naylor SL,Sakaguchi AY,Bell GI,Shows TB

    更新日期:1983-11-01 00:00:00

  • The human ERG1 channel polymorphism, K897T, creates a phosphorylation site that inhibits channel activity.

    abstract::Single-nucleotide polymorphisms (SNPs) in the human ether-a-go-go-related gene 1, hERG1, are associated with cardiac arrhythmias. The Kv11.1 channels encoded by hERG1 are also essential for rhythmic excitability of the pituitary, where they are regulated by thyroid hormone through a signal transduction cascade involvi...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0802250105

    authors: Gentile S,Martin N,Scappini E,Williams J,Erxleben C,Armstrong DL

    更新日期:2008-09-23 00:00:00

  • Seminoma-derived Nagao isozyme is encoded by a germ-cell alkaline phosphatase gene.

    abstract::A full-length placental alkaline phosphatase (PLAP) cDNA was used to identify and clone the PLAP-like Nagao isozyme gene from human genomic libraries. The entire nucleotide sequence of the gene reveals the existence of 11 exons interrupted by 10 small introns (76-427 base pairs). Putative regulatory sequences have bee...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.85.9.3024

    authors: Millán JL,Manes T

    更新日期:1988-05-01 00:00:00

  • Dynamic contrast-enhanced magnetic resonance imaging reveals stress-induced angiogenesis in MCF7 human breast tumors.

    abstract::The mechanism of contrast enhancement of tumors using magnetic resonance imaging was investigated in MCF7 human breast cancer implanted in nude mice. Dynamic contrast-enhanced images recorded at high spatial resolution were analyzed by an image analysis method based on a physiological model, which included the blood c...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.93.13.6247

    authors: Furman-Haran E,Margalit R,Grobgeld D,Degani H

    更新日期:1996-06-25 00:00:00

  • Application of a polarizable force field to calculations of relative protein-ligand binding affinities.

    abstract::An explicitly polarizable force field based exclusively on quantum data is applied to calculations of relative binding affinities of ligands to proteins. Five ligands, differing by replacement of an atom or functional group, in complexes with three serine proteases-trypsin, thrombin, and urokinase-type plasminogen act...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0803847105

    authors: Khoruzhii O,Donchev AG,Galkin N,Illarionov A,Olevanov M,Ozrin V,Queen C,Tarasov V

    更新日期:2008-07-29 00:00:00

  • Deletions of a DNA sequence in retinoblastomas and mesenchymal tumors: organization of the sequence and its encoded protein.

    abstract::Retinoblastoma is a childhood tumor that can arise because of mutant alleles acquired as somatic or germinal mutations. The mutant allele can be carried in the germ line. The mutations creating these alleles act by inactivating copies of a recessive oncogene located within band q14 of chromosome 13 and termed the RB1 ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.84.24.9059

    authors: Friend SH,Horowitz JM,Gerber MR,Wang XF,Bogenmann E,Li FP,Weinberg RA

    更新日期:1987-12-01 00:00:00

  • Strong triaxial coupling and anomalous Poisson effect in collagen networks.

    abstract::While cells within tissues generate and sense 3D states of strain, the current understanding of the mechanics of fibrous extracellular matrices (ECMs) stems mainly from uniaxial, biaxial, and shear tests. Here, we demonstrate that the multiaxial deformations of fiber networks in 3D cannot be inferred solely based on t...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1815659116

    authors: Ban E,Wang H,Franklin JM,Liphardt JT,Janmey PA,Shenoy VB

    更新日期:2019-04-02 00:00:00

  • Isolation and expression of human cytokine synthesis inhibitory factor cDNA clones: homology to Epstein-Barr virus open reading frame BCRFI.

    abstract::We have demonstrated the existence of human cytokine synthesis inhibitory factor (CSIF) [interleukin 10 (IL-10)]. cDNA clones encoding human IL-10 (hIL-10) were isolated from a tetanus toxin-specific human T-cell clone. Like mouse IL-10, hIL-10 exhibits strong DNA and amino acid sequence homology to an open reading fr...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.88.4.1172

    authors: Vieira P,de Waal-Malefyt R,Dang MN,Johnson KE,Kastelein R,Fiorentino DF,deVries JE,Roncarolo MG,Mosmann TR,Moore KW

    更新日期:1991-02-15 00:00:00

  • The crystal structure of human IRE1 luminal domain reveals a conserved dimerization interface required for activation of the unfolded protein response.

    abstract::The unfolded protein response (UPR) is an evolutionarily conserved mechanism by which all eukaryotic cells adapt to the accumulation of unfolded proteins in the endoplasmic reticulum (ER). Inositol-requiring kinase 1 (IRE1) and PKR-related ER kinase (PERK) are two type I transmembrane ER-localized protein kinase recep...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0606480103

    authors: Zhou J,Liu CY,Back SH,Clark RL,Peisach D,Xu Z,Kaufman RJ

    更新日期:2006-09-26 00:00:00

  • Functional analysis of protein N-myristoylation: metabolic labeling studies using three oxygen-substituted analogs of myristic acid and cultured mammalian cells provide evidence for protein-sequence-specific incorporation and analog-specific redistributio

    abstract::Covalent attachment of myristic acid (C14:0) to the NH2-terminal glycine residue of a number of cellular, viral, and oncogene-encoded proteins is essential for full expression of their biological function. Substitution of oxygen for methylene groups in this fatty acid does not produce a significant change in chain len...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.87.21.8511

    authors: Johnson DR,Cox AD,Solski PA,Devadas B,Adams SP,Leimgruber RM,Heuckeroth RO,Buss JE,Gordon JI

    更新日期:1990-11-01 00:00:00

  • Maize AMEIOTIC1 is essential for multiple early meiotic processes and likely required for the initiation of meiosis.

    abstract::Molecular mechanisms that initiate meiosis have been studied in fungi and mammals, but little is known about the mechanisms directing the meiosis transition in other organisms. To elucidate meiosis initiation in plants, we characterized and cloned the ameiotic1 (am1) gene, which affects the transition to meiosis and p...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0810115106

    authors: Pawlowski WP,Wang CJ,Golubovskaya IN,Szymaniak JM,Shi L,Hamant O,Zhu T,Harper L,Sheridan WF,Cande WZ

    更新日期:2009-03-03 00:00:00

  • Differentiation of a human leukemia cell line and expression of collagenase inhibitor.

    abstract::A human collagenase inhibitor (CI) of Mr 28,500 has been extensively characterized in skin fibroblasts and identified in a variety of connective tissues. Because human alveolar macrophages synthesize and secrete both a collagenase and CI that are immunologically and functionally identical to their counterparts in fibr...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.82.16.5380

    authors: Bar-Shavit Z,Teitelbaum SL,Stricklin GP,Eisen AZ,Kahn AJ,Welgus HG

    更新日期:1985-08-01 00:00:00

  • Tropical forests were the primary sources of new agricultural land in the 1980s and 1990s.

    abstract::Global demand for agricultural products such as food, feed, and fuel is now a major driver of cropland and pasture expansion across much of the developing world. Whether these new agricultural lands replace forests, degraded forests, or grasslands greatly influences the environmental consequences of expansion. Althoug...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 历史文章,杂志文章

    doi:10.1073/pnas.0910275107

    authors: Gibbs HK,Ruesch AS,Achard F,Clayton MK,Holmgren P,Ramankutty N,Foley JA

    更新日期:2010-09-21 00:00:00

  • A cluster of hydrophobic amino acid residues required for fast Na(+)-channel inactivation.

    abstract::The inward Na+ current underlying the action potential in nerve is terminated by inactivation. The preceding report shows that deletions within the intracellular linker between domains III and IV remove inactivation, but mutation of conserved basic and paired acidic amino acids has little effect. Here we show that sub...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.89.22.10910

    authors: West JW,Patton DE,Scheuer T,Wang Y,Goldin AL,Catterall WA

    更新日期:1992-11-15 00:00:00

  • Divergent effects of new cyclooxygenase inhibitors on gastric ulcer healing: Shifting the angiogenic balance.

    abstract::Delayed gastric ulcer healing is a well recognized problem associated with the use of cyclooxygenase (COX) inhibitors. In contrast, NO-releasing COX inhibitors do not interfere with ulcer healing. These divergent effects may in part be due to differences in their effects on platelets, which are known to influence ulce...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.202392199

    authors: Ma L,del Soldato P,Wallace JL

    更新日期:2002-10-01 00:00:00

  • Molecular cloning and nucleotide sequence of a full-length cDNA for human alpha enolase.

    abstract::We previously purified a 48-kDa protein (p48) that specifically reacts with an antiserum directed against the 12 carboxyl-terminal amino acids of the c-myc gene product. Using an antiserum directed against the purified p48, we have cloned a cDNA from a human expression library. This cDNA hybrid-selects an mRNA that tr...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.83.18.6741

    authors: Giallongo A,Feo S,Moore R,Croce CM,Showe LC

    更新日期:1986-09-01 00:00:00

  • Differential expression of the ToxR regulon in classical and E1 Tor biotypes of Vibrio cholerae is due to biotype-specific control over toxT expression.

    abstract::The two major disease-causing biotypes of Vibrio cholerae, classical and El Tor, exhibit differences in their epidemic nature. Their behavior in the laboratory also differs in that El Tor strains produce two major virulence factors, cholera toxin (CT) and the toxin coregulated pilus (TCP), only under very restricted g...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.93.15.7991

    authors: DiRita VJ,Neely M,Taylor RK,Bruss PM

    更新日期:1996-07-23 00:00:00

  • High-frequency expression of a conserved kappa light-chain variable-region gene in chronic lymphocytic leukemia.

    abstract::Malignant B lymphocytes from several patients with chronic lymphocytic leukemia (CLL) were examined for reactivity with murine monoclonal antibody 17.109. This antibody, prepared against the rheumatoid factor (RF) paraprotein Sie, recognizes a crossreactive idiotype on 48% of human IgM RF paraproteins, but does not re...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.84.9.2916

    authors: Kipps TJ,Fong S,Tomhave E,Chen PP,Goldfien RD,Carson DA

    更新日期:1987-05-01 00:00:00

  • Geospatial analysis of nonmedical vaccine exemptions and pertussis outbreaks in the United States.

    abstract::Because of increased numbers of recorded pertussis cases in the United States, this study sought to understand the role of nonmedical vaccine exemptions and waning immunity may have had on the resurgence of pertussis in the United States at the community level. We used geospatial scan statistics, SaTScan, version 9.4,...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1700240114

    authors: Aloe C,Kulldorff M,Bloom BR

    更新日期:2017-07-03 00:00:00

  • Synaptonemal complexes at premeiotic interphase in the mouse spermatocyte.

    abstract::Male mice were injected intraperitoneally with 125 microCi (1 Ci = 3.7 X 10(10) becquerels) of [3H]thymidine at 1-hr intervals and killed 1 hr after the second injection. Testes were prepared for bright-field and electron microscopic autoradiography. Primary spermatocytes, identified by light microscopy to be at the p...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.77.11.6720

    authors: Grell RF,Oakberg EF,Generoso EE

    更新日期:1980-11-01 00:00:00

  • BMP-SMAD-ID promotes reprogramming to pluripotency by inhibiting p16/INK4A-dependent senescence.

    abstract::Fibrodysplasia ossificans progressiva (FOP) patients carry a missense mutation in ACVR1 [617G > A (R206H)] that leads to hyperactivation of BMP-SMAD signaling. Contrary to a previous study, here we show that FOP fibroblasts showed an increased efficiency of induced pluripotent stem cell (iPSC) generation. This positiv...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1603668113

    authors: Hayashi Y,Hsiao EC,Sami S,Lancero M,Schlieve CR,Nguyen T,Yano K,Nagahashi A,Ikeya M,Matsumoto Y,Nishimura K,Fukuda A,Hisatake K,Tomoda K,Asaka I,Toguchida J,Conklin BR,Yamanaka S

    更新日期:2016-11-15 00:00:00

  • IFNalpha kinoid vaccine-induced neutralizing antibodies prevent clinical manifestations in a lupus flare murine model.

    abstract::A major involvement of IFNalpha in the etiopathogenesis of systemic lupus erythematosus has been suggested by clinical observations, including the increase of serum levels of this cytokine in patients with active disease. Supporting this hypothesis, we have shown that expression of IFNalpha from a recombinant adenovir...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0900615106

    authors: Zagury D,Le Buanec H,Mathian A,Larcier P,Burnett R,Amoura Z,Emilie D,Peltre G,Bensussan A,Bizzini B,Gallo RC,Koutouzov S

    更新日期:2009-03-31 00:00:00

  • The homodimer of prostate-specific membrane antigen is a functional target for cancer therapy.

    abstract::Prostate-specific membrane antigen (PSMA) is a type 2 integral membrane glycoprotein that serves as an attractive target for cancer immunotherapy by virtue of its abundant and restricted expression on the surface of prostate carcinomas and the neovasculature of most other solid tumors. However, relatively little is kn...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1735443100

    authors: Schülke N,Varlamova OA,Donovan GP,Ma D,Gardner JP,Morrissey DM,Arrigale RR,Zhan C,Chodera AJ,Surowitz KG,Maddon PJ,Heston WD,Olson WC

    更新日期:2003-10-28 00:00:00

  • Subcompartments of the G1 phase of cell cycle detected by flow cytometry.

    abstract::Cellular DNA and RNA were simultaneously quantitated in individual cells of cycling and quiescent populations by flow cytometry. Based on differences in RNA content, two distinct subcompartments, G1A and G1B, were recognized in the G1 phase of exponentially growing cells. After mitosis, cells reside in the low-RNA, G1...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.77.11.6696

    authors: Darzynkiewicz Z,Sharpless T,Staiano-Coico L,Melamed MR

    更新日期:1980-11-01 00:00:00

  • Interaction between like-charged colloidal spheres in electrolyte solutions.

    abstract::How colloidal particles interact with each other is one of the key issues that determines our ability to interpret experimental results for phase transitions in colloidal dispersions and our ability to apply colloid science to various industrial processes. The long-accepted theories for answering this question have be...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.95.26.15169

    authors: Wu J,Bratko D,Prausnitz JM

    更新日期:1998-12-22 00:00:00

  • Autoreactive epitopes defined by diabetes-associated human monoclonal antibodies are localized in the middle and C-terminal domains of the smaller form of glutamate decarboxylase.

    abstract::The gamma-aminobutyrate-synthesizing enzyme glutamate decarboxylase (GAD; L-glutamate 1-carboxy-lyase, EC 4.1.1.15) is a major target of autoantibodies associated with both early and late stages of pancreatic beta-cell destruction and development of type 1 diabetes. We have used five monoclonal anti-islet-cell antibod...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.90.7.2832

    authors: Richter W,Shi Y,Baekkeskov S

    更新日期:1993-04-01 00:00:00