Transcription frequency modulates the efficiency of an attenuator preceding the rpoBC RNA polymerase genes of Escherichia coli: possible autogenous control.

Abstract:

:Expression of the rpoBC genes encoding the beta and beta' RNA polymerase subunits of Escherichia coli is autogenously regulated. Although previous studies have demonstrated a post-transcriptional feedback mechanism, complex transcriptional controls of rpoBC expression may also contribute. We show that an attenuator (rpoBa) separating the ribosomal protein (rpl) genes from the rpoBC genes in the rplKAJLrpoBC gene cluster is modulated in its efficiency in response to changes in the frequency of transcription initiated by promoters located upstream. A series of rplJLrpoBalacZ transcriptional fusions was constructed on lambda vectors in which transcription into the rpoBa attenuator was varied by using a variety of promoters with different strengths. beta-galactosidase assays performed on monolysogens of the recombinant phage show that with transcription increasing over a 40-fold range, readthrough of rpoBa decreases from 61% to 19%. In contrast, two other well-characterized terminators show nearly constant efficiencies over a similar range of transcription frequencies. Using a set of phage P22 ant promoter variants with single-nucleotide changes in the promoter consensus sequences also demonstrates that the modulation of rpoBa function appears to be unrelated to the phenomenon of 'factor-independent antitermination' reported by others. The implications for autogenous control of RNA polymerase synthesis are discussed.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Steward KL,Linn T

doi

10.1093/nar/20.18.4773

keywords:

subject

Has Abstract

pub_date

1992-09-25 00:00:00

pages

4773-9

issue

18

eissn

0305-1048

issn

1362-4962

journal_volume

20

pub_type

杂志文章
  • Peripheral re-localization of constitutive heterochromatin advances its replication timing and impairs maintenance of silencing marks.

    abstract::The replication of the genome is a highly organized process, both spatially and temporally. Although a lot is known on the composition of the basic replication machinery, how its activity is regulated is mostly unknown. Several chromatin properties have been proposed as regulators, but a potential role of the nuclear ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky368

    authors: Heinz KS,Casas-Delucchi CS,Török T,Cmarko D,Rapp A,Raska I,Cardoso MC

    更新日期:2018-07-06 00:00:00

  • Partial purification and characterization of two cytoplasmic DNA polymerases from ungerminated wheat.

    abstract::Two DNA polymerases have been purified from the 105,000 x g supernatant of ungerminated wheat. The purification stages included: high speed centrifugation, salt fractionation, DEAE-cellulose chromatography, Sephadex G-150 filtration and phosphocellulose chromatography. Several properties of the two enzyme (called A an...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/2.11.2077

    authors: Castroviejo M,Tarragó-Litvak L,Litvak S

    更新日期:1975-11-01 00:00:00

  • The role of TFIIB-RNA polymerase II interaction in start site selection in yeast cells.

    abstract::Previous studies have established a critical role of both TFIIB and RNA polymerase II (RNAPII) in start site selection in the yeast Saccharomyces cerevisiae. However, it remains unclear how the TFIIB-RNAPII interaction impacts on this process since such an interaction can potentially influence both preinitiation compl...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkf422

    authors: Zhang DY,Carson DJ,Ma J

    更新日期:2002-07-15 00:00:00

  • Primary structure and regulation of vegetative specific genes of Dictyostelium discoideum.

    abstract::We have examined the expression and structure of several genes belonging to two classes of vegetative specific genes of the simple eukaryote, Dictyostelium discoideum. In amebae grown on bacteria, deactivation of all vegetative specific genes occurred at the onset of development and very little mRNA exists by 8 to 10 ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/17.23.9679

    authors: Singleton CK,Manning SS,Ken R

    更新日期:1989-12-11 00:00:00

  • Complete DNA sequence of the short repeat region in the genome of herpes simplex virus type 1.

    abstract::We report the complete DNA sequence of the short repeat region in the genome of herpes simplex virus type 1, as 6633 base pairs of composition 79.5% G+C. This contains immediate early gene 3, encoding the IE175 protein, an important transcriptional activator of later virus genes. The IE175 coding region was identified...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/14.4.1727

    authors: McGeoch DJ,Dolan A,Donald S,Brauer DH

    更新日期:1986-02-25 00:00:00

  • PreCisIon: PREdiction of CIS-regulatory elements improved by gene's positION.

    abstract::Conventional approaches to predict transcriptional regulatory interactions usually rely on the definition of a shared motif sequence on the target genes of a transcription factor (TF). These efforts have been frustrated by the limited availability and accuracy of TF binding site motifs, usually represented as position...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks1286

    authors: Elati M,Nicolle R,Junier I,Fernández D,Fekih R,Font J,Képès F

    更新日期:2013-02-01 00:00:00

  • Interaction of N-terminal domain of U1A protein with an RNA stem/loop.

    abstract::The U1A protein is a sequence-specific RNA binding protein found in the U1 snRNP particle where it binds to stem/loop II of U1 snRNA. U1A contains two 'RNP' or 'RRM' (RNA Recognition Motif) domains, which are common to many RNA-binding proteins. The N-terminal RRM has been shown to bind specifically to the U1 RNA stem...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/20.16.4283

    authors: Hall KB,Stump WT

    更新日期:1992-08-25 00:00:00

  • The presence of pseudouridine in the anticodon alters the genetic code: a possible mechanism for assignment of the AAA lysine codon as asparagine in echinoderm mitochondria.

    abstract::It has been inferred from DNA sequence analyses that in echinoderm mitochondria not only the usual asparagine codons AAU and AAC, but also the usual lysine codon AAA, are translated as asparagine by a single mitochondrial (mt) tRNAAsn with the anticodon GUU. Nucleotide sequencing of starfish mt tRNAAsn revealed that t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/27.7.1683

    authors: Tomita K,Ueda T,Watanabe K

    更新日期:1999-04-01 00:00:00

  • A 5' UTR GGN repeat controls localisation and translation of a potassium leak channel mRNA through G-quadruplex formation.

    abstract::RNA G-quadruplexes (G4s) are secondary structures proposed to function as regulators of post-transcriptional mRNA localisation and translation. G4s within some neuronal mRNAs are known to control distal localisation and local translation, contributing to distinct local proteomes that facilitate the synaptic remodellin...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa699

    authors: Maltby CJ,Schofield JPR,Houghton SD,O'Kelly I,Vargas-Caballero M,Deinhardt K,Coldwell MJ

    更新日期:2020-09-25 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

  • Structural rearrangements in mRNA upon its binding to human 80S ribosomes revealed by EPR spectroscopy.

    abstract::The model mRNA (MR), 11-mer RNA containing two nitroxide spin labels at the 5'- and 3'-terminal nucleotides and prone to form a stable homodimer (MR)2, was used for Electron Paramagnetic Resonance study of structural rearrangements in mRNA occurring upon its binding to human 80S ribosomes. The formation of two differe...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkx1136

    authors: Malygin AA,Graifer DM,Meschaninova MI,Venyaminova AG,Timofeev IO,Kuzhelev AA,Krumkacheva OA,Fedin MV,Karpova GG,Bagryanskaya EG

    更新日期:2018-01-25 00:00:00

  • BseSI, a restriction endonuclease from Bacillus stearothermophilus Jo 10-553, which recognizes the novel hexanucleotide sequence 5'-G(G/T)GC(A/C)C-3'.

    abstract::A new restriction endonuclease Bse SI has been isolated from Bacillus stearothermophilus Jo10-553. Bse SI recognizes a degenerate hexanucleotide sequence 5'-G(G/T)GC(A/C)C-3' and cleaves DNA to produce 3[prime]-protruding tetranucleotide ends. ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/27.13.2644

    authors: Steponaviciene D,Maneliene Z,Petrusyte M,Janulaitis A

    更新日期:1999-07-01 00:00:00

  • Identification of putative transcriptional regulatory networks in Entamoeba histolytica using Bayesian inference.

    abstract::Few transcriptional regulatory networks have been described in non-model organisms. In Entamoeba histolytica seminal aspects of pathogenesis are transcriptionally controlled, however, little is known about transcriptional regulatory networks that effect gene expression in this parasite. We used expression data from tw...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkm028

    authors: Hackney JA,Ehrenkaufer GM,Singh U

    更新日期:2007-01-01 00:00:00

  • Noncoding RNAs database (ncRNAdb).

    abstract::The noncoding RNA database (ncRNAdb) was created as a source of information on RNA molecules, which do not possess protein-coding capacity. It is now widely accepted that, in addition to constitutively expressed, housekeeping or infrastructural RNAs, there is a wide variety of RNAs participating in mechanisms involved...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl994

    authors: Szymanski M,Erdmann VA,Barciszewski J

    更新日期:2007-01-01 00:00:00

  • Transcription of satellite 2 DNA from the newt is driven by a snRNA type of promoter.

    abstract::The transcriptional promoter of satellite 2 from the eastern newt, Notophthalmus viridescens, was analyzed by assaying the activity of deleted or mutated satellite 2 clones in Xenopus laevis oocytes. Two elements in the promoter were found to be important for transcription. These elements have sequences that are simil...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/22.22.4697

    authors: Coats SR,Zhang Y,Epstein LM

    更新日期:1994-11-11 00:00:00

  • PLAST-ncRNA: Partition function Local Alignment Search Tool for non-coding RNA sequences.

    abstract::Alignment-based programs are valuable tools for finding potential homologs in genome sequences. Previously, it has been shown that partition function posterior probabilities attuned to local alignment achieve a high accuracy in identifying distantly similar non-coding RNA sequences that are hidden in a large genome. H...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkq487

    authors: Chikkagoudar S,Livesay DR,Roshan U

    更新日期:2010-07-01 00:00:00

  • Tpk3 and Snf1 protein kinases regulate Rgt1 association with Saccharomyces cerevisiae HXK2 promoter.

    abstract::Hexokinase 2 is an essential factor for signalling repression through the Saccharomyces cerevisiae high-glucose sensing pathway. The main regulatory mechanism that controls the HXK2 gene expression in yeast is mediated by the Rgt1 and Med8 transcription factors, which repress HXK2 expression in low-glucose containing ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl028

    authors: Palomino A,Herrero P,Moreno F

    更新日期:2006-03-09 00:00:00

  • NMR structure of a vestigial nuclease provides insight into the evolution of functional transitions in viral dsDNA packaging motors.

    abstract::Double-stranded DNA viruses use ATP-powered molecular motors to package their genomic DNA. To ensure efficient genome encapsidation, these motors regulate functional transitions between initiation, translocation, and termination modes. Here, we report structural and biophysical analyses of the C-terminal domain of the...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa874

    authors: Mahler BP,Bujalowski PJ,Mao H,Dill EA,Jardine PJ,Choi KH,Morais MC

    更新日期:2020-11-18 00:00:00

  • The use of oligodeoxynucleotide probes in chaotrope-based hybridization solutions.

    abstract::Hybridization solutions containing chaotropes may be used to modulate the thermal stability (Tm or Td) of oligodeoxynucleotide (ODN) duplexes or hybrids over a 90 degrees C range. Modulation of Td allows formulation of hybridization solutions that permit ambient temperature hybridization using most combinations of pro...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/19.19.5143

    authors: Van Ness J,Chen L

    更新日期:1991-10-11 00:00:00

  • An hnRNP-like RNA-binding protein affects alternative splicing by in vivo interaction with transcripts in Arabidopsis thaliana.

    abstract::Alternative splicing (AS) of pre-mRNAs is an important regulatory mechanism shaping the transcriptome. In plants, only few RNA-binding proteins are known to affect AS. Here, we show that the glycine-rich RNA-binding protein AtGRP7 influences AS in Arabidopsis thaliana. Using a high-resolution RT-PCR-based AS panel, we...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks873

    authors: Streitner C,Köster T,Simpson CG,Shaw P,Danisman S,Brown JW,Staiger D

    更新日期:2012-12-01 00:00:00

  • Transmission of dynamic supercoiling in linear and multi-way branched DNAs and its regulation revealed by a fluorescent G-quadruplex torsion sensor.

    abstract::DNA supercoiling is an important regulator of gene activity. The transmission of transcription-generated supercoiling wave along a DNA helix provides a way for a gene being transcribed to communicate with and regulate its neighboring genes. Currently, the dynamic behavior of supercoiling transmission remains unclear o...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky534

    authors: Xia Y,Zheng KW,He YD,Liu HH,Wen CJ,Hao YH,Tan Z

    更新日期:2018-08-21 00:00:00

  • Random DNA fragmentation with endonuclease V: application to DNA shuffling.

    abstract::The enzyme endonuclease V nicks uracil-containing DNA at the second or third phosphodiester bond 3' to uracil sites. I applied the enzyme to random fragmentation of DNA to revise the complex DNA shuffling protocol. The merit of using endonuclease V is that cleavage occurs at random sites and the length of the fragment...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gnf139

    authors: Miyazaki K

    更新日期:2002-12-15 00:00:00

  • HDOCK: a web server for protein-protein and protein-DNA/RNA docking based on a hybrid strategy.

    abstract::Protein-protein and protein-DNA/RNA interactions play a fundamental role in a variety of biological processes. Determining the complex structures of these interactions is valuable, in which molecular docking has played an important role. To automatically make use of the binding information from the PDB in docking, her...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkx407

    authors: Yan Y,Zhang D,Zhou P,Li B,Huang SY

    更新日期:2017-07-03 00:00:00

  • The hyperthermophilic partners Nanoarchaeum and Ignicoccus stabilize their tRNA T-loops via different but structurally equivalent modifications.

    abstract::The universal L-shaped tertiary structure of tRNAs is maintained with the help of nucleotide modifications within the D- and T-loops, and these modifications are most extensive within hyperthermophilic species. The obligate-commensal Nanoarchaeum equitans and its phylogenetically-distinct host Ignicoccus hospitalis gr...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa411

    authors: Rose S,Auxilien S,Havelund JF,Kirpekar F,Huber H,Grosjean H,Douthwaite S

    更新日期:2020-07-09 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

    doi:10.1093/nar/20.22.6043

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

    更新日期:1992-11-25 00:00:00

  • Coding and spacer sequences in the 5.8S-2S region of Sciara coprophila ribosomal DNA.

    abstract::The sequence of 436 nucleotides around the region coding for 5.8S RNA in the Sciara coprophila rDNA transcription unit (1) has been determined. Regions coding for 5.8S and 2S RNAs have been identified; they are 80 - 90% homologous to the corresponding Drosophila sequences and are separated by a 22 nucleotide long spac...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/8.16.3565

    authors: Jordan BR,Latil-Damotte M,Jourdan R

    更新日期:1980-08-25 00:00:00

  • Semisynthesis of site-specifically succinylated histone reveals that succinylation regulates nucleosome unwrapping rate and DNA accessibility.

    abstract::Posttranslational modifications (PTMs) of histones represent a crucial regulatory mechanism of nucleosome and chromatin dynamics in various of DNA-based cellular processes, such as replication, transcription and DNA damage repair. Lysine succinylation (Ksucc) is a newly identified histone PTM, but its regulation and f...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa663

    authors: Jing Y,Ding D,Tian G,Kwan KCJ,Liu Z,Ishibashi T,Li XD

    更新日期:2020-09-25 00:00:00

  • RPA complexes in Caenorhabditis elegans meiosis; unique roles in replication, meiotic recombination and apoptosis.

    abstract::Replication Protein A (RPA) is a critical complex that acts in replication and promotes homologous recombination by allowing recombinase recruitment to processed DSB ends. Most organisms possess three RPA subunits (RPA1, RPA2, RPA3) that form a trimeric complex critical for viability. The Caenorhabditis elegans genome...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa1293

    authors: Hefel A,Honda M,Cronin N,Harrell K,Patel P,Spies M,Smolikove S

    更新日期:2021-01-21 00:00:00

  • A new method for predicting signal sequence cleavage sites.

    abstract::A new method for identifying secretory signal sequences and for predicting the site of cleavage between a signal sequence and the mature exported protein is described. The predictive accuracy is estimated to be around 75-80% for both prokaryotic and eukaryotic proteins. ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/14.11.4683

    authors: von Heijne G

    更新日期:1986-06-11 00:00:00

  • Identification of proteins interacting with newly replicated DNA in SV40-infected cells by UV-induced DNA-protein cross-linking.

    abstract::Protein species interacting with newly replicated DNA were analyzed using a photo cross-linking technique. Nascent DNA was labeled in vitro with [alpha-32P]dCTP and BrdUTP in SV40-infected CV-1 cells made permeable with saponin. The labeled cells were then irradiated with UV light (254 nm) and were treated extensively...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/11.14.4793

    authors: Tsutsui K,Watanabe S,Katagiri M,Oda T

    更新日期:1983-07-25 00:00:00