TITLE

A Triplex-Mediated Knot between Separated Polypurine–Polypyrimidine Tracts in Circular DNA Blocks Transcription by Escherichia coli RNA Polymerase

AUTHOR(S)
Ashley, Carolyn; Lee, Jeremy S.
PUB. DATE
April 2000
SOURCE
DNA & Cell Biology;Apr2000, Vol. 19 Issue 4, p235
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Polypurine–polypyrimidine tracts are overrepresented in eukaryotes and many have the potential to form triplex DNA. Transmolecular triplexes form between separated but complementary polypurine–polypyrimidine tracts in duplex DNA. Transmolecular triplexes (T-loops) were studied previously using a circular plasmid containing a pair of separated polypurine–polypyrimidine tracts designed to able to form a triplex with each other. T-Loops formed when the nicked plasmid was incubated at low pH in the presence of spermine. When the pH was raised to 8, the T-loops were constrained by a hydrogen-bonded knot composed of multistranded and single-stranded regions. The present experiments used T-loops as a model system to investigate the influence of transmolecular triplex formation on transcription. T-Loops and control open circular, linear, and supercoiled plasmid forms were isolated from bands on agarose gels. Transcription assays were carried out with the isolated plasmid forms and Escherichia coli RNA polymerase holoenzyme and the core enzyme, which lacked sigma[sup 70]. Transcription was significantly inhibited in T-loop forms compared with control plasmid forms. There was no evidence that the single-stranded regions of T-loops facilitated nonspecific initiation of transcription. Instead, the multistranded component of the hydrogen-bonded knot at the root of the T-loop structure inhibited transcription.
ACCESSION #
5322740

 

Related Articles

  • IscR Regulates RNase LS Activity by Repressing rnlA Transcription. Otsuka, Yuichi; Miki, Kumiko; Koga, Mitsunori; Katayama, Natsu; Morimoto, Wakako; Takahashi, Yasuhiro; Yonesaki, Tetsuro // Genetics;Jul2010, Vol. 185 Issue 3, p823 

    The Escherichia coli endoribonuclease LS was originally identified as a potential antagonist of bacteriophage T4. When the T4 dmd gene is defective, RNase LS cleaves T4 mRNAs and antagonizes T4 reproduction. This RNase also plays an important role in RNA metabolisms in E. coli. rnlA is an...

  • Oligomerization of the E. coli Core RNA Polymerase: Formation of (α2ββ'ω)2 -- DNA Complexes and Regulation of the Oligomerization by Auxiliary Subunits. Kansara, Seema G.; Sukhodolets, Maxim V. // PLoS ONE;2011, Vol. 6 Issue 4, p1 

    In this work, using multiple, dissimilar physico-chemical techniques, we demonstrate that the Escherichia coli RNA polymerase core enzyme obtained through a classic purification procedure forms stable (α2ββ′ω)2 complexes in the presence or absence of short DNA probes. Multiple...

  • A system for heterologous expression and isolation of Escherichia coli RNA polymerase and its components. Khodak, Yu. A.; Koroleva, O. N.; Drutsa, V. L. // Biochemistry (00062979);Feb2007, Vol. 72 Issue 2, p178 

    A set of plasmid vectors for expression of all major Escherichia coli RNA polymerase subunits as fusion proteins with intein-and chitin-binding domains, allowing protein purification in accordance with IMPACT technology, was constructed. It is demonstrated that the fusion subunits α, β, or...

  • Repression of deoP2 in Escherichia coli by CytR: conversion of a transcription activator into a repressor. Shin, Minsang; Kang, Soim; Hyun, Seok-Jin; Fujita, Nobuyuki; Ishihama, Akira; Valentin-Hansen, Poul; Choy, Hyon E. // EMBO Journal;10/1/2001, Vol. 20 Issue 19, p5392 

    In the deoP2 promoter of Escherichia coli, a transcription activator, cAMP-CRP, binds at two sites, centered at -41.5 and -93.5 from the start site of transcription, while a repressor, CytR, binds to a space between the two cAMP-CRP complexes. The mechanisms for the cAMP-CRP-mediated...

  • Transcription through a simple DNA repeat blocks replication elongation. Krasilnikova, Maria M.; Samadashwily, George M.; Krasilnikov, Andrey S.; Mirkin, Sergei M. // EMBO Journal;9/1/98, Vol. 17 Issue 17, p5095 

    The influence of d(G) n ··d(C) n repeats on plasmid replication in Escherichia coli cells was analyzed using electrophoretic analysis of replication intermediates. These repeats impeded the replication fork in a length- and orientation-dependent manner. Unexpectedly, the replication arrest...

  • A structural model of the E. coli PhoB Dimer in the transcription initiation complex.  // BMC Structural Biology;2012, Vol. 12 Issue 1, p3 

    The article offers information on a study on the structural model of Escherichia coli (E. Coli) PhoB Dimer in the transcription initiation complex. It states that Motif Binding Geometries (MBG) approach demonstrated its utility on RNA polymerase initiating transcription under conditions of...

  • Stochastic sequence-level model of coupled transcription and translation in prokaryotes. Mäkelä, Jarno; Lloyd-Price, Jason; Yli-Harja, Olli; Ribeiro, Andre S. // BMC Bioinformatics;2011, Vol. 12 Issue 1, p121 

    Background: In prokaryotes, transcription and translation are dynamically coupled, as the latter starts before the former is complete. Also, from one transcript, several translation events occur in parallel. To study how events in transcription elongation affect translation elongation and...

  • Characterization of the Escherichia coli σS core regulon by Chromatin Immunoprecipitation-sequencing (ChIP-seq) analysis. Peano, Clelia; Petiti, Luca; De Bellis, Gianluca; Wolf, Johannes; Egli, Thomas; Demol, Julien; Geiselmann, Johannes; Lacour, Stephan; Rossi, Elio; Landini, Paolo // Scientific Reports;5/29/2015, p10469 

    In bacteria, selective promoter recognition by RNA polymerase is achieved by its association with σ factors, accessory subunits able to direct RNA polymerase 'core enzyme' (E) to different promoter sequences. Using Chromatin Immunoprecipitation-sequencing (ChIP-seq), we searched for promoters...

  • Revisiting operons: an analysis of the landscape of transcriptional units in E. coli. Xizeng Mao; Qin Ma; Bingqiang Liu; Xin Chen; Hanyuan Zhang; Ying Xu // BMC Bioinformatics;11/4/2015, Vol. 16, p1 

    Background: Bacterial operons are considerably more complex than what were thought. At least their components are dynamically rather than statically defined as previously assumed. Here we present a computational study of the landscape of the transcriptional units (TUs) of E. coli K12, revealed...

Share

Read the Article

Courtesy of THE LIBRARY OF VIRGINIA

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics