Literature DB >> 1868834

Flexibility of the DNA enhances promoter affinity of Escherichia coli RNA polymerase.

W Werel1, P Schickor, H Heumann.   

Abstract

Two types of mechanisms are discussed for the formation of active protein-DNA complexes: contacts with specific bases and interaction via specific DNA structures within the cognate DNA. We have studied the effect of a single nucleoside deletion on the interaction of Escherichia coli RNA polymerase with a strong promoter. This study reveals three patterns of interaction which can be attributed to different sites of the promoter, (i) direct base contact with the template strand in the '-35 region' (the 'recognition domain'), (ii) a DNA structure dependent interaction in the '-10 region' (the 'melting domain'), and (iii) an interaction which is based on a defined spatial relationship between the two domains of a promoter, namely the 'recognition domain' and the 'melting domain'.

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Year:  1991        PMID： 1868834      PMCID： PMC452957          DOI： 10.1002/j.1460-2075.1991.tb07800.x

Source DB:  PubMed          Journal:  EMBO J        ISSN： 0261-4189            Impact factor:   11.598


  22 in total

1.  Altered promoter recognition by mutant forms of the sigma 70 subunit of Escherichia coli RNA polymerase.

Authors:  D A Siegele; J C Hu; W A Walter; C A Gross
Journal:  J Mol Biol       Date:  1989-04-20       Impact factor: 5.469

2.  Hydroxyl radical "footprinting": high-resolution information about DNA-protein contacts and application to lambda repressor and Cro protein.

Authors:  T D Tullius; B A Dombroski
Journal:  Proc Natl Acad Sci U S A       Date:  1986-08       Impact factor: 11.205

3.  Hydroxyl radical interference: a new method for the study of protein-DNA interactions.

Authors:  G Chalepakis; M Beato
Journal:  Nucleic Acids Res       Date:  1989-02-25       Impact factor: 16.971

4.  Molecular structure of nicked DNA: a substrate for DNA repair enzymes.

Authors:  J Aymami; M Coll; G A van der Marel; J H van Boom; A H Wang; A Rich
Journal:  Proc Natl Acad Sci U S A       Date:  1990-04       Impact factor: 11.205

5.  Missing contact probing of DNA-protein interactions.

Authors:  A Brunelle; R F Schleif
Journal:  Proc Natl Acad Sci U S A       Date:  1987-10       Impact factor: 11.205

6.  Topological unwinding of strong and weak promoters by RNA polymerase. A comparison between the lac wild-type and the UV5 sites of Escherichia coli.

Authors:  M Amouyal; H Buc
Journal:  J Mol Biol       Date:  1987-06-20       Impact factor: 5.469

7.  The missing nucleoside experiment: a new technique to study recognition of DNA by protein.

Authors:  J J Hayes; T D Tullius
Journal:  Biochemistry       Date:  1989-11-28       Impact factor: 3.162

8.  Molecular characterization of the GCN4-DNA complex.

Authors:  M R Gartenberg; C Ampe; T A Steitz; D M Crothers
Journal:  Proc Natl Acad Sci U S A       Date:  1990-08       Impact factor: 11.205

9.  Use of the hydroxyl radical and gel electrophoresis to study DNA structure.

Authors:  G E Shafer; M A Price; T D Tullius
Journal:  Electrophoresis       Date:  1989 May-Jun       Impact factor: 3.535

10.  Topography of intermediates in transcription initiation of E.coli.

Authors:  P Schickor; W Metzger; W Werel; H Lederer; H Heumann
Journal:  EMBO J       Date:  1990-07       Impact factor: 11.598
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  16 in total

1.  Topography of lacUV5 initiation complexes.

Authors:  V Studitsky; K Brodolin; Y Liu; A Mirzabekov
Journal:  Nucleic Acids Res       Date:  2001-02-01       Impact factor: 16.971

2.  Gapped DNA is anisotropically bent.

Authors:  Hong Guo; Thomas D Tullius
Journal:  Proc Natl Acad Sci U S A       Date:  2003-03-18       Impact factor: 11.205

3.  Temperature-dependence of open-complex formation at two Escherichia coli promoters with extended -10 sequences.

Authors:  H D Burns; T A Belyaeva; S J Busby; S D Minchin
Journal:  Biochem J       Date:  1996-07-01       Impact factor: 3.857

4.  Real-time characterization of intermediates in the pathway to open complex formation by Escherichia coli RNA polymerase at the T7A1 promoter.

Authors:  Bianca Sclavi; Evgeny Zaychikov; Anastasia Rogozina; Ferdinand Walther; Malcolm Buckle; Hermann Heumann
Journal:  Proc Natl Acad Sci U S A       Date:  2005-02-28       Impact factor: 11.205

5.  Different thermal energy requirement for open complex formation by Escherichia coli RNA polymerase at two related promoters.

Authors:  E Grimes; S Busby; S Minchin
Journal:  Nucleic Acids Res       Date:  1991-11-25       Impact factor: 16.971

6.  Cra-dependent transcriptional activation of the icd gene of Escherichia coli.

Authors:  J F Prost; D Nègre; C Oudot; K Murakami; A Ishihama; A J Cozzone; J C Cortay
Journal:  J Bacteriol       Date:  1999-02       Impact factor: 3.490

7.  Transposase makes critical contacts with, and is stimulated by, single-stranded DNA at the P element termini in vitro.

Authors:  E L Beall; D C Rio
Journal:  EMBO J       Date:  1998-04-01       Impact factor: 11.598

8.  DNA flexibility of the UP element is a major determinant for transcriptional activation at the Escherichia coli acetate promoter.

Authors:  D Nègre; C Bonod-Bidaud; C Oudot; J F Prost; A Kolb; A Ishihama; A J Cozzone; J C Cortay
Journal:  Nucleic Acids Res       Date:  1997-02-15       Impact factor: 16.971

9.  Spacing of promoter elements regulates the basal expression of the soxS gene and converts SoxR from a transcriptional activator into a repressor.

Authors:  E Hidalgo; B Demple
Journal:  EMBO J       Date:  1997-03-03       Impact factor: 11.598

10.  Effect of mutations in the -10 region of the phoE promoter in Escherichia coli on regulation of gene expression.

Authors:  M Scholten; J Tommassen
Journal:  Mol Gen Genet       Date:  1994-10-28
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