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PMID: 3290898 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

One-dimensional diffusion of Escherichia coli DNA-dependent RNA polymerase: a mechanism to facilitate promoter location.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 85 ·No. 13 ·1988-07-00 ·Pages 4610-4

Ricchetti M, Metzger W, Heumann H

Abstract

The mechanism of promoter location by DNA-dependent RNA polymerase of Escherichia coli was investigated. The occupancies of DNA fragments carrying the A1 promoter of bacteriophage T7 were analyzed as a function of the length of flanking sequences adjacent to the promoter. Competition between the promoters on different fragments showed qualitatively that DNA sequences downstream of the promoter enhanced promoter occupancy, whereas upstream flanking sequences had little or no influence on occupancy. This was studied quantitatively by using a set of DNA fragments with four identical A1 promoters (I-IV) equidistant from each other, but with different lengths of flanking sequences upstream from promoter I and downstream from promoter IV. The relative occupancies of these promoters showed that downstream DNA sequences of up to 250 base pairs increased the occupancy of the adjacent promoter, whereas upstream sequences longer than 70 base pairs had little or no effect on occupancy. Promoter occupancies measured as a function of the length of the downstream flanking DNA sequences were fit by a published theory that takes into account an enhancement of signal-sequence location by linear diffusion.

MeSH Terms
Bacterial Proteins/metabolism DNA, Viral/genetics Diffusion Escherichia coli/enzymology Genes, Viral Promoter Regions, Genetic RNA Polymerase I/metabolism T-Phages/genetics
Chemicals
Bacterial Proteins DNA, Viral RNA Polymerase I
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Ricchetti M
Max-Planck-Institut für Biochemie, Martinsried, Federal Republic of Germany.
Metzger W
Heumann H
References (22)
22 references, click to expand
  1. Rate enhancement by guided diffusion. Chain length dependence of repressor-operator association rates.
    Biophys Chem. 1978 May;8(2):135-50 PMID: 667313
  2. A new method of large scale preparation of highly purified DNA-dependent RNA-polymerase from E. coli.
    Hoppe Seylers Z Physiol Chem. 1970 Feb;351(2):221-4 PMID: 4907251
  3. Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli lac repressor--operator interaction: kinetic measurements and conclusions.
    Biochemistry. 1981 Nov 24;20(24):6961-77 PMID: 7032584
  4. Dynamics of DNA polymerase III holoenzyme of Escherichia coli in replication of a multiprimed template.
    J Biol Chem. 1985 Oct 15;260(23):12875-83 PMID: 2413035
  5. Binding of Escherichia coli RNA polymerase holoenzyme to bacteriophage T7 DNA. Measurements of binding at bacteriophage T7 promoter A1 using a template competition assay.
    J Mol Biol. 1982 Feb 15;155(1):1-29 PMID: 7042985
  6. Reconstitution of bacterial DNA-dependent RNA-polymerase from isolated subunits as a tool for the elucidation of the role of the subunits in transcription.
    FEBS Lett. 1970 Dec;11(3):165-168 PMID: 11945477
  7. Association kinetics with coupled diffusion III. Ionic-strength dependence of the lac repressor-operator association.
    Biophys Chem. 1978 Sep;8(4):271-80 PMID: 728534
  8. Diffusion controlled reaction rates in spheroidal geometry. Application to repressor--operator association and membrane bound enzymes.
    Biophys Chem. 1974 Oct;2(3):255-63 PMID: 4474030
  9. A simple procedure for resolution of Escherichia coli RNA polymerase holoenzyme from core polymerase.
    Arch Biochem Biophys. 1977 Aug;182(2):404-8 PMID: 332084
  10. The use of thin acrylamide gels for DNA sequencing.
    FEBS Lett. 1978 Mar 1;87(1):107-10 PMID: 631324
  11. Nitrocellulose filter binding studies of the interactions of Escherichia coli RNA polymerase holoenzyme with deoxyribonucleic acid restriction fragments: evidence for multiple classes of nonpromoter interactions, some of which display promoter-like properties.
    Biochemistry. 1982 Aug 31;21(18):4318-31 PMID: 6289878
  12. Deuterium incorporation into Escherichia coli proteins. A neutron-scattering study of DNA-dependent RNA polymerase.
    Eur J Biochem. 1986 May 2;156(3):655-9 PMID: 3516697
  13. A steady state assay for the RNA polymerase initiation reaction.
    J Biol Chem. 1978 Dec 25;253(24):8941-8 PMID: 363712
  14. The one-dimensional diffusion coefficient of proteins absorbed on DNA hydrodynamic considerations.
    Biophys Chem. 1975 May;9(4):413-4 PMID: 16997207
  15. Physical studies on ribonucleic acid polymerase from Escherichia coli B.
    Biochemistry. 1970 Dec 22;9(26):5055-64 PMID: 4921542
  16. Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory.
    Biochemistry. 1981 Nov 24;20(24):6929-48 PMID: 7317363
  17. Linear diffusion of restriction endonucleases on DNA.
    J Biol Chem. 1985 May 25;260(10):6160-6 PMID: 2987217
  18. Large-scale preparation of a DNA fragment containing the strong promoter A1 of the phage T7.
    Biochim Biophys Acta. 1987 Jul 14;909(2):126-32 PMID: 2439122
  19. Diffusion-driven mechanisms of protein translocation on nucleic acids. 2. The Escherichia coli repressor--operator interaction: equilibrium measurements.
    Biochemistry. 1981 Nov 24;20(24):6948-60 PMID: 6274381
  20. Facilitated diffusion during catalysis by EcoRI endonuclease. Nonspecific interactions in EcoRI catalysis.
    J Biol Chem. 1985 Oct 25;260(24):13130-7 PMID: 2997157
  21. Visualization of intermediary transcription states in the complex between Escherichia coli DNA-dependent RNA polymerases and a promoter-carrying DNA fragment using the gel retardation method.
    Eur J Biochem. 1986 Aug 1;158(3):575-9 PMID: 3525164
  22. Electron microscopic studies of the binding of Escherichia coli RNA polymerase to DNA. II. Formation of multiple promoter-like complexes at non-promoter sites.
    J Mol Biol. 1980 Jan 5;136(1):79-93 PMID: 6988596
Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.85.13.4610
Published
1988-07-00
Pages
4610-4
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC280484
Subset
IM
External Links
PubMed source DOI: 10.1073/pnas.85.13.4610 PMC Full Text View journal details
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