Structure of a bacterial RNA polymerase holoenzyme open promoter complex

  1. Brian Bae
  2. Andrey Feklistov
  3. Agnieszka Lass-Napiorkowska
  4. Robert Landick
  5. Seth A Darst  Is a corresponding author
  1. The Rockefeller University, United States
  2. Saint Louis University School of Medicine, United States
  3. University of Wisconsin-madison, United States

Abstract

Initiation of transcription is a primary means for controlling gene expression. In bacteria, the RNA polymerase (RNAP) holoenzyme binds and unwinds promoter DNA, forming the transcription bubble of the open promoter complex (RPo). We have determined crystal structures, refined to 4.14 Å-resolution, of RPo containing Thermus aquaticus RNAP holoenzyme and promoter DNA that includes the full transcription bubble. The structures, combined with biochemical analyses, reveal key features supporting the formation and maintenance of the double-strand/single-strand DNA junction at the upstream edge of the -10 element where bubble formation initiates. The results also reveal RNAP interactions with duplex DNA just upstream of the -10 element and potential protein/DNA interactions that direct the DNA template strand into the RNAP active site. Addition of an RNA primer to yield a 4 base-pair post-translocated RNA:DNA hybrid mimics an initially transcribing complex at the point where steric clash initiates abortive initiation and σA dissociation.

Article and author information

Author details

  1. Brian Bae

    Laboratory for Molecular Biophysics, The Rockefeller University, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Andrey Feklistov

    Laboratory for Molecular Biophysics, The Rockefeller University, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Agnieszka Lass-Napiorkowska

    Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Robert Landick

    Department of Biochemistry, University of Wisconsin-madison, Madison, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Seth A Darst

    Laboratory for Molecular Biophysics, The Rockefeller University, New York, United States
    For correspondence
    darst@rockefeller.edu
    Competing interests
    The authors declare that no competing interests exist.

Copyright

© 2015, Bae et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 17,710
    views
  • 1,454
    downloads
  • 204
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Citations by DOI

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Brian Bae
  2. Andrey Feklistov
  3. Agnieszka Lass-Napiorkowska
  4. Robert Landick
  5. Seth A Darst
(2015)
Structure of a bacterial RNA polymerase holoenzyme open promoter complex
eLife 4:e08504.
https://doi.org/10.7554/eLife.08504

Share this article

https://doi.org/10.7554/eLife.08504