1. Biochemistry and Chemical Biology
  2. Structural Biology and Molecular Biophysics
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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
Research Article
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Cite this article as: eLife 2015;4:e08504 doi: 10.7554/eLife.08504

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.

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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.

Reviewing Editor

  1. Stephen C Harrison, Harvard Medical School, United States

Publication history

  1. Received: May 4, 2015
  2. Accepted: September 3, 2015
  3. Accepted Manuscript published: September 8, 2015 (version 1)
  4. Version of Record published: October 5, 2015 (version 2)

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.

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Further reading

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    2. Structural Biology and Molecular Biophysics

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    A key point to regulate gene expression is at transcription initiation, and activators play a major role. CarD, an essential activator in Mycobacterium tuberculosis, is found in many bacteria, including Thermus species, but absent in Escherichia coli. To delineate the molecular mechanism of CarD, we determined crystal structures of Thermus transcription initiation complexes containing CarD. The structures show CarD interacts with the unique DNA topology presented by the upstream double-stranded/single-stranded DNA junction of the transcription bubble. We confirm that our structures correspond to functional activation complexes, and extend our understanding of the role of a conserved CarD Trp residue that serves as a minor groove wedge, preventing collapse of the transcription bubble to stabilize the transcription initiation complex. Unlike E. coli RNAP, many bacterial RNAPs form unstable promoter complexes, explaining the need for CarD.

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