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The orientation of DNA in an archaeal transcription initiation complex

Nature Structural Biology volume 7, pages 782–785 (2000)Cite this article

Abstract

RNA polymerase from the hyperthermophile archaeon Pyrococcus furiosus (Pfu) forms specific and transcriptionally active complexes with its conjugate transcription factors TBP (the archaeal TATA binding protein homolog) and TFB (the archaeal homolog of eukaryotic RNA polymerase II and III transcription factors TFIIB and Brf) at the Pfu glutamate dehydrogenase promoter. A photochemical crosslinking method was used to map the vicinity of the catalytic subunits of Pfu RNA polymerase to DNA locations distributed along the polymerase–promoter interface. The largest component of this archaeal polymerase is split into two subunits, A′ and A″, whose relatively sharp boundary of DNA crosslinking (probed on the transcribed strand) is centered five to six base pairs downstream of the transcriptional start site. A strong argument based on this information, on the well-defined homology between the core bacterial, archaeal and eukaryotic RNA polymerase subunits, and on the recently determined structure of a bacterial RNA polymerase specifies the directionality of DNA in the archaeal transcription complex and its trajectory downstream of the transcriptional start site.

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Figure 1: The Pfu gdh promoter, initiation complexes and transcription.
Figure 2: Position-specific crosslinking of the gdh promoter to the catalytic subunits of Pfu RNAP.
Figure 3: Model of the DNA trajectory.

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Acknowledgements

We are grateful to S.A. Darst for providing coordinates of Taq RNA polymerase, to V. Nikiforov for sharing data on sequence alignments, to W. Liu for generous help in generating Fig. 3, to J. Buschdorf and B. Goede for valuable materials and to G.A. Kassavetis for advice. Research support at UCSD from the NIGMS, at Kiel from the DFG and the Fonds der Chemischen Industrie, and a National Research Service postdoctoral fellowship from the NIH to M.S.B. are also gratefully acknowledged.

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Authors and Affiliations

  1. Department of Biology and Center for Molecular Genetics, University of California, San Diego, La Jolla, 92093-0634, California , USA

    Michael S. Bartlett & E. Peter Geiduschek

  2. Institut für Allgemeine Mikrobiologie, Universität Kiel, Am Botanischen Garten 1-9, Kiel, D-24118, Germany

    Michael Thomm

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  1. Michael S. Bartlett
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Correspondence to Michael S. Bartlett.

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Bartlett, M., Thomm, M. & Geiduschek, E. The orientation of DNA in an archaeal transcription initiation complex . Nat Struct Mol Biol 7, 782–785 (2000). https://doi.org/10.1038/79020

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