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Molecular mechanism of promoter opening by RNA polymerase III

Nature volume 553, pages 295300 (18 January 2018) | Download Citation

Abstract

RNA polymerase III (Pol III) and transcription factor IIIB (TFIIIB) assemble together on different promoter types to initiate the transcription of small, structured RNAs. Here we present structures of Pol III preinitiation complexes, comprising the 17-subunit Pol III and the heterotrimeric transcription factor TFIIIB, bound to a natural promoter in different functional states. Electron cryo-microscopy reconstructions, varying from 3.7 Å to 5.5 Å resolution, include two early intermediates in which the DNA duplex is closed, an open DNA complex, and an initially transcribing complex with RNA in the active site. Our structures reveal an extremely tight, multivalent interaction between TFIIIB and promoter DNA, and explain how TFIIIB recruits Pol III. Together, TFIIIB and Pol III subunit C37 activate the intrinsic transcription factor-like activity of the Pol III-specific heterotrimer to initiate the melting of double-stranded DNA, in a mechanism similar to that of the Pol II system.

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Acknowledgements

C.W.M. and R.W. acknowledge support from the European Research Council Advanced Grant (ERC-2013-AdG340964-POL1PIC). M.K.V. acknowledges support from the EMBL International PhD program. H.K. acknowledges support from the European Union’s Horizon 2020 program under the Marie Sklodowska-Curie grant agreement no. 703432. We thank F. Baudin for help with the transcription assay, A. J. Jakobi for extensive help with setting up LocScaling of cryo-EM maps and model refinement, T. Hoffmann and J. Pecar for setting up the high performance computing for RELION 2.0, and N. A. Hoffmann, J. Kosinski, L. Tafur and Y. Sadian for discussions. We thank A. Vannini for giving us access to the coordinates of PDB entry 5N9G before publication.

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Affiliations

  1. European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany

    • Matthias K. Vorländer
    • , Heena Khatter
    • , Rene Wetzel
    • , Wim J. H. Hagen
    •  & Christoph W. Müller

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Contributions

C.W.M. initiated and supervised the project. M.K.V. designed and carried out experiments, data processing and model building. H.K. helped in the initial stages of electron microscopy preparation. W.J.H.H. collected cryo-EM datasets. R.W. was responsible for yeast fermentation and helped with cloning. M.K.V. and C.W.M. prepared the manuscript with input from the other authors.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Christoph W. Müller.

Reviewer Information Nature thanks R. Maraia and the other anonymous reviewer(s) for their contribution to the peer review of this work.

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    Mechanism of promoter opening by RNA Pol III

    The video shows the proposed model of promoter opening including the transition between the structures reported in this work and the modelled “closed complex/open clamp” intermediate.

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https://doi.org/10.1038/nature25440

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