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High-resolution structure of TBP with TAF1 reveals anchoring patterns in transcriptional regulation

Nature Structural & Molecular Biology volume 20, pages 1008–1014 (2013)Cite this article

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Abstract

The general transcription factor TFIID provides a regulatory platform for transcription initiation. Here we present the crystal structure (1.97 Å) and NMR analysis of yeast TAF1 N-terminal domains TAND1 and TAND2 bound to yeast TBP, together with mutational data. We find that yeast TAF1-TAND1, which in itself acts as a transcriptional activator, binds TBP's concave DNA-binding surface by presenting similar anchor residues to TBP as does Mot1 but from a distinct structural scaffold. Furthermore, we show how TAF1-TAND2 uses an aromatic and acidic anchoring pattern to bind a conserved TBP surface groove traversing the basic helix region, and we find highly similar TBP-binding motifs also presented by the structurally distinct TFIIA, Mot1 and Brf1 proteins. Our identification of these anchoring patterns, which can be easily disrupted or enhanced, provides insight into the competitive multiprotein TBP interplay critical to transcriptional regulation.

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Figure 1: Structure and dynamics of yTBP-yTAF1 binding.
Figure 2: TATA-box mimicry of yTAF1-TAND1.
Figure 3: Electrostatic and hydrophobic anchoring of yTAF1-TAND2 to yTBP.
Figure 4: Multiple acidic residues in TAND2 affect yeast growth.
Figure 5: Similar TBP-anchoring residues in yTAF1-TAND1 and Mot1 despite reverse sequence tracing.
Figure 6: Conserved surface-groove and anchoring residues in competitive TBP binding.

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Acknowledgements

This work was supported by the Swedish Research Council (621-2011-6028 and 621-2012-5250 to M.S.; 621-2012-5136 to P.L.), VINNOVA (P32045-1 to M.S.), the Swedish Cancer Foundation (11 0681 to M.S.), the Swedish Child Cancer Foundation (PROJ09/092 to M.S.), the Forum Scientium Award (C.A.), the Canadian Institutes for Health Research (MT-13611 to M.I.), the grant-in-Aid for Scientific Research from Japan Society for the Promotion of Science (23370077 to T.K.) and equipment grants to Linköping University from the Knut and Alice Wallenberg foundation. M.I. is supported as a Canada Research Chair. We thank H.Th.M. Timmers, L. Penn, C.H. Arrowsmith and P. de Graaf for critical discussion and acknowledge the Swedish NMR Centre, the Protein Science Facility and beamline ID14-1 at the European Synchrotron Radiation Facility.

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  1. Marina I Siponen

    Present address: Present address: Laboratoire de Bioénergétique Cellulaire, CEA Cadarache, Saint Paul lez Durance, France.,

  2. Cecilia Andresen and Sara Helander: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden

    Madhanagopal Anandapadamanaban, Cecilia Andresen, Sara Helander, Patrik Lundström & Maria Sunnerhagen

  2. Division of Molecular and Cellular Biology, Graduate School of Nanobioscience, Yokohama City University, Yokohama, Japan

    Yoshifumi Ohyama & Tetsuro Kokubo

  3. Department of Medical Biochemistry and Biophysics, Protein Science Facility, Karolinska Institutet, Stockholm, Sweden

    Marina I Siponen & Martin Moche

  4. Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada

    Mitsuhiko Ikura

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  1. Madhanagopal Anandapadamanaban
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Contributions

M.I. and M.S. conceived of and designed the study. Experiments and data evaluation were designed and performed by M.A., M.I.S. and M.M. (crystallography), Y.O. and T.K. (yeast mutations) and M.A., C.A., S.H., P.L. and M.S. (NMR). M.A., C.A., S.H., M.M. and M.S. wrote the paper. All authors discussed the interpretation and implications of the results and edited the manuscript at all stages.

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Correspondence to Maria Sunnerhagen.

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Anandapadamanaban, M., Andresen, C., Helander, S. et al. High-resolution structure of TBP with TAF1 reveals anchoring patterns in transcriptional regulation. Nat Struct Mol Biol 20, 1008–1014 (2013). https://doi.org/10.1038/nsmb.2611

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